Contacts of the helix formed by residues 85 - 98 (chain A) in PDB entry 1NVB
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 SER 85 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82A VAL 3.7 9.5 + - - -
83A SER 3.4 3.0 + - - -
84A LYS* 1.3 75.7 - - - +
86A ARG* 1.3 65.4 + - - +
87A GLN* 3.6 10.8 + - - +
88A THR* 2.9 25.5 + - - -
89A LYS* 3.0 23.4 + - - +
120A LEU* 4.4 0.3 - - - +
155A ILE* 4.1 10.1 - - - +
156A ASP 4.0 10.1 - - - -
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Residues in contact with ARG 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A SER* 1.3 73.6 - - - +
87A GLN* 1.3 63.5 + - - +
89A LYS* 3.3 7.8 + - - +
90A ALA* 2.9 26.1 + - - +
155A ILE* 3.6 19.8 - - + +
156A ASP 4.6 1.5 + - - +
157A THR* 3.6 35.3 - - - +
158A PRO* 4.7 7.9 - - - +
164A ILE* 4.2 17.5 - - + +
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Residues in contact with GLN 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A ARG* 4.7 6.7 - - - +
85A SER* 3.6 10.9 - - - +
86A ARG* 1.3 80.6 - - - +
88A THR* 1.3 67.1 + - - +
90A ALA* 3.2 6.7 + - - +
91A ASP* 2.7 60.6 + - - +
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Residues in contact with THR 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A TYR* 5.7 0.4 - - + -
77A ARG* 3.1 46.9 + - + +
82A VAL 3.7 3.1 + - - -
83A SER* 3.1 36.3 + - - +
85A SER* 2.9 17.5 + - - -
87A GLN* 1.3 75.4 - - - +
89A LYS* 1.3 65.8 + - - +
91A ASP* 3.1 11.1 + - - +
92A ILE* 3.2 16.5 + - + +
120A LEU* 3.7 15.7 - - + -
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Residues in contact with LYS 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A SER 3.0 16.8 + - - +
86A ARG* 3.7 7.4 - - - +
88A THR* 1.3 77.3 - - - +
90A ALA* 1.3 63.9 + - - +
92A ILE* 3.4 3.2 + - - +
93A GLU* 2.8 57.0 + - - +
120A LEU* 4.0 15.0 - - + +
123A PHE* 3.3 54.0 - - + -
124A VAL* 3.7 19.2 - - + +
127A THR* 3.0 22.4 + - - +
155A ILE* 4.4 4.0 - - + -
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Residues in contact with ALA 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A ARG 2.9 18.6 + - - +
87A GLN* 3.3 6.7 - - - +
89A LYS* 1.3 77.7 - - - +
91A ASP* 1.3 54.9 + - - +
93A GLU* 3.1 15.7 + - - +
94A ASP* 2.7 45.3 + - - +
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Residues in contact with ASP 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A TYR* 3.6 10.3 - - - +
77A ARG* 2.9 30.0 + - - +
87A GLN* 2.7 44.6 + - - +
88A THR 3.1 0.6 + - - +
90A ALA* 1.3 74.6 - - - +
92A ILE* 1.3 60.7 + - - +
94A ASP* 3.8 11.6 - - - +
95A TRP* 2.9 31.0 + - - +
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Residues in contact with ILE 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A VAL* 4.5 28.3 - - + -
75A TYR* 3.7 36.8 - - + +
88A THR* 3.2 14.6 + - + +
89A LYS 3.7 5.2 - - - +
91A ASP* 1.3 76.1 - - - +
93A GLU* 1.3 57.8 + - - +
95A TRP* 3.3 4.0 + - + +
96A MET* 2.9 38.8 + - + +
120A LEU* 3.5 39.5 - - + -
121A THR* 5.4 0.9 - - - +
124A VAL* 4.0 27.1 - - + -
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Residues in contact with GLU 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A LYS* 2.8 50.1 + - - +
90A ALA* 3.1 15.4 + - - +
92A ILE* 1.3 74.7 - - - +
94A ASP* 1.3 69.1 + - - +
96A MET* 3.0 16.4 + - - +
97A LEU* 3.0 23.8 + - + +
124A VAL* 3.8 20.9 - - + +
127A THR* 3.1 13.3 + - - -
128A TYR* 4.2 16.0 + - + -
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Residues in contact with ASP 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A ALA* 2.7 30.2 + - - +
91A ASP* 3.9 11.9 - - - +
93A GLU* 1.3 73.8 - - - +
95A TRP* 1.3 58.5 + - - +
97A LEU* 3.6 13.4 + - - +
98A SER* 2.9 28.9 + - - -
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Residues in contact with TRP 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A VAL* 3.5 26.7 - - + -
73A LEU* 3.4 32.8 - - + -
74A ILE 3.4 30.5 + - - -
75A TYR* 3.5 33.8 - + + -
91A ASP 2.9 19.1 + - - +
92A ILE* 3.4 4.9 - - + +
94A ASP* 1.3 77.3 - - - +
96A MET* 1.3 84.9 + - + +
98A SER* 2.7 23.7 + - - -
99A GLN* 3.0 39.1 + - - +
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Residues in contact with MET 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A VAL* 4.1 13.7 - - + -
92A ILE* 2.9 26.8 + - + +
93A GLU 3.6 3.6 - - - +
95A TRP* 1.3 98.1 - - + +
97A LEU* 1.3 61.7 + - - +
99A GLN* 3.3 13.6 + - - +
103A CYS* 3.2 28.9 + - + -
107A THR* 3.6 30.7 - - + -
109A VAL* 4.0 15.3 - - + -
124A VAL* 4.3 17.5 - - - -
128A TYR* 3.4 45.5 - - + +
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Residues in contact with LEU 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A GLU* 3.0 26.7 + - + +
94A ASP* 3.9 11.4 - - - +
96A MET* 1.3 75.9 - - - +
98A SER* 1.3 58.0 + - - +
99A GLN 3.2 1.7 + - - -
102A PRO* 3.0 32.3 - - + +
128A TYR* 3.3 29.6 + - + +
129A MET* 4.0 20.6 - - + -
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Residues in contact with SER 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A ASP 2.9 15.3 + - - -
95A TRP* 2.7 26.4 + - - -
97A LEU* 1.3 75.5 - - - +
99A GLN* 1.3 69.9 + - - +
100A ASN* 5.3 0.7 - - - +
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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