Contacts of the helix formed by residues 37 - 55 (chain E) in PDB entry 3V5I
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 ASP 37 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35E GLN* 2.9 28.8 + - + +
36E ILE* 1.3 75.0 - - - +
38E ASP* 1.3 67.6 + - - +
39E ASN* 2.9 22.8 + - - +
40E VAL* 3.0 13.0 + - - +
41E ALA* 2.8 22.2 + - - +
70E SER* 4.4 5.8 - - - -
73E ALA* 3.6 11.0 - - - -
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Residues in contact with ASP 38 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37E ASP* 1.3 76.2 - - - +
39E ASN* 1.3 57.9 + - - +
41E ALA* 3.8 3.0 - - - +
42E ASN* 2.9 29.8 + - - +
70E SER* 4.4 5.9 + - - -
72E THR* 4.7 2.9 + - - -
73E ALA* 3.7 14.7 + - - +
33F GLY 3.2 21.5 - - - +
34F SER* 4.8 2.2 - - - -
65F ASN* 3.5 36.9 + - - +
67F PRO* 4.0 19.4 - - - +
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Residues in contact with ASN 39 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37E ASP* 2.9 10.9 + - - +
38E ASP* 1.3 75.9 - - - +
40E VAL* 1.3 71.1 + - + +
42E ASN* 3.1 6.9 + - - +
43E SER* 2.9 24.7 + - - -
21F TYR* 3.9 3.3 + - - +
33F GLY 4.3 7.3 - - - +
34F SER* 4.9 7.8 - - - -
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Residues in contact with VAL 40 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32E LEU* 3.7 29.4 - - + -
34E SER* 3.5 19.5 - - - +
35E GLN* 3.5 21.3 - - - +
36E ILE* 4.5 6.5 - - + -
37E ASP* 3.0 17.6 + - - +
39E ASN* 1.3 84.9 - - + +
41E ALA* 1.3 59.5 + - - +
43E SER* 3.1 5.5 + - - -
44E ILE* 2.9 36.1 + - + +
77E ILE* 5.2 0.7 - - + -
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Residues in contact with ALA 41 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36E ILE* 5.0 0.8 - - + +
37E ASP 2.8 16.8 + - - +
38E ASP* 3.8 4.9 - - - +
40E VAL* 1.3 76.2 - - - +
42E ASN* 1.3 58.2 + - - +
44E ILE* 3.2 0.5 + - - +
45E VAL* 2.8 36.4 + - - +
73E ALA* 3.5 34.5 - - + +
76E ALA* 4.5 4.7 - - + -
77E ILE* 3.9 17.4 - - + +
65F ASN* 4.5 7.2 - - - +
93F ILE* 6.3 0.2 - - - -
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Residues in contact with ASN 42 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38E ASP 2.9 20.5 + - - +
39E ASN* 3.1 8.0 + - - +
41E ALA* 1.3 76.1 - - - +
43E SER* 1.3 57.0 + - - +
45E VAL* 4.0 2.1 - - - +
46E SER* 2.9 33.3 + - - -
21F TYR* 3.3 22.9 + - - +
31F MET* 3.4 39.8 - - - +
32F LEU 4.4 2.2 + - - -
33F GLY* 3.8 27.8 + - - +
65F ASN* 5.5 3.1 - - - +
93F ILE* 5.1 7.4 - - - +
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Residues in contact with SER 43 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39E ASN 2.9 11.4 + - - -
40E VAL* 3.3 11.9 - - - -
42E ASN* 1.3 75.3 - - - +
44E ILE* 1.3 65.5 - - - +
46E SER* 3.4 3.6 + - - -
47E GLN* 3.0 43.2 + - - +
4F ILE* 3.7 25.0 + - - +
5F PRO* 3.9 5.7 - - - +
20F ILE* 4.7 1.7 - - - +
21F TYR* 3.2 17.3 + - - -
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Residues in contact with ILE 44 (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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30E ILE* 3.7 28.7 - - + -
31E MET 4.1 12.6 - - - +
32E LEU* 4.5 18.4 - - + -
40E VAL* 2.9 33.0 + - + +
41E ALA 3.9 2.0 - - - +
43E SER* 1.3 70.0 + - - +
45E VAL* 1.3 69.1 + - - +
47E GLN* 2.9 21.7 + - - +
48E LEU* 2.9 23.4 + - + +
62E LEU* 4.6 10.1 - - + -
77E ILE* 3.9 37.5 - - + -
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Residues in contact with VAL 45 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41E ALA 2.8 25.5 + - - +
42E ASN* 4.0 3.1 - - - +
44E ILE* 1.3 71.8 - - - +
46E SER* 1.3 65.2 + - - +
48E LEU* 3.1 7.3 + - - +
49E LEU* 2.9 32.0 + - + +
76E ALA* 3.7 18.8 - - + +
77E ILE* 4.2 6.7 - - - +
80E THR* 3.5 36.8 - - + +
31F MET* 3.9 13.5 - - + -
63F TYR* 5.3 2.2 - - + -
93F ILE* 3.8 26.2 - - + -
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Residues in contact with SER 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 ASN 2.9 19.2 + - - -
43E SER 3.6 4.7 - - - -
44E ILE 3.2 0.2 - - - -
45E VAL* 1.3 79.5 - - - +
47E GLN* 1.3 58.7 + - - +
49E LEU* 3.4 1.5 + - - +
50E PHE* 2.9 30.1 + - - +
20F ILE* 4.1 13.5 - - - -
