Contacts of the helix formed by residues 31 - 54 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27E LEU* 2.8 33.1 + - + +
30E SER* 1.3 93.7 + - - +
32E HIS* 1.3 64.8 - - + +
33E HIS 3.6 0.4 - - - -
34E ALA* 3.9 2.0 - - - +
35E THR* 2.8 30.4 + - - -
172F ASN* 3.5 46.0 - - + +
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Residues in contact with HIS 32 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27E LEU 3.1 17.5 + - - -
28E HIS* 3.3 26.7 - + + +
31E LYS* 1.3 79.1 - - + +
33E HIS* 1.3 68.2 + - - +
35E THR* 3.1 15.9 + - - -
36E TYR* 3.2 25.4 + - + -
164E HIS* 3.7 34.3 + + + +
163F GLU* 4.0 7.4 + - - -
167F TYR* 2.5 45.4 + + - -
172F ASN* 3.9 16.1 - - + +
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Residues in contact with HIS 33 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6E LEU* 3.8 9.4 - - + +
7E PRO* 3.8 12.4 - - + +
28E HIS 2.9 15.6 + - - +
29E HIS* 3.3 15.5 - - - +
32E HIS* 1.3 73.3 - - - +
34E ALA* 1.3 64.0 + - - +
36E TYR* 3.1 19.1 + - + +
37E VAL* 3.1 19.0 + - + +
73E HIS* 3.1 34.0 + - - -
76E HIS* 3.0 31.6 - + + +
77E THR* 3.4 18.4 - - - -
80E TRP* 2.9 27.5 + + - +
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Residues in contact with ALA 34 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6E LEU* 3.8 27.1 - - + +
29E HIS 3.3 3.8 + - - -
30E SER 3.5 24.5 - - - +
31E LYS 3.6 2.7 + - - +
32E HIS 3.2 0.8 - - - -
33E HIS* 1.3 78.7 - - - +
35E THR* 1.3 57.2 + - - +
37E VAL* 3.4 7.0 + - - +
38E LYS* 3.0 28.2 + - - +
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Residues in contact with THR 35 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31E LYS 2.8 17.8 + - - -
32E HIS* 3.1 12.1 + - - -
33E HIS 3.1 0.2 - - - -
34E ALA* 1.3 77.7 - - - +
36E TYR* 1.3 65.6 + - + +
38E LYS* 3.5 7.4 + - + +
39E GLY* 3.0 23.2 + - - -
69E ASN* 4.3 3.5 - - - +
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Residues in contact with TYR 36 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32E HIS* 3.2 29.7 + - + -
33E HIS* 3.1 13.9 + - - +
35E THR* 1.3 77.7 - - + +
37E VAL* 1.3 57.1 + - - +
39E GLY 3.1 0.5 + - - -
40E ALA* 2.7 37.0 + - - +
68E PHE* 4.0 17.6 - + - -
69E ASN* 3.5 26.7 - - - +
72E GLY* 4.0 11.0 - - - -
73E HIS* 3.8 18.4 - - - +
76E HIS* 3.6 24.2 - + - -
145E HIS* 2.7 38.2 + + - -
162E TRP* 3.8 18.5 - - - -
164E HIS* 4.4 6.1 - + - -
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Residues in contact with VAL 37 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4E TYR* 3.7 24.1 - - - +
5E THR* 4.1 0.7 - - - -
6E LEU* 3.9 26.5 - - + +
33E HIS* 3.1 17.8 + - + +
34E ALA* 3.6 9.4 - - - +
36E TYR* 1.3 80.3 - - - +
38E LYS* 1.3 65.5 + - - +
40E ALA* 3.3 6.4 + - - +
41E ASN* 3.1 26.7 + - - +
73E HIS* 3.5 37.5 - - + +
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Residues in contact with LYS 38 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34E ALA 3.0 16.6 + - - +
35E THR* 3.9 6.7 - - - +
36E TYR 3.2 0.2 - - - -
37E VAL* 1.3 79.5 - - - +
39E GLY* 1.3 60.9 + - - +
41E ASN* 3.2 7.8 + - + +
42E ASP* 2.9 59.1 + - - +
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Residues in contact with GLY 39 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35E THR 3.0 15.9 + - - -
36E TYR 3.1 3.6 + - - -
38E LYS* 1.3 81.7 - - - +
40E ALA* 1.3 55.5 + - - +
42E ASP* 3.8 7.2 - - - +
43E ALA* 3.0 29.3 + - - +
65E ASN* 5.6 0.2 - - - +
69E ASN* 3.6 22.9 + - - -
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Residues in contact with ALA 40 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4E TYR* 3.8 24.2 - - + -
36E TYR 2.7 19.6 + - - +
37E VAL* 3.8 7.4 - - - +
38E LYS 3.2 0.2 - - - -
39E GLY* 1.3 69.3 - - - +
41E ASN* 1.3 66.9 + - - +
43E ALA* 3.3 5.7 + - - +
44E VAL* 3.1 27.0 + - - +
66E LEU* 4.7 1.9 - - + +
69E ASN* 3.4 18.1 - - - +
70E LEU* 4.1 15.7 - - + +
73E HIS* 5.0 2.2 - - + -
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Residues in contact with ASN 41 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3E GLU* 3.7 26.6 + - + +
4E TYR* 2.8 57.5 + - - +
37E VAL* 3.1 19.2 + - - +
38E LYS* 3.7 7.9 - - + +
40E ALA* 1.3 76.9 - - - +
42E ASP* 1.3 63.5 + - - +
44E VAL* 3.1 10.1 + - - +
45E ALA* 3.0 22.6 + - - +
136G LYS* 4.8 1.4 + - - -
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Residues in contact with ASP 42 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38E LYS* 2.9 61.2 + - - +
39E GLY* 3.8 7.4 - - - +
41E ASN* 1.3 73.0 - - - +
43E ALA* 1.3 57.6 + - - +
45E ALA* 3.1 8.9 + - - +
