Contacts of the helix formed by residues 47 - 75 (chain G) in PDB entry 2YW7
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with PHE 47 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A TRP* 5.3 6.1 - + - -
151A PHE* 3.8 14.4 - + - -
154A ALA* 3.6 18.8 - - + -
155A HIS* 3.0 46.7 - + - -
42G VAL* 3.8 13.9 - - + -
43G VAL* 3.8 23.1 - - - +
44G GLY 3.0 32.3 + - - +
46G ASN* 1.3 74.4 - - - +
48G ILE* 1.3 70.4 + - + +
49G GLY 3.4 0.2 - - - -
50G VAL* 3.3 5.8 - - - +
51G HIS* 3.0 68.4 + + - -
102G VAL* 3.6 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 48 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A PHE* 3.8 24.2 - - + -
155A HIS* 4.0 12.8 - - + +
45G PRO 5.7 0.7 - - - +
46G ASN* 3.1 2.2 - - - -
47G PHE* 1.3 103.2 - - + +
49G GLY* 1.3 54.6 + - - +
50G VAL 2.9 5.2 - - - -
51G HIS* 3.8 14.4 - - + +
52G GLU* 2.6 64.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 49 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46G ASN* 3.6 14.8 + - - +
47G PHE 3.4 0.8 - - - -
48G ILE* 1.3 77.9 - - - +
50G VAL* 1.3 60.3 + - - +
52G GLU* 4.0 10.8 + - - +
53G MET* 3.4 25.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 50 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38G VAL* 4.6 4.5 - - + -
42G VAL* 4.0 24.2 - - + -
46G ASN 4.3 1.6 - - - +
47G PHE 3.3 8.0 + - - +
48G ILE 2.9 0.6 - - - -
49G GLY* 1.3 75.4 - - - +
51G HIS* 1.3 67.6 + - - +
52G GLU 3.0 1.1 - - - -
53G MET* 2.7 18.6 + - + +
54G ILE* 2.8 40.0 + - + +
102G VAL* 3.7 41.3 - - + -
106G LEU* 3.7 22.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 51 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A TRP* 5.0 12.5 - + - -
39G HIS* 2.8 59.3 + + - +
40G TRP* 5.8 0.4 - - - -
42G VAL* 3.4 12.0 + - + +
47G PHE* 3.0 59.4 + + - +
48G ILE* 2.9 20.6 + - + +
50G VAL* 1.3 75.1 - - - +
52G GLU* 1.3 60.7 + - + +
54G ILE* 4.4 0.2 - - - -
55G ASP* 2.9 34.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 52 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A GLU* 5.7 1.2 - - - +
48G ILE* 2.6 44.4 + - + +
49G GLY* 4.0 10.2 + - - +
51G HIS* 1.3 73.0 - - + +
53G MET* 1.3 57.5 + - - +
55G ASP* 4.3 6.1 - - - +
56G PRO* 3.6 18.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 53 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49G GLY 3.4 16.4 + - - +
50G VAL* 2.7 25.2 + - - +
52G GLU* 1.3 74.3 - - - +
54G ILE* 1.3 67.4 + - + +
55G ASP 3.6 0.4 - - - -
56G PRO* 4.2 9.0 - - - +
57G GLN* 3.7 4.7 - - - +
106G LEU* 4.9 15.9 - - - -
148G PHE* 3.3 32.6 - - + -
151G PHE* 3.4 54.1 - - + +
152G VAL* 3.6 34.5 - - + +
154G ALA 6.2 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 54 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35G LEU* 3.6 27.8 - - + +
38G VAL* 3.9 7.6 - - + -
39G HIS* 4.0 17.7 - - + -
50G VAL* 2.8 43.0 + - + +
51G HIS* 4.3 2.5 - - - +
53G MET* 1.3 88.1 - - + +
55G ASP* 1.3 55.1 + - - +
57G GLN* 2.9 7.9 + - - +
58G VAL* 2.6 54.6 + - + +
106G LEU* 5.6 0.2 - - + -
109G LEU* 3.9 27.4 - - + -
148G PHE* 4.4 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 55 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36G LYS* 3.7 14.5 + - - +
39G HIS* 3.2 24.3 + - - -
51G HIS* 2.9 20.5 - - - +
52G GLU* 4.3 5.2 - - - +
54G ILE* 1.3 79.2 - - - +
56G PRO* 1.3 73.5 - - + +
58G VAL* 3.0 15.5 + - - +
59G GLU* 3.1 19.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 56 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52G GLU 3.6 20.2 - - - +
53G MET* 4.2 8.1 - - - +
54G ILE 3.8 0.9 - - - -
