Contacts of the helix formed by residues 57 - 65 (chain J) in PDB entry 6I3N
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 GLU 57 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32I ARG* 2.9 31.8 + - - -
35I LEU* 4.4 0.7 - - - +
36I PHE* 5.6 0.2 - - - -
55J ASP 3.9 1.6 + - - -
56J PHE* 1.3 78.3 - - - +
58J TYR* 1.3 68.5 + - - +
59J LEU* 3.3 22.7 - - + +
60J GLU* 3.3 21.0 + - + +
61J ILE* 3.2 20.9 + - - +
23M ALA* 4.2 11.0 - - - +
26M ASN* 6.1 0.7 - - - -
116M TYR* 3.3 31.0 + - + -
119M LYS* 3.3 32.9 + - + +
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Residues in contact with TYR 58 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39I VAL* 6.2 0.7 - - + -
56J PHE 4.0 0.2 + - - -
57J GLU* 1.3 76.4 - - - +
59J LEU* 1.3 73.9 + - + +
61J ILE* 3.3 8.1 + - + +
62J ARG* 2.9 49.5 + - + +
65J GLU* 5.7 0.9 - - - -
22M LEU 4.9 0.2 - - - -
23M ALA* 4.0 15.1 + - - +
25M LEU 3.7 16.6 - - - +
26M ASN* 4.0 13.0 - - - +
27M MET* 3.6 34.5 - - + -
30M ARG* 3.5 41.7 - - - -
73M ARG* 4.1 4.3 + - - -
76M ASP* 2.5 38.5 + - - -
79M GLN* 4.9 6.5 - - + -
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Residues in contact with LEU 59 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32I ARG* 4.9 1.1 - - - +
35I LEU* 3.5 44.7 - - + +
36I PHE* 3.7 40.6 - - + -
39I VAL* 4.1 15.4 - - + +
57J GLU* 3.3 17.7 - - - +
58J TYR* 1.3 90.1 - - + +
60J GLU* 1.3 60.3 + - - +
62J ARG* 3.7 3.1 - - + +
63J GLN* 2.9 28.8 + - - +
23M ALA* 3.9 18.8 - - + -
79M GLN* 4.8 12.3 - - + +
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Residues in contact with GLU 60 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42F GLN 4.7 0.3 - - - +
43F VAL* 3.2 48.5 - - + +
32I ARG* 4.4 3.5 + - - -
35I LEU* 3.4 31.5 - - - +
56J PHE* 4.1 12.8 - - + -
57J GLU* 3.3 37.4 + - + +
59J LEU* 1.3 74.7 - - - +
61J ILE* 1.3 60.4 + - - +
63J GLN* 3.2 7.3 + - - +
64J LEU* 2.9 33.7 + - - +
119M LYS* 4.0 8.8 + - - +
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Residues in contact with ILE 61 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47J TRP* 3.5 11.0 - - + -
48J THR* 3.8 32.5 - - + +
51J ALA* 3.7 24.5 - - + -
52J GLU* 4.0 15.7 - - + +
56J PHE* 4.0 17.0 - - + +
57J GLU 3.2 17.0 + - - +
58J TYR* 3.7 8.1 - - - +
60J GLU* 1.3 74.2 - - - +
62J ARG* 1.3 58.5 + - - +
64J LEU* 3.2 8.4 + - + +
65J GLU* 2.9 29.7 + - - +
26M ASN* 5.8 0.9 - - + -
27M MET* 3.9 29.2 - - + +
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Residues in contact with ARG 62 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39I VAL* 3.7 42.6 - - + +
40I ARG 4.6 12.3 + - - +
40J ARG* 5.1 0.8 - - - +
58J TYR* 2.9 43.1 + - + +
59J LEU* 3.7 8.7 - - - +
61J ILE* 1.3 77.4 - - - +
63J GLN* 1.3 59.6 + - - +
65J GLU* 2.4 45.4 + - - +
66J THR* 3.6 17.7 - - - +
73M ARG* 3.3 41.7 - - - +
76M ASP* 3.8 7.6 + - - +
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Residues in contact with GLN 63 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42F GLN* 3.4 36.5 - - + +
43F VAL* 3.3 25.1 - - - +
34I SER 6.4 0.2 - - - -
35I LEU* 4.3 15.3 - - + -
38I ASN* 4.6 21.7 - - - +
39I VAL* 5.7 1.5 - - - +
68I ALA* 6.1 2.4 - - - +
69I ASP* 5.9 3.0 - - - +
59J LEU 2.9 17.2 + - - +
60J GLU* 3.2 4.4 + - - +
62J ARG* 1.3 76.4 - - - +
64J LEU* 1.3 65.7 + - - +
66J THR* 2.7 33.4 + - + +
67J GLN* 4.2 17.0 + - - +
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Residues in contact with LEU 64 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41F THR* 6.0 0.4 - - - +
43F VAL* 4.2 14.1 - - + -
47J TRP* 3.9 16.2 - - + -
51J ALA* 5.4 1.1 - - + -
56J PHE* 5.2 5.6 - - + -
60J GLU 2.9 21.9 + - - +
61J ILE* 3.2 9.1 + - + +
63J GLN* 1.3 83.6 - - - +
65J GLU* 1.3 64.5 + - - +
66J THR 3.2 0.7 + - - -
67J GLN* 3.5 35.5 + - - +
70J PRO* 3.3 19.7 - - - +
73J ARG* 3.9 22.0 - - + +
74J LEU* 3.7 35.4 - - + -
77J ALA* 5.0 4.9 - - + -
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Residues in contact with GLU 65 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40J ARG* 2.6 36.8 + - - +
47J TRP* 3.5 24.2 - - + -
48J THR* 4.3 4.9 - - - +
58J TYR* 5.7 1.0 - - - -
61J ILE* 2.9 20.7 + - - +
62J ARG* 2.4 48.8 + - - +
63J GLN 3.2 0.6 - - - -
64J LEU* 1.3 78.3 - - - +
66J THR* 1.3 62.4 + - + +
67J GLN 3.9 3.8 - - - +
70J PRO* 4.6 5.5 - - - +
27M MET* 4.6 8.1 - - - +
73M ARG* 5.5 0.2 + - - -
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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
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Atomic class I II III IV V VI VII VIII
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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