46E LYS* 2.9 33.9 + - + +
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Residues in contact with ALA 43 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39E GLY 3.0 19.2 + - - +
40E ALA 3.6 4.9 - - - +
42E ASP* 1.3 75.3 - - - +
44E VAL* 1.3 64.7 + - - +
46E LYS* 3.3 7.6 + - - +
47E LEU* 3.3 29.1 + - - +
62E ASN* 4.5 3.8 + - - +
65E ASN* 4.0 13.7 - - + +
66E LEU* 3.6 37.9 - - + +
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Residues in contact with VAL 44 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4E TYR* 4.0 20.4 - - + -
40E ALA 3.1 13.4 + - - +
41E ASN* 3.1 9.6 + - - +
43E ALA* 1.3 78.1 - - - +
45E ALA* 1.3 63.2 + - + +
47E LEU* 3.3 17.7 + - - +
48E GLU* 3.3 27.0 + - - +
51E ARG* 4.9 0.7 + - - -
66E LEU* 4.0 17.5 - - + -
136G LYS* 4.5 16.6 - - + +
138G LEU* 4.7 13.7 - - + -
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Residues in contact with ALA 45 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41E ASN 3.0 12.7 + - - +
42E ASP* 3.5 10.1 - - - +
44E VAL* 1.3 79.9 - - + +
46E LYS* 1.3 63.8 + - + +
48E GLU* 2.9 27.8 + - - +
49E GLU* 2.9 15.5 + - - +
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Residues in contact with LYS 46 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42E ASP* 2.9 19.1 + - + +
43E ALA* 3.3 6.0 + - - +
45E ALA* 1.3 76.6 - - + +
47E LEU* 1.3 51.5 + - - +
49E GLU* 3.5 34.1 + - - +
50E ALA* 2.8 34.4 + - - +
62E ASN* 3.6 29.4 - - - +
57H SER* 5.9 3.2 + - - -
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Residues in contact with LEU 47 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43E ALA 3.3 17.7 + - - +
44E VAL* 3.6 10.8 - - - +
45E ALA 3.0 0.8 - - - -
46E LYS* 1.3 75.7 - - - +
48E GLU* 1.3 54.9 + - - +
50E ALA* 3.1 8.0 + - + +
51E ARG* 2.7 53.5 + - - +
56E HIS* 4.9 1.1 - - + -
59E ILE* 4.3 13.9 - - + -
62E ASN* 3.8 40.2 - - + +
63E GLU* 4.7 3.4 - - - +
66E LEU* 4.1 22.4 - - + -
112G GLN* 4.0 26.9 - - + +
138G LEU* 6.3 1.3 - - + -
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Residues in contact with GLU 48 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44E VAL* 3.3 24.9 + - - +
45E ALA* 2.9 18.4 + - - +
47E LEU* 1.3 76.9 - - - +
49E GLU* 1.3 60.0 + - - +
51E ARG* 3.0 25.5 + - - +
52E ALA* 2.8 31.3 + - - +
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Residues in contact with GLU 49 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45E ALA 2.9 11.2 + - - +
46E LYS* 3.8 34.9 + - - +
48E GLU* 1.3 83.8 - - - +
50E ALA* 1.3 60.3 + - - +
52E ALA* 3.5 5.3 + - - +
53E LYS* 3.1 57.8 + - + +
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Residues in contact with ALA 50 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46E LYS 2.8 19.2 + - - +
47E LEU* 3.5 8.7 - - + +
48E GLU 3.1 0.2 - - - -
49E GLU* 1.3 77.3 - - - +
51E ARG* 1.3 62.1 + - - +
53E LYS* 5.2 2.0 - - - +
54E GLU* 3.1 3.3 + - - -
55E ASP 3.1 45.2 + - - +
56E HIS* 3.9 19.1 - - + +
62E ASN* 4.3 11.9 - - - +
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Residues in contact with ARG 51 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44E VAL 4.9 0.8 + - - -
47E LEU* 2.7 27.4 + - - +
48E GLU* 3.0 39.4 + - - +
50E ALA* 1.3 76.8 - - - +
52E ALA* 1.3 65.0 + - - +
54E GLU* 3.4 10.9 + - - +
56E HIS* 4.0 16.2 - - + +
102G ALA 3.7 14.0 + - - -
103G PHE* 3.6 46.0 + - - +
108G LYS* 3.9 41.2 - - + +
112G GLN* 2.7 42.3 + - - +
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Residues in contact with ALA 52 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48E GLU 2.8 14.8 + - - +
49E GLU* 3.8 7.0 - - - +
51E ARG* 1.3 78.9 - - - +
53E LYS* 1.3 65.7 + - + +
54E GLU* 3.1 8.4 + - - +
108G LYS* 4.1 15.5 + - - +
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Residues in contact with LYS 53 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49E GLU* 3.1 44.3 + - + +
50E ALA* 4.5 0.9 - - - +
52E ALA* 1.3 77.3 - - + +
54E GLU* 1.3 76.8 + - - +
55E ASP* 3.3 22.4 + - + +
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Residues in contact with GLU 54 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50E ALA 3.1 7.1 + - - -
51E ARG* 3.4 8.2 + - - +
52E ALA 3.1 13.8 - - - +
53E LYS* 1.3 83.3 - - - +
55E ASP* 1.3 58.0 + - - +
56E HIS* 4.1 5.8 - - - -
108G LYS* 5.4 7.4 - - + -
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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) + - + + + + + -
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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