Contacts of the helix formed by residues 77 - 92 (chain B) in PDB entry 3NAV
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 THR 77 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53B PRO* 5.7 1.6 - - - -
75B LYS* 3.6 10.9 + - + +
76B THR* 1.3 78.6 - - - +
78B PRO* 1.3 73.1 - - + +
79B ASP* 3.5 9.7 + - - +
80B ILE* 3.2 28.7 + - + +
81B CYS* 2.8 33.1 + - - -
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Residues in contact with PRO 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A GLU* 5.9 2.2 - - - +
52B MET* 4.1 22.2 - - + -
53B PRO* 5.6 4.9 - - + +
77B THR* 1.3 89.3 - - + +
79B ASP* 1.3 64.6 + - - +
81B CYS* 3.0 2.9 + - + +
82B PHE* 2.9 32.4 + - + -
105B LEU* 4.6 28.9 - - + +
109B ARG* 3.7 21.3 - - - +
114B PHE* 6.2 0.7 - - + -
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Residues in contact with ASP 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77B THR* 3.2 9.2 + - - +
78B PRO* 1.3 81.4 - - - +
80B ILE* 1.3 58.1 + - + +
82B PHE* 3.3 7.3 + - - +
83B GLU* 3.0 39.1 + - - +
109B ARG* 2.8 41.2 + - - +
117B ARG* 3.1 15.6 + - - +
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Residues in contact with ILE 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B PRO* 4.2 18.6 - - + -
75B LYS 3.5 24.7 - - - +
76B THR* 4.2 13.9 - - + -
77B THR* 3.2 19.7 + - + +
79B ASP* 1.3 75.5 - - + +
81B CYS* 1.3 66.5 + - - +
83B GLU* 2.9 20.5 + - + +
84B LEU* 2.8 42.1 + - + +
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Residues in contact with CYS 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B ILE* 3.7 26.8 - - + +
52B MET* 3.7 36.3 - - + -
53B PRO* 3.7 12.6 - - - -
76B THR* 3.6 20.2 - - - -
77B THR 2.8 24.4 + - - -
78B PRO 3.0 6.9 + - - +
80B ILE* 1.3 71.7 - - - +
82B PHE* 1.3 63.9 + - - +
84B LEU* 3.2 1.7 + - - +
85B ILE* 3.0 28.8 + - - +
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Residues in contact with PHE 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B MET* 3.6 27.6 - - + -
78B PRO* 2.9 28.5 + - + -
79B ASP* 3.7 6.5 - - - +
81B CYS* 1.3 77.6 - - - +
83B GLU* 1.3 55.9 + - - +
85B ILE* 3.4 8.3 + - + +
86B ALA* 2.9 28.9 + - - +
99B LEU* 4.5 3.6 - - + -
109B ARG* 4.9 3.8 - - - -
114B PHE* 3.8 28.3 - + - -
117B ARG* 3.6 54.1 - - + +
118B CYS* 3.7 28.0 - - - -
121B ALA* 3.8 15.4 - - + +
123B VAL* 4.9 0.4 - - + -
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Residues in contact with GLU 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B ASP* 3.0 30.4 + - - +
80B ILE* 2.9 21.4 + - + +
82B PHE* 1.3 78.1 - - - +
84B LEU* 1.3 63.4 + - + +
86B ALA* 3.3 6.8 + - - +
87B GLN* 3.2 34.0 + - - +
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Residues in contact with LEU 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B ILE* 3.7 24.0 - - + -
26B GLY* 4.6 4.5 - - - +
30B PRO* 3.9 35.9 - - + +
31B GLU* 5.6 2.5 - - - +
33B SER* 4.6 4.9 - - - +
34B LEU* 3.8 16.7 - - + +
37B MET* 4.1 14.4 - - + -
80B ILE* 2.8 32.2 + - + +
81B CYS 3.7 5.4 - - - +
83B GLU* 1.3 74.5 - - + +
85B ILE* 1.3 66.8 + - - +
87B GLN* 3.1 22.8 + - - +
88B ILE* 3.0 27.9 + - - +