55G ASP* 1.3 95.4 - - + +
57G GLN* 1.3 56.7 + - + +
59G GLU* 3.3 10.9 + - + +
60G LEU* 3.0 27.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 57 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35G LEU* 3.6 9.4 - - + -
53G MET 3.7 2.7 - - - +
54G ILE* 2.9 8.4 + - - +
56G PRO* 1.3 77.7 - - + +
58G VAL* 1.3 61.1 + - - +
60G LEU* 3.2 22.3 + - - +
61G VAL* 3.0 47.4 + - - +
113G TYR* 3.0 34.6 + - - +
144G GLU 4.9 1.8 + - - +
145G LEU* 4.0 9.7 - - - +
148G PHE* 3.1 51.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 58 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32G HIS* 4.4 6.2 - - + +
35G LEU* 3.7 22.4 - - + -
36G LYS* 4.1 23.8 - - + +
54G ILE* 2.6 42.0 + - + +
55G ASP* 3.0 11.2 + - - +
57G GLN* 1.3 73.5 - - - +
59G GLU* 1.3 66.6 + - - +
60G LEU 3.3 0.2 + - - -
61G VAL* 3.4 2.4 + - - +
62G ARG* 3.0 60.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 59 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B GLU* 4.8 5.8 - - - +
62B ARG* 5.0 0.9 + - - -
36G LYS* 5.4 5.0 + - - -
55G ASP* 3.1 17.1 + - + +
56G PRO* 3.3 9.8 + - + +
58G VAL* 1.3 79.6 - - - +
60G LEU* 1.3 56.5 + - - +
62G ARG* 3.9 31.7 + - - +
63G GLY* 3.0 23.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 60 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56G PRO 3.0 14.4 + - - +
57G GLN* 3.3 29.2 - - - +
58G VAL 3.1 0.2 - - - -
59G GLU* 1.3 75.7 - - - +
61G VAL* 1.3 53.3 + - - +
63G GLY* 2.7 23.2 + - - -
64G TYR* 2.8 68.5 + - + +
144G GLU* 4.1 19.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 61 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28G TYR* 3.2 41.1 - - + +
31G LEU* 3.5 30.5 - - + -
32G HIS* 3.9 11.4 - - + -
35G LEU* 4.1 7.2 - - + -
57G GLN* 3.0 37.6 + - - +
58G VAL 4.0 0.4 - - - +
60G LEU* 1.3 70.8 - - - +
62G ARG* 1.3 66.7 + - - +
64G TYR* 2.9 12.6 + - + +
65G ALA* 2.9 22.2 + - - +
145G LEU* 4.6 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 62 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B HIS* 5.1 4.0 + - - -
36B LYS* 5.1 5.3 + - - +
40B TRP* 5.6 0.3 - - - -
59B GLU* 4.3 3.4 + - - -
62B ARG* 3.3 64.6 - - - +
66B ASP* 5.7 0.4 + - - -
32G HIS* 3.5 41.2 + - + +
36G LYS* 4.1 25.7 - - - +
58G VAL* 3.0 39.4 + - - +
59G GLU* 3.9 29.3 + - - +
61G VAL* 1.3 76.4 - - - +
63G GLY* 1.3 64.3 + - - +
65G ALA* 3.2 4.3 + - - +
66G ASP* 2.9 23.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 63 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59G GLU 3.0 13.3 + - - -
60G LEU* 2.7 11.1 + - - -
62G ARG* 1.3 75.4 - - - +
64G TYR* 1.3 63.9 + - - -
66G ASP* 3.0 11.9 - - - +
67G GLU* 3.0 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 64 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28G TYR* 3.3 27.4 - + + -
60G LEU* 2.8 51.4 + - + +
61G VAL* 2.9 13.0 + - + +
63G GLY* 1.3 70.1 - - - +
65G ALA* 1.3 68.5 - - - +
67G GLU* 3.1 11.4 + - - +
68G VAL* 3.0 21.8 + - - +
141G HIS* 3.5 52.6 - + + +
144G GLU* 2.7 36.2 - - + +
145G LEU* 4.0 24.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 65 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B TRP* 4.4 7.0 - - + -
25G LEU* 3.8 18.3 - - + +
28G TYR* 3.4 13.8 - - + -
29G ASN* 3.9 14.4 - - - +
32G HIS* 5.1 1.3 - - + +
61G VAL 2.9 10.9 + - - +
62G ARG* 3.4 11.4 - - - +
64G TYR* 1.3 75.6 - - - +
66G ASP* 1.3 67.5 + - - +
67G GLU 2.8 1.6 + - - -
68G VAL* 3.0 11.8 + - - +
69G ALA* 2.8 25.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 66 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B LYS* 3.0 32.6 + - - -
