Contacts of the helix formed by residues 75 - 90 (chain A) in PDB entry 6NSV
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 GLN 75 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70A TYR* 2.8 39.6 + - + +
73A MET* 3.6 38.2 + - - +
74A GLN* 1.3 75.2 - - - +
76A HIS* 1.3 59.4 - - - +
78A GLN* 3.2 33.4 + - + +
79A ALA* 2.9 24.4 + - - +
144B LYS* 3.4 37.2 + - - +
145B LYS* 4.9 5.6 - - + +
148B ASN* 4.1 13.1 - - - +
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Residues in contact with HIS 76 (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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71A LEU* 4.0 21.1 - - + -
74A GLN* 3.2 31.1 + - - -
75A GLN* 1.3 73.8 - - - +
77A GLU* 1.3 58.3 + - - +
78A GLN* 3.8 0.4 + - - -
79A ALA* 3.3 8.6 + - - +
80A LEU* 2.9 28.6 + - - +
103A CYS* 3.8 8.2 - - + +
106A GLU* 3.8 28.2 + - + +
107A MET* 3.9 26.2 - - + +
202A NA 2.3 31.6 - - - -
106B GLU* 5.9 4.3 - - - -
145B LYS* 3.9 12.6 + - - +
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Residues in contact with GLU 77 (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 GLN 3.3 0.2 - - - -
76A HIS* 1.3 77.5 - - + +
78A GLN* 1.3 75.2 + - - +
80A LEU* 3.3 9.5 + - - +
81A ALA* 3.0 23.2 + - - +
107A MET* 3.5 25.3 - - + +
152B GLU* 3.9 24.2 - - - +
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Residues in contact with GLN 78 (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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70A TYR* 3.6 32.1 - - + -
75A GLN* 3.2 44.5 + - + +
76A HIS 3.8 0.2 + - - -
77A GLU* 1.3 88.3 + - - +
79A ALA* 1.3 63.9 + - - +
81A ALA* 3.4 6.4 + - - +
82A ASP* 3.1 20.4 + - - +
85A ARG* 4.7 1.0 + - - -
145B LYS* 5.7 1.7 - - - -
148B ASN* 5.1 10.9 - - - +
152B GLU* 5.2 7.1 + - - -
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Residues in contact with ALA 79 (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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67A ALA* 3.5 32.8 - - + +
70A TYR* 3.7 9.5 - - + -
71A LEU* 4.1 9.6 - - + -
75A GLN 2.9 13.3 + - - +
76A HIS 3.5 4.3 - - - +
78A GLN* 1.3 76.1 - - - +
80A LEU* 1.3 62.9 + - - +
82A ASP 3.2 1.4 + - - -
83A CYS* 2.9 26.7 + - - -
103A CYS* 3.4 23.3 - - - -
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Residues in contact with LEU 80 (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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76A HIS 2.9 13.7 + - - +
77A GLU* 3.5 10.8 - - - +
78A GLN 3.3 0.2 - - - -
79A ALA* 1.3 74.9 - - - +
81A ALA* 1.3 67.0 + - + +
83A CYS* 3.1 8.3 + - - +
84A ARG* 3.0 46.1 + - + +
100A LEU* 3.7 20.9 - - + -
103A CYS* 3.7 10.5 - - + -
104A GLN* 4.3 17.0 - - + +
107A MET* 4.2 22.2 - - + -
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Residues in contact with ALA 81 (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 GLU 3.0 16.3 + - - +
78A GLN* 3.7 6.1 - - - +
79A ALA 3.2 0.2 - - - -
80A LEU* 1.3 81.5 - - + +
82A ASP* 1.3 62.3 + - - +
84A ARG* 3.2 10.6 + - - +
85A ARG* 3.0 50.4 + - - +
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Residues in contact with ASP 82 (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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63A TYR* 3.4 38.0 - - - +
66A ARG* 2.7 45.5 + - - +
67A ALA* 3.9 4.5 - - + -
70A TYR* 3.2 16.1 - - - -
78A GLN 3.1 12.8 + - - +
79A ALA 3.6 7.0 - - - +
81A ALA* 1.3 76.4 - - - +
83A CYS* 1.3 63.3 + - - +
85A ARG* 2.8 23.1 + - - +
86A ALA* 2.9 19.8 + - - +
