Contacts of the helix formed by residues 31 - 54 (chain G) in PDB entry 1GN2
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 31 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A ALA 5.6 2.4 + - - -
198A THR 5.7 1.8 + - - -
199A SER* 4.3 16.8 + - - +
27G LEU* 2.8 33.3 + - + +
29G HIS 3.3 0.4 - - - -
30G SER* 1.3 92.3 + - - +
32G HIS* 1.3 64.0 + - - +
33G HIS 3.6 0.4 - - - -
34G ALA* 3.6 2.0 + - - +
35G THR* 2.8 30.4 + - - -
172H ASN* 3.6 44.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 32 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27G LEU 3.1 18.8 + - - -
28G HIS* 3.3 25.6 - - + +
31G LYS* 1.3 77.1 - - - +
33G HIS* 1.3 67.0 + - - +
35G THR* 3.1 15.7 + - - -
36G TYR* 3.2 26.5 + - + -
164G HIS* 3.7 34.8 + + + +
163H GLU* 4.3 5.6 - - - -
167H TYR* 2.5 39.5 + + - -
172H ASN* 3.7 23.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 33 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6G LEU* 3.8 9.0 - - + +
7G PRO* 3.8 11.3 - - + +
28G HIS 2.9 15.6 + - - +
29G HIS* 3.3 16.1 + - - +
31G LYS 3.6 0.2 - - - -
32G HIS* 1.3 73.1 - - - +
34G ALA* 1.3 63.2 + - - +
36G TYR* 3.1 19.1 + - + +
37G VAL* 3.1 19.9 + - + +
73G HIS* 3.1 34.1 + - - -
76G HIS* 3.0 31.4 - + + +
77G THR* 3.4 18.2 - - - -
80G TRP* 2.9 27.7 + + - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 34 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6G LEU* 3.8 26.4 - - + +
29G HIS 3.3 3.8 + - - -
30G SER 3.5 24.2 - - - +
31G LYS 3.9 1.8 - - - +
32G HIS 3.2 0.8 - - - -
33G HIS* 1.3 79.1 - - - +
35G THR* 1.3 57.7 + - - +
37G VAL* 3.4 7.5 + - - +
38G LYS* 3.0 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 35 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31G LYS 2.8 17.4 + - - -
32G HIS* 3.1 12.9 + - - +
33G HIS 3.1 0.4 - - - -
34G ALA* 1.3 77.9 - - - +
36G TYR* 1.3 65.3 + - + +
38G LYS* 3.5 6.8 + - + +
39G GLY* 3.0 23.2 + - - -
69G ASN* 4.3 3.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 36 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32G HIS* 3.2 29.2 + - + +
33G HIS* 3.1 13.1 + - - +
35G THR* 1.3 79.3 - - + +
37G VAL* 1.3 57.0 + - - +
39G GLY 3.1 0.2 + - - -
40G ALA* 2.7 36.8 + - - +
68G PHE* 4.0 18.4 - + - -
69G ASN* 3.5 26.3 - - - +
72G GLY* 4.0 11.2 - - - -
73G HIS* 3.8 19.1 - - - +
76G HIS* 3.6 24.9 - + - -
145G HIS* 2.7 37.9 + + - -
162G TRP* 3.8 18.9 - - - -
164G HIS* 4.4 5.9 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 37 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4G TYR* 3.7 24.6 - - - +
5G THR* 4.1 0.4 - - - -
6G LEU* 3.9 25.6 - - + +
33G HIS* 3.1 18.0 + - + +
34G ALA* 3.6 9.2 - - - +
36G TYR* 1.3 81.1 - - - +
38G LYS* 1.3 65.1 + - - +
40G ALA* 3.3 6.1 + - - +
41G ASN* 3.1 26.8 + - - +
73G HIS* 3.5 37.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 38 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34G ALA 3.0 16.4 + - - +
35G THR* 3.9 7.2 - - + +
36G TYR 3.2 0.2 - - - -
37G VAL* 1.3 79.1 - - - +
39G GLY* 1.3 60.6 + - - +
41G ASN* 3.2 7.4 + - + +
42G ASP* 2.9 60.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 39 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35G THR 3.0 15.3 + - - -
36G TYR 3.1 3.6 + - - -
38G LYS* 1.3 83.1 - - - +
40G ALA* 1.3 55.8 + - - +
42G ASP* 3.8 7.4 - - - +
43G ALA* 3.0 29.5 + - - +
65G ASN* 5.6 0.2 - - - +
69G ASN* 3.6 22.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 40 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4G TYR* 3.8 24.5 - - + -
36G TYR 2.7 20.7 + - - +
37G VAL* 3.8 7.4 - - - +
38G LYS 3.2 0.2 - - - -
39G GLY* 1.3 70.2 - - - +
41G ASN* 1.3 66.3 + - - +
43G ALA* 3.3 5.5 + - - +
44G VAL* 3.1 27.4 + - - +
66G LEU* 4.7 2.4 - - + +
69G ASN* 3.4 19.0 - - - +
70G LEU* 4.1 15.3 - - + +
73G HIS* 5.0 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 41 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136E LYS* 4.7 1.7 + - - -
3G GLU* 3.7 26.3 + - + +
4G TYR* 2.8 58.2 + - - +
37G VAL* 3.1 18.8 + - - +
38G LYS* 3.7 8.5 - - + +
40G ALA* 1.3 76.8 - - - +
42G ASP* 1.3 63.1 + - - +
44G VAL* 3.1 10.1 + - - +
45G ALA* 3.0 22.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 42 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38G LYS* 2.9 61.5 + - - +
