Contacts of the helix formed by residues 45 - 66 (chain G) in PDB entry 1P7G
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 LYS 45 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188E ASN* 3.6 45.4 - - + +
41G LEU* 3.0 28.2 + - + +
44G GLN* 1.3 88.1 - - + +
46G HIS* 1.3 61.7 + - - +
48G GLN* 3.5 2.1 + - - +
49G GLY* 2.8 27.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 46 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179E GLU* 3.9 3.6 - - - -
183E TYR* 2.7 32.5 + + - -
188E ASN* 3.6 22.8 - - + +
41G LEU 3.3 23.2 + - - -
42G HIS* 3.4 26.0 - - + +
45G LYS* 1.3 79.0 - - + +
47G HIS* 1.3 64.7 + - - +
49G GLY* 3.0 11.0 + - - -
50G TYR* 3.2 28.5 + - + +
180G HIS* 2.9 47.5 + + + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 47 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20G LEU* 3.4 11.0 - - + +
21G PRO* 3.5 29.1 - - + +
42G HIS 2.9 16.9 + - - +
43G HIS* 3.3 15.0 - - - +
45G LYS 3.6 0.2 - - - -
46G HIS* 1.3 72.2 - - - +
48G GLN* 1.3 64.8 + - - +
50G TYR* 2.8 20.7 + + - -
51G VAL* 3.1 6.8 + - + +
86G GLY 4.4 0.7 - - - -
87G HIS* 2.9 40.4 + - - -
90G HIS* 3.5 29.9 - + + +
91G SER* 3.8 7.0 - - - -
94G TRP* 3.0 24.1 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 48 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20G LEU* 3.5 33.4 - - + +
43G HIS 3.1 9.3 + - - +
44G GLN 2.8 29.2 - - - +
45G LYS 3.7 0.9 - - - +
46G HIS 3.3 0.4 - - - -
47G HIS* 1.3 76.2 - - - +
49G GLY* 1.3 57.1 + - - +
51G VAL* 3.2 13.6 + - - +
52G ASN* 2.5 62.3 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
45G LYS 2.8 15.8 + - - -
46G HIS 3.0 5.3 + - - -
48G GLN* 1.3 78.3 - - - +
50G TYR* 1.3 60.2 + - - +
52G ASN* 3.4 10.4 - - - +
53G GLY* 2.8 23.9 + - - -
83G HIS* 3.5 7.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 50 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46G HIS* 3.2 27.9 + - + +
47G HIS* 2.8 13.4 + - - +
49G GLY* 1.3 73.8 - - - +
51G VAL* 1.3 67.0 + - - +
54G ALA* 2.9 26.2 + - - +
82G PHE* 3.8 12.1 - + - -
83G HIS* 3.2 39.7 - + - +
86G GLY* 3.9 11.2 - - - -
87G HIS* 3.8 8.7 - - - +
90G HIS* 3.4 33.9 - + - -
161G HIS* 3.1 29.4 + + - -
178G TRP* 4.3 5.7 - - - -
180G HIS* 3.2 27.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 51 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18G TYR* 3.2 36.3 - - + +
19G THR* 3.6 7.0 - - - -
20G LEU* 3.8 19.7 - - + +
47G HIS* 3.1 14.8 + - + +
48G GLN* 3.5 16.4 - - - +
50G TYR* 1.3 77.1 - - - +
52G ASN* 1.3 65.4 + - - +
54G ALA* 3.4 5.6 - - - +
55G ASN* 3.0 29.3 + - - +
87G HIS* 3.3 37.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 52 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48G GLN* 2.5 52.4 + - - +
49G GLY* 3.4 13.0 - - - +
50G TYR 3.2 0.2 - - - -
51G VAL* 1.3 78.0 - - - +
53G GLY* 1.3 57.9 + - - +
55G ASN* 3.3 7.9 + - - +
56G ALA* 3.0 27.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 53 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49G GLY 2.8 15.1 + - - -
52G ASN* 1.3 70.4 - - - +
54G ALA* 1.3 64.4 + - - +
56G ALA* 3.3 9.3 + - - +
57G ALA* 3.0 22.5 + - - +
79G ASP* 5.6 0.9 - - - +
83G HIS* 3.5 33.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 54 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18G TYR* 4.1 20.4 - - + -
50G TYR 2.9 19.5 + - - +
51G VAL* 3.2 6.7 + - - +
53G GLY* 1.3 76.6 - - - +
55G ASN* 1.3 59.0 + - - +
57G ALA* 3.2 9.4 + - - +
58G LEU* 3.0 29.8 + - - +
80G LEU* 3.8 5.6 - - + +
83G HIS* 3.2 12.9 - - + +
84G LEU* 4.0 18.2 - - + +
87G HIS* 5.3 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 55 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17G ARG* 3.4 28.7 + - - +
18G TYR* 2.7 55.8 + - - -
51G VAL* 3.0 22.8 + - - +
52G ASN* 3.7 6.5 + - - +
54G ALA* 1.3 75.0 - - - +
56G ALA* 1.3 58.9 + - - +
58G LEU* 3.2 7.3 + - - +
59G GLU* 2.9 29.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 56 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52G ASN 3.0 14.1 + - - +
53G GLY* 3.6 13.5 - - - +
54G ALA 3.3 0.2 - - - -
55G ASN* 1.3 75.1 - - - +
57G ALA* 1.3 62.0 + - - +
59G GLU* 3.4 7.2 + - - +