21F TYR* 3.5 12.4 - - - -
24F LEU* 3.5 22.4 - - - +
31F MET* 3.5 28.0 - - - +
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Residues in contact with GLN 47 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25E LEU* 4.0 26.9 - - + +
29E ILE 4.8 0.5 - - - +
30E ILE* 3.4 40.0 - - + +
31E MET 4.8 2.4 + - - +
43E SER* 3.0 41.3 + - - +
44E ILE* 2.9 17.8 + - - +
46E SER* 1.3 75.4 - - - +
48E LEU* 1.3 59.2 + - - +
50E PHE* 3.3 2.9 + - - +
51E LEU* 2.9 33.3 + - - +
5F PRO* 3.7 19.4 - - + +
20F ILE* 4.1 15.7 - - + -
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Residues in contact with LEU 48 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30E ILE* 3.7 20.4 - - + -
44E ILE* 2.9 30.0 + - + +
45E VAL* 3.4 8.3 - - - +
47E GLN* 1.3 74.3 - - - +
49E LEU* 1.3 66.4 + - - +
51E LEU* 3.2 4.9 + - - +
52E GLN* 3.0 23.4 + - - +
60E ILE* 4.2 9.0 - - + -
62E LEU* 5.8 2.7 - - + -
77E ILE* 4.6 3.6 - - + +
80E THR* 3.8 27.6 - - + -
81E ILE* 3.9 24.9 - - + +
84E ILE* 4.2 16.6 - - + +
88E VAL* 4.1 26.7 - - + -
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Residues in contact with LEU 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 VAL* 2.9 35.6 + - + +
46E SER 4.0 3.4 - - - +
48E LEU* 1.3 71.4 - - - +
50E PHE* 1.3 63.6 + - - +
52E GLN* 3.3 11.5 + - - +
53E ALA* 3.1 23.2 + - - +
80E THR* 4.5 7.6 - - + -
83E HIS* 5.3 7.0 - - + +
84E ILE* 4.2 19.5 - - + -
24F LEU* 4.6 18.6 - - + -
29F ILE* 4.9 9.4 - - + -
31F MET* 4.8 1.8 - - - -
63F TYR* 3.5 49.4 - - + +
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Residues in contact with PHE 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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25E LEU* 4.3 12.6 - - + -
26E LYS* 6.2 0.9 - - - -
46E SER 2.9 18.8 + - - +
47E GLN 3.5 4.3 - - - +
49E LEU* 1.3 79.1 - - - +
51E LEU* 1.3 80.2 + - + +
53E ALA* 3.1 17.1 + - + +
54E GLN* 3.1 49.7 + - + +
7F VAL* 3.4 28.5 - - + -
9F GLU* 5.3 0.2 - - - -
20F ILE* 3.9 15.5 - - + -
23F ARG* 3.4 49.8 - - + -
24F LEU* 3.6 15.9 - - + +
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Residues in contact with LEU 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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25E LEU* 3.7 36.1 - - + +
28E ARG* 3.0 56.3 + - + +
30E ILE* 4.1 9.0 - - + -
47E GLN 2.9 17.0 + - - +
48E LEU 3.2 0.9 + - - +
50E PHE* 1.3 92.8 - - + +
52E GLN* 1.3 62.7 + - - +
54E GLN* 3.3 5.8 + - + +
55E ASP 3.1 11.3 + - - +
60E ILE* 3.7 43.7 - - + -
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Residues in contact with GLN 52 (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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48E LEU 3.0 13.0 + - - +
49E LEU* 3.6 15.9 - - - +
51E LEU* 1.3 78.1 - - - +
53E ALA* 1.3 64.1 + - - +
54E GLN 3.1 1.2 + - - -
55E ASP 3.1 23.1 + - - -
56E SER* 3.4 12.8 + - - -
60E ILE* 4.8 1.0 - - - +
83E HIS* 4.5 5.5 + - - -
84E ILE* 3.3 24.2 - - + +
85E LYS* 2.8 43.4 - - - +
86E PRO* 3.9 16.8 - - + -
193F GLU* 4.8 2.6 + - - -
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Residues in contact with ALA 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 LEU 3.1 11.2 + - - +
50E PHE* 3.5 11.4 - - + +
52E GLN* 1.3 78.3 - - - +
54E GLN* 1.3 63.1 + - + +
23F ARG* 5.6 4.9 - - - +
27F ASP* 4.2 18.6 - - - +
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Residues in contact with GLN 54 (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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28E ARG* 4.2 7.6 - - - +
50E PHE* 3.1 44.0 + - + +
51E LEU* 3.4 11.9 - - + +
52E GLN 3.1 0.6 - - - -
53E ALA* 1.3 82.0 + - - +
55E ASP* 1.3 63.0 + - + +
9F GLU* 5.3 2.8 + - - -
23F ARG* 3.8 24.7 - - - +
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Residues in contact with ASP 55 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28E ARG* 2.8 41.5 + - - +
51E LEU 3.1 3.5 + - - +
52E GLN 3.1 4.4 + - - +
54E GLN* 1.3 85.0 - - + +
56E SER* 1.3 58.0 + - - +
57E GLU* 2.8 38.7 + - - +
58E LYS* 2.8 42.7 + - - +
86E PRO* 3.8 1.0 - - - +
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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