39G GLY* 3.8 7.6 - - - +
41G ASN* 1.3 73.6 - - - +
43G ALA* 1.3 58.3 + - - +
45G ALA* 3.1 8.5 + - - +
46G LYS* 2.9 35.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 43 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39G GLY 3.0 17.9 + - - +
40G ALA 3.6 5.2 - - - +
41G ASN 3.2 0.2 - - - -
42G ASP* 1.3 74.9 - - - +
44G VAL* 1.3 64.6 + - - +
46G LYS* 3.3 7.9 + - - +
47G LEU* 3.3 28.2 + - - +
62G ASN* 4.5 4.8 + - - +
65G ASN* 4.0 12.3 - - + +
66G LEU* 3.6 39.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 44 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136E LYS* 4.4 17.9 - - + +
138E LEU* 4.7 13.9 - - + -
4G TYR* 4.0 20.0 - - + -
40G ALA 3.1 13.8 + - - +
41G ASN* 3.1 10.1 + - - +
43G ALA* 1.3 78.8 - - - +
45G ALA* 1.3 64.2 + - - +
47G LEU* 3.3 17.7 + - - +
48G GLU* 3.3 26.9 + - - +
51G ARG* 4.9 1.0 + - - -
66G LEU* 4.0 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 45 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41G ASN 3.0 12.7 + - - +
42G ASP* 3.1 9.8 + - - +
44G VAL* 1.3 79.5 - - - +
46G LYS* 1.3 63.8 + - - +
48G GLU* 2.9 27.6 + - - +
49G GLU* 2.9 14.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 46 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42G ASP* 2.9 19.7 + - + +
43G ALA* 3.3 5.8 + - - +
45G ALA* 1.3 76.4 - - + +
47G LEU* 1.3 53.2 + - - +
49G GLU* 3.5 33.0 + - - +
50G ALA* 2.8 34.4 + - - +
62G ASN* 3.6 29.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 47 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112E GLN* 3.9 28.3 - - - +
138E LEU* 6.1 2.7 - - + -
43G ALA 3.3 17.9 + - - +
44G VAL* 3.6 10.5 - - - +
45G ALA 3.0 0.6 - - - -
46G LYS* 1.3 75.1 - - - +
48G GLU* 1.3 56.5 + - - +
50G ALA* 3.1 7.8 + - + +
51G ARG* 2.7 53.1 + - - +
56G HIS* 4.9 1.3 - - + +
59G ILE* 4.3 12.8 - - + -
62G ASN* 3.8 39.5 - - + +
63G GLU* 4.7 3.1 - - - +
66G LEU* 4.1 22.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 48 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102E ALA 5.6 0.2 - - - +
44G VAL* 3.3 25.0 + - - +
45G ALA* 2.9 17.7 + - - +
47G LEU* 1.3 76.5 - - - +
49G GLU* 1.3 60.5 + - - +
51G ARG* 3.0 26.3 + - - +
52G ALA* 2.8 30.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 49 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45G ALA 2.9 11.5 + - - +
46G LYS* 3.8 36.5 + - - +
48G GLU* 1.3 83.4 - - - +
50G ALA* 1.3 60.9 + - - +
52G ALA* 3.5 5.5 + - - +
53G LYS* 3.1 59.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 50 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46G LYS 2.8 19.5 + - - +
47G LEU* 3.5 9.0 - - + +
48G GLU 3.1 0.2 - - - -
49G GLU* 1.3 76.5 - - - +
51G ARG* 1.3 63.0 + - - +
53G LYS* 3.7 2.6 + - - +
54G GLU* 3.1 3.5 + - - -
55G ASP* 3.1 45.0 + - - +
56G HIS* 3.9 19.2 - - + +
62G ASN* 4.3 12.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 51 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102E ALA 3.6 19.8 + - - -
103E PHE* 3.5 44.1 + - - +
108E LYS* 3.8 39.4 - - + +
112E GLN* 2.9 41.6 + - - +
44G VAL 4.9 0.6 + - - -
47G LEU* 2.7 27.3 + - - +
48G GLU* 3.0 39.4 + - - +
50G ALA* 1.3 77.0 - - - +
52G ALA* 1.3 63.9 + - - +
54G GLU* 3.4 10.4 + - - +
56G HIS* 4.0 16.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 52 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108E LYS* 4.0 17.2 + - - +
48G GLU 2.8 15.0 + - - +
49G GLU* 3.8 7.4 - - - +
51G ARG* 1.3 78.5 - - - +
53G LYS* 1.3 64.7 + - + +
54G GLU* 3.1 9.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 53 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49G GLU* 3.1 44.3 + - + +
50G ALA* 5.2 0.7 - - - +
52G ALA* 1.3 77.0 - - + +
54G GLU* 1.3 77.4 + - - +
55G ASP* 4.1 22.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 54 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108E LYS* 5.2 9.2 - - + -
50G ALA 3.1 7.1 + - - -
51G ARG* 3.4 9.1 + - - +
52G ALA 3.1 13.0 - - - +
53G LYS* 1.3 83.1 - - - +
55G ASP* 1.3 58.4 + - - +
56G HIS* 4.1 6.7 + - - -
----------------------------------------------------------
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