60G LYS* 3.3 38.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 57 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53G GLY 3.0 11.4 + - - +
54G ALA 3.3 9.0 - - - +
55G ASN 3.1 0.2 - - - -
56G ALA* 1.3 78.3 - - - +
58G LEU* 1.3 61.9 + - - +
60G LYS* 3.3 12.2 + - - +
61G LEU* 3.1 26.2 + - - +
76G VAL* 3.6 12.7 - - + +
79G ASP* 4.6 5.4 - - + -
80G LEU* 3.5 41.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 58 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152F GLN* 3.6 2.7 - - - +
154F LEU* 3.7 28.9 - - + -
15G THR* 4.0 20.3 - - + +
16G LYS 2.9 30.5 - - - +
17G ARG* 3.9 17.3 - - - +
18G TYR* 3.4 25.1 - - + -
54G ALA 3.0 13.1 + - - +
55G ASN* 3.2 9.4 + - - +
57G ALA* 1.3 74.5 - - - +
59G GLU* 1.3 59.5 + - - +
61G LEU* 3.2 18.8 + - + +
62G GLU* 2.8 28.9 + - - +
65G ARG* 5.4 0.4 - - - +
80G LEU* 4.2 8.1 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
17G ARG* 3.7 20.3 + - - +
55G ASN 2.9 13.3 + - - +
56G ALA* 3.7 10.8 - - - +
57G ALA 3.3 0.2 - - - -
58G LEU* 1.3 75.9 - - - +
60G LYS* 1.3 62.9 + - + +
62G GLU* 2.8 20.7 + - - +
63G LYS* 2.8 55.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 60 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56G ALA* 3.3 27.1 + - - +
57G ALA* 3.6 10.5 - - - +
59G GLU* 1.3 80.5 - - + +
61G LEU* 1.3 62.4 + - - +
63G LYS* 3.4 9.1 + - - +
64G PHE* 3.2 16.5 + - - +
70G GLN 5.3 1.4 - - - +
71G ILE* 3.4 13.9 - - + +
76G VAL* 4.1 27.3 - - + +
79G ASP* 4.6 15.0 + - - +
72H ASP* 5.1 7.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 61 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128F GLU* 3.8 25.4 - - + +
154F LEU* 5.0 0.9 - - + -
155F ILE 5.6 0.7 - - - +
57G ALA 3.1 17.7 + - - +
58G LEU* 3.5 19.3 - - + +
60G LYS* 1.3 76.5 - - - +
62G GLU* 1.3 57.5 + - - +
64G PHE* 3.5 2.4 + - - +
65G ARG* 2.9 57.7 + - - +
71G ILE* 3.5 20.6 - - + -
73G ILE* 5.0 2.0 - - + -
76G VAL* 3.7 11.0 - - + -
77G LEU* 3.9 14.8 - - + -
80G LEU* 3.6 31.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 62 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13G VAL* 4.2 7.4 - - + -
14G THR* 3.8 5.4 - - - +
15G THR* 3.5 30.0 + - + +
17G ARG* 3.3 19.2 + - - -
58G LEU 2.8 12.3 + - - +
59G GLU* 2.8 21.5 + - - +
61G LEU* 1.3 74.7 - - - +
63G LYS* 1.3 57.6 + - - +
64G PHE 2.9 4.5 - - - -
65G ARG* 3.1 8.3 + - - +
66G LYS* 2.9 71.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 63 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59G GLU* 2.8 41.3 + - + +
60G LYS* 3.4 8.7 + - - +
62G GLU* 1.3 76.1 - - - +
64G PHE* 1.3 57.6 + - - +
66G LYS 4.0 1.3 - - - -
68G GLU* 2.9 54.6 + - + +
69G ALA* 3.0 39.3 + - + -
70G GLN 5.8 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 64 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124F LYS* 3.0 27.7 + - + -
127F GLU* 3.0 48.5 - - + -
128F GLU* 3.3 44.2 - - + -
131F GLN* 3.9 10.8 - - - -
60G LYS 3.2 12.1 + - - +
61G LEU 3.5 8.5 - - - +
62G GLU 2.9 0.2 - - - -
63G LYS* 1.3 77.9 - - - +
65G ARG* 1.3 59.8 + - + +
66G LYS 2.9 4.3 - - - -
67G GLY* 2.9 18.9 + - - -
69G ALA 3.9 14.1 - - - +
70G GLN* 5.1 6.3 - - - +
71G ILE* 3.5 41.7 - - + -
73G ILE* 5.5 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 65 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118F PHE* 3.0 34.6 + - - +
119F PHE* 3.4 24.1 - - + +
120F GLY* 5.3 0.2 - - - -
124F LYS* 3.5 33.8 - - + +
128F GLU* 3.1 40.1 + - - +
152F GLN* 5.5 1.0 + - - -
153F LEU 4.6 8.1 + - - -
154F LEU* 4.8 5.9 - - - +
155F ILE 4.9 2.2 - - - +
13G VAL* 3.3 34.0 - - + +
15G THR* 3.4 22.6 - - - +
58G LEU* 5.5 0.4 - - - +
61G LEU* 2.9 45.2 + - - +
62G GLU* 3.1 1.3 + - - +
64G PHE* 1.3 78.3 - - + +
66G LYS* 1.3 57.9 + - - +
67G GLY 3.4 1.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 66 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13G VAL* 2.9 44.6 + - + +
14G THR* 5.5 0.6 - - - +
62G GLU* 2.9 45.1 + - + +
64G PHE 2.9 1.4 - - - -
65G ARG* 1.3 80.1 - - - +
67G GLY* 1.3 52.4 + - - +
68G GLU* 2.7 45.0 + - + +
----------------------------------------------------------
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