39B HIS* 5.6 1.9 + - - -
40B TRP* 3.2 26.3 + - - +
62G ARG 2.9 11.2 + - - +
63G GLY* 3.0 18.4 - - - +
65G ALA* 1.3 75.5 - - - +
67G GLU* 1.3 60.3 + - + +
69G ALA* 3.3 4.2 - - - +
70G GLU* 3.3 28.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 67 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63G GLY 3.0 19.1 + - - +
64G TYR* 3.4 13.1 - - - +
65G ALA 2.8 4.4 + - - -
66G ASP* 1.3 69.4 - - + +
68G VAL* 1.3 59.1 + - - +
69G ALA 3.0 3.8 - - - -
70G GLU* 2.9 34.7 + - - +
71G ARG* 3.1 10.9 + - - +
137G LEU* 3.0 23.7 - - + +
141G HIS* 3.0 25.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 68 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21G LEU* 3.1 49.1 - - + +
24G GLN* 4.4 5.4 - - + -
25G LEU* 4.0 13.5 - - + +
28G TYR* 3.8 17.3 - - + -
64G TYR 3.0 11.0 + - - +
65G ALA* 3.1 23.8 - - - +
67G GLU* 1.3 76.5 - - - +
69G ALA* 1.3 58.7 + - - +
71G ARG* 3.5 3.0 - - - +
72G ILE* 2.9 26.4 + - + +
137G LEU* 4.0 17.6 - - + +
138G LEU* 5.4 1.3 - - + -
141G HIS* 5.2 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 69 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B TRP* 3.5 41.5 - - + -
25G LEU* 4.8 3.6 - - + -
65G ALA 2.8 11.3 + - - +
66G ASP 3.3 12.1 - - - +
68G VAL* 1.3 75.0 - - - +
70G GLU* 1.3 67.0 + - - +
72G ILE* 2.9 19.0 + - - +
73G ALA* 3.1 8.3 + - - +
79G PRO* 3.4 20.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 70 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B TRP* 5.3 4.2 - - + -
66G ASP* 3.3 15.9 - - - +
67G GLU* 2.9 23.5 + - - +
69G ALA* 1.3 76.3 - - + +
71G ARG* 1.3 58.4 + - - +
73G ALA* 2.9 11.0 + - - +
74G THR* 2.9 34.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 71 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21G LEU* 3.3 21.8 - - + -
67G GLU 3.1 8.5 + - - +
68G VAL* 3.5 15.0 - - - +
69G ALA 3.1 0.2 - - - -
70G GLU* 1.3 79.5 - - - +
72G ILE* 1.3 56.7 + - - +
74G THR* 3.4 19.4 + - - +
75G LEU* 3.1 61.0 + - - +
131G ASP* 2.8 34.6 + - - -
133G VAL* 3.3 27.7 - - - +
134G SER* 2.6 17.8 + - - +
137G LEU* 4.1 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 72 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18G ALA* 4.6 12.3 - - + +
21G LEU* 3.6 25.6 - - + +
22G GLN* 3.7 38.4 - - + +
25G LEU* 4.4 11.2 - - + -
68G VAL* 2.9 26.0 - - + +
69G ALA* 2.9 9.2 + - - +
71G ARG* 1.3 75.2 - - - +
73G ALA* 1.3 57.7 + - - +
75G LEU* 4.2 4.9 + - - +
76G GLY 4.0 1.4 + - - -
77G LYS* 3.1 38.6 + - + +
78G SER 3.7 25.6 - - - +
79G PRO* 4.3 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 73 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B TRP 4.5 12.1 - - - +
99B ARG* 3.9 14.4 + - - +
69G ALA 3.1 9.3 + - - +
70G GLU* 2.9 12.7 + - - +
72G ILE* 1.3 77.1 - - - +
74G THR* 1.3 64.9 + - - +
76G GLY* 3.2 13.3 + - - -
77G LYS 3.9 9.9 - - - +
79G PRO* 4.4 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 74 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70G GLU* 2.9 21.0 + - - +
71G ARG* 3.7 26.3 - - - +
73G ALA* 1.3 73.9 - - - +
75G LEU* 1.3 56.7 + - + +
76G GLY* 2.8 15.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 75 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14G ALA* 4.4 31.1 - - + +
17G VAL* 3.8 29.4 - - + -
18G ALA* 5.1 6.1 - - + +
21G LEU* 3.9 13.0 - - + -
71G ARG* 3.1 52.3 + - - +
72G ILE* 4.3 5.4 - - - +
73G ALA 3.4 0.4 - - - -
74G THR* 1.3 75.5 - - + +
76G GLY* 1.3 63.6 + - - +
77G LYS* 3.6 5.6 - - + +
131G ASP* 4.0 4.9 - - - +
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il