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Residues in contact with CYS 83 (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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64A THR* 5.1 1.8 - - - -
67A ALA* 3.9 9.9 - - - -
79A ALA 2.9 19.0 + - - -
80A LEU* 3.1 8.5 + - - +
82A ASP* 1.3 76.3 - - - +
84A ARG* 1.3 57.4 + - - +
86A ALA* 3.3 7.3 + - - +
87A LEU* 3.0 34.7 + - - +
96A ALA* 3.7 17.4 - - - +
99A PHE* 3.7 20.0 - - - -
100A LEU* 3.6 40.6 - - + -
103A CYS* 4.8 0.7 - - - -
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Residues in contact with ARG 84 (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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80A LEU* 3.0 36.4 + - + +
81A ALA* 3.6 9.6 - - - +
83A CYS* 1.3 77.3 - - - +
85A ARG* 1.3 62.8 + - + +
87A LEU* 3.3 15.4 + - - +
88A GLU* 3.1 29.8 + - - +
100A LEU* 3.3 28.7 - - + +
104A GLN* 3.7 24.0 - - - +
112A GLU* 4.9 5.5 + - - -
116A ASN* 5.1 1.8 + - - +
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Residues in contact with ARG 85 (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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63A TYR* 3.6 36.3 - - + -
66A ARG* 3.9 9.0 - - - +
70A TYR* 6.0 0.4 - - - -
78A GLN 4.7 1.0 + - - -
81A ALA* 3.0 27.6 + - - +
82A ASP* 2.8 45.1 + - - +
84A ARG* 1.3 76.4 - - + +
86A ALA* 1.3 63.7 + - - +
88A GLU* 3.2 22.0 + - - +
89A LEU* 3.4 19.0 + - + +
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Residues in contact with ALA 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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60A ALA* 3.6 28.1 - - + +
63A TYR* 4.0 5.5 - - + +
64A THR* 3.5 32.5 - - + -
82A ASP 2.9 12.3 + - - +
83A CYS 3.5 7.6 - - - +
85A ARG* 1.3 77.8 - - - +
87A LEU* 1.3 57.7 + - - +
89A LEU* 2.9 4.5 + - - -
90A ASP 2.8 27.8 + - - +
93A SER* 5.4 0.9 - - - +
96A ALA* 4.1 4.3 - - + -
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Residues in contact with LEU 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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83A CYS 3.0 23.0 + - - +
84A ARG* 3.3 17.0 + - - +
86A ALA* 1.3 75.5 - - - +
88A GLU* 1.3 62.5 + - - +
89A LEU 3.4 0.3 + - - -
90A ASP 3.8 11.4 - - - +
91A GLY* 3.5 24.1 + - - +
93A SER 4.6 0.4 - - - +
96A ALA* 3.8 19.7 - - + +
97A HIS* 3.3 41.1 - - + +
100A LEU* 3.9 28.5 - - + -
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Residues in contact with GLU 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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84A ARG* 3.1 18.2 + - - +
85A ARG* 3.4 15.8 - - - +
87A LEU* 1.3 79.2 - - - +
89A LEU* 1.3 62.7 + - + +
91A GLY 5.4 0.2 + - - -
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Residues in contact with LEU 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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57A PRO 3.8 7.9 - - - +
58A LEU* 3.8 45.5 - - + +
59A VAL 4.0 1.3 - - - +
60A ALA* 3.9 13.5 - - + +
63A TYR* 3.5 35.2 - - + +
85A ARG* 3.4 11.6 + - + +
86A ALA 2.9 7.1 + - - +
88A GLU* 1.3 84.6 - - + +
90A ASP* 1.4 58.6 + - - +
91A GLY 4.1 0.9 - - - -
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Residues in contact with ASP 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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60A ALA* 3.6 20.5 - - + +
86A ALA 2.8 13.6 + - - +
87A LEU* 3.7 7.0 - - - +
89A LEU* 1.4 73.5 - - - +
91A GLY* 1.3 62.6 + - - +
92A GLN* 3.1 21.3 + - - +
93A SER* 3.1 35.5 + - - -
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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