Contacts of the helix formed by residues 37 - 55 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35G GLN* 3.0 28.0 + - + +
36G ILE* 1.3 76.2 - - - +
38G ASP* 1.3 59.9 + - - +
39G ASN* 2.9 21.0 + - - +
40G VAL* 3.0 14.3 + - - +
41G ALA* 2.8 29.3 + - - +
70G SER* 4.4 5.2 - - - -
73G ALA* 3.6 10.7 - - - +
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Residues in contact with ASP 38 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A GLY 3.3 21.2 - - - +
34A SER* 4.9 1.6 - - - -
65A ASN* 3.7 24.9 + - - +
67A PRO* 4.1 21.8 - - - +
37G ASP* 1.3 77.8 - - - +
39G ASN* 1.3 59.2 + - - +
41G ALA* 3.9 2.4 - - - +
42G ASN* 2.9 29.8 + - - +
70G SER* 4.3 5.8 + - - -
72G THR* 4.6 3.6 + - - -
73G ALA* 3.6 19.0 + - - +
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Residues in contact with ASN 39 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A TYR* 4.2 2.8 + - - -
33A GLY 4.8 4.9 - - - +
34A SER* 5.3 6.2 - - - -
37G ASP* 2.9 10.3 + - - +
38G ASP* 1.3 75.3 - - - +
40G VAL* 1.3 71.4 + - + +
42G ASN* 3.1 6.5 + - - +
43G SER* 2.9 24.1 + - - -
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Residues in contact with VAL 40 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32G LEU* 3.6 31.4 - - + -
34G SER* 3.5 12.8 - - - +
35G GLN* 3.5 28.5 - - - +
36G ILE* 4.5 5.8 - - + -
37G ASP* 3.0 20.8 + - - +
39G ASN* 1.3 78.2 - - + +
41G ALA* 1.3 65.6 + - - +
43G SER* 3.0 8.8 + - - -
44G ILE* 2.8 34.5 + - + +
77G ILE* 5.1 1.6 - - + -
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Residues in contact with ALA 41 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A ASN* 4.7 3.6 - - - +
36G ILE* 5.0 0.6 - - + +
37G ASP 2.8 16.5 + - - +
38G ASP* 3.9 4.3 - - - +
40G VAL* 1.3 76.8 - - - +
42G ASN* 1.3 58.1 + - - +
45G VAL* 2.8 37.1 + - - +
73G ALA* 3.4 34.3 - - + +
76G ALA* 4.5 9.4 - - + -
77G ILE* 3.9 17.7 - - + +
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Residues in contact with ASN 42 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A TYR* 3.1 28.6 + - - +
31A MET* 3.5 36.1 - - - +
32A LEU 4.6 1.6 + - - -
33A GLY* 3.8 27.0 + - - +
65A ASN* 5.6 4.9 - - - +
93A ILE* 5.3 5.0 - - - +
38G ASP 2.9 19.9 + - - +
39G ASN* 3.5 7.2 - - - +
41G ALA* 1.3 75.8 - - - +
43G SER* 1.3 59.6 + - - +
45G VAL* 4.0 3.5 - - - +
46G SER* 3.1 29.5 + - - -
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Residues in contact with SER 43 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A ILE* 3.4 28.1 + - - +
5A PRO* 3.6 6.8 - - - +
20A ILE* 4.9 1.4 - - - +
21A TYR* 3.4 15.0 + - - -
39G ASN 2.9 12.2 + - - -
40G VAL* 3.4 9.2 - - - -
42G ASN* 1.3 76.1 - - - +
44G ILE* 1.3 68.2 + - - +
46G SER* 3.4 4.5 + - - -
47G GLN* 2.9 42.8 + - - +
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Residues in contact with ILE 44 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30G ILE* 3.7 28.5 - - + -
31G MET 4.0 13.7 - - - +
32G LEU* 4.4 17.3 - - + -
40G VAL* 2.8 32.4 + - + +
41G ALA 3.8 2.0 - - - +
43G SER* 1.3 70.5 - - - +
45G VAL* 1.3 65.1 + - - +
47G GLN* 3.0 15.1 + - - +
48G LEU* 2.9 32.3 + - + +
62G LEU* 4.6 10.8 - - + -
77G ILE* 3.9 39.9 - - + -
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Residues in contact with VAL 45 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A MET* 3.8 21.8 - - + -
63A TYR* 5.6 1.6 - - + -
93A ILE* 3.9 17.7 - - + -
41G ALA 2.8 27.2 + - - +
42G ASN* 4.0 3.6 - - - +
44G ILE* 1.3 71.4 - - - +
46G SER* 1.3 63.3 + - - +
48G LEU* 3.0 13.2 + - - +
49G LEU* 2.9 31.8 + - + +
76G ALA* 3.7 21.5 - - + +
77G ILE* 4.1 6.3 - - - +
80G THR* 3.6 31.2 - - + +
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Residues in contact with SER 46 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A ILE* 3.8 26.9 - - - +
21A TYR* 3.3 19.6 - - - -
24A LEU* 3.7 22.5 - - - +
31A MET* 3.7 8.5 - - - +
42G ASN 3.1 17.5 + - - -
43G SER 3.6 4.0 - - - -
45G VAL* 1.3 79.5 - - - +
47G GLN* 1.3 58.4 + - - +
49G LEU* 3.3 2.7 + - - +