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Residues in contact with ILE 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B ILE* 3.8 21.5 - - + -
37B MET* 4.9 1.5 - - - +
50B LEU* 4.3 11.4 - - + -
52B MET* 4.4 5.6 - - + -
81B CYS 3.0 24.4 + - - +
82B PHE* 3.6 16.2 - - + +
84B LEU* 1.3 77.7 - - + +
86B ALA* 1.3 62.8 + - - +
87B GLN 3.3 0.2 + - - -
88B ILE* 3.3 7.8 + - - +
89B ARG* 3.0 20.4 + - - +
97B ILE* 4.3 17.8 - - + +
99B LEU* 3.7 28.0 - - + -
121B ALA* 3.7 18.4 - - + +
123B VAL* 3.9 23.1 - - + +
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Residues in contact with ALA 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82B PHE 2.9 18.5 + - - +
83B GLU* 3.3 8.5 + - - +
84B LEU 3.2 0.4 - - - -
85B ILE* 1.3 76.3 - - - +
87B GLN* 1.3 58.6 + - + +
89B ARG* 3.4 3.7 + - - +
90B ALA* 3.1 27.4 + - - +
120B LYS 5.2 2.5 - - - +
121B ALA* 3.7 22.9 - - - +
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Residues in contact with GLN 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B LEU* 3.2 30.9 - - + +
83B GLU* 3.2 23.6 + - - +
84B LEU* 3.1 26.0 + - - +
86B ALA* 1.3 76.5 - - + +
88B ILE* 1.3 63.6 + - - +
90B ALA* 3.4 6.5 + - - +
91B ARG* 3.2 24.8 + - - +
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Residues in contact with ILE 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B LEU* 3.9 24.0 - - + +
37B MET* 3.6 38.8 - - + -
38B GLN* 4.0 19.5 - - + +
41B ILE* 3.9 16.8 - - + -
48B LEU* 4.4 9.6 - - + -
50B LEU* 6.3 0.2 - - + -
84B LEU 3.0 14.5 + - - +
85B ILE* 3.7 8.7 - - - +
87B GLN* 1.3 74.6 - - - +
89B ARG* 1.3 58.0 + - - +
91B ARG* 3.5 0.6 + - + -
92B ASN* 2.7 46.5 + - + +
97B ILE* 4.2 16.4 - - + -
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Residues in contact with ARG 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3B ARG* 3.3 29.8 - - - +
85B ILE 3.0 17.2 + - - +
86B ALA 3.6 4.9 - - - +
87B GLN 3.2 0.2 - - - -
88B ILE* 1.3 76.2 - - - +
90B ALA* 1.3 64.1 + - - +
92B ASN 2.9 39.3 + - - -
93B PRO* 3.3 14.4 + - - +
95B THR 2.8 24.6 + - - -
97B ILE* 3.6 21.1 - - + +
121B ALA 3.7 17.0 - - - +
122B GLY* 2.8 26.4 + - - -
124B ASP* 2.6 30.1 + - - -
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Residues in contact with ALA 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86B ALA 3.1 16.3 + - - +
87B GLN* 3.7 7.9 - - - +
88B ILE 3.4 0.2 - - - -
89B ARG* 1.3 77.9 - - - +
91B ARG* 1.3 61.0 + - - +
92B ASN 3.6 0.2 + - - -
93B PRO* 4.0 11.8 - - - +
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Residues in contact with ARG 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B GLN* 3.3 44.1 - - - +
42B ASP* 4.3 11.3 + - - -
87B GLN 3.2 14.6 + - - +
88B ILE* 4.8 0.9 - - + -
90B ALA* 1.3 80.9 - - - +
92B ASN* 1.3 62.7 + - - +
93B PRO* 3.6 7.3 - - - +
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Residues in contact with ASN 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B GLN* 2.8 43.1 + - - -
41B ILE* 3.5 23.1 - - + +
88B ILE* 2.7 37.7 + - + +
89B ARG* 2.9 20.3 + - - +
91B ARG* 1.3 90.2 + - - +
93B PRO* 1.3 66.8 - - - +
94B GLU 3.0 4.6 + - - -
95B THR* 3.1 21.8 + - - +
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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