50G PHE* 2.9 31.0 + - - +
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Residues in contact with GLN 47 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A ILE* 5.4 0.4 - - - +
5A PRO* 3.6 25.0 - - + +
20A ILE* 4.3 11.0 - - + -
25G LEU* 3.8 24.0 - - + +
29G ILE 4.9 0.2 - - - +
30G ILE* 3.4 41.2 - - + +
31G MET 4.8 1.8 + - - -
43G SER* 2.9 44.9 + - - +
44G ILE* 3.4 17.6 - - - +
46G SER* 1.3 73.2 - - - +
48G LEU* 1.3 57.4 + - - +
50G PHE* 3.6 1.7 - - - +
51G LEU* 2.9 33.6 + - - +
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Residues in contact with LEU 48 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30G ILE* 3.8 20.2 - - + -
44G ILE* 2.9 30.7 + - + +
45G VAL* 3.3 8.5 - - - +
47G GLN* 1.3 75.0 - - - +
49G LEU* 1.3 62.2 + - - +
51G LEU* 3.2 5.5 + - - +
52G GLN* 3.1 22.7 + - - +
60G ILE* 4.3 9.4 - - + -
62G LEU* 6.0 2.7 - - + -
77G ILE* 4.5 2.9 - - + +
80G THR* 3.8 27.8 - - + -
81G ILE* 3.8 24.9 - - + +
84G ILE* 4.1 17.2 - - + +
88G VAL* 4.1 28.3 - - + -
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Residues in contact with LEU 49 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A LEU* 4.4 23.6 - - + -
29A ILE* 4.8 9.0 - - + -
31A MET* 4.7 2.0 - - - -
63A TYR* 3.9 43.5 - - + +
45G VAL* 2.9 31.7 + - + +
46G SER 3.8 5.4 - - - +
48G LEU* 1.3 72.2 - - - +
50G PHE* 1.3 63.2 + - - +
52G GLN* 3.4 13.1 + - - +
53G ALA* 3.1 23.0 + - - +
80G THR* 4.4 9.0 - - + -
83G HIS* 5.4 7.4 - - + +
84G ILE* 4.2 18.8 - - + -
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Residues in contact with PHE 50 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A VAL* 3.4 37.7 - - + -
9A GLU* 5.4 0.2 - - - -
20A ILE* 3.6 21.3 - - + -
23A ARG* 3.6 33.7 - - + -
24A LEU* 3.9 12.9 - - + +
25G LEU* 4.3 13.0 - - + -
26G LYS* 6.3 0.9 - - - -
46G SER 2.9 17.9 + - - +
47G GLN 3.6 4.5 - - - +
49G LEU* 1.3 77.4 - - - +
51G LEU* 1.3 80.1 + - + +
53G ALA* 3.3 7.9 + - + +
54G GLN* 3.1 58.4 + - + +
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Residues in contact with LEU 51 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25G LEU* 3.6 35.7 - - + +
26G LYS 5.8 0.2 - - - +
28G ARG* 3.0 60.3 + - + +
30G ILE* 4.1 10.5 - - + -
47G GLN 2.9 16.5 + - - +
48G LEU 3.2 4.7 + - - +
50G PHE* 1.3 94.0 - - + +
52G GLN* 1.3 61.2 + - - +
54G GLN* 3.3 4.8 + - + +
55G ASP 3.0 11.8 + - - +
60G ILE* 3.8 36.8 - - + -
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Residues in contact with GLN 52 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193A GLU* 5.0 2.6 + - - -
48G LEU 3.1 11.9 + - - +
49G LEU* 3.7 15.0 - - - +
50G PHE 3.2 0.2 - - - -
51G LEU* 1.3 75.1 - - - +
53G ALA* 1.3 64.3 + - - +
55G ASP* 3.1 24.5 + - - -
56G SER* 3.4 12.3 + - - -
60G ILE* 4.8 0.6 - - - +
83G HIS* 4.7 4.4 + - - -
84G ILE* 3.4 24.0 - - + +
85G LYS* 2.9 42.4 - - - +
86G PRO* 3.9 19.1 - - + -
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Residues in contact with ALA 53 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A ARG* 5.3 7.6 - - - +
24A LEU* 6.3 1.1 - - + -
27A ASP* 4.4 16.8 - - - +
49G LEU 3.1 10.4 + - - +
50G PHE* 3.6 12.1 - - + +
52G GLN* 1.3 78.5 + - - +
54G GLN* 1.3 63.3 + - + +
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Residues in contact with GLN 54 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A GLU* 5.3 2.8 + - - -
23A ARG* 4.2 16.0 - - - +
28G ARG* 4.2 8.1 - - - +
50G PHE* 3.1 53.0 + - + +
51G LEU* 3.4 10.8 - - + +
52G GLN 3.1 0.8 - - - -
53G ALA* 1.3 81.2 + - - +
55G ASP* 1.3 61.1 + - + +
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Residues in contact with ASP 55 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28G ARG* 2.9 39.1 + - - +
51G LEU 3.0 4.0 - - - +
52G GLN* 3.1 5.8 + - - +
54G GLN* 1.3 82.6 - - + +
56G SER* 1.3 58.7 + - - +
57G GLU* 2.7 40.0 + - - +
58G LYS* 2.8 44.3 + - - +
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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