Contacts of the helix formed by residues 78 - 93 (chain B) in PDB entry 6WNX
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 78 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A MET 4.6 7.5 - - - +
2A LEU* 4.5 28.9 - - + +
77B VAL* 1.3 78.8 - - - +
79B GLN* 1.3 64.9 + - - +
80B GLY* 3.2 7.8 + - - +
81B THR* 2.6 45.1 + - - -
82B LEU* 3.0 15.6 + - - +
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Residues in contact with GLN 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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2A LEU 3.4 18.5 + - - +
3A GLN* 3.0 8.8 - - - +
4A ARG* 3.0 29.9 + - - +
6A PHE* 3.5 16.5 - - + -
77B VAL 3.8 0.2 + - - -
78B ASP* 1.3 72.0 - - - +
80B GLY* 1.3 54.0 + - - +
82B LEU* 3.2 11.2 + - - +
83B PHE* 2.8 32.6 + - - +
108B MET* 3.4 33.1 - - + +
120B THR* 3.1 24.4 + - - +
121B PHE* 3.4 20.0 - - - -
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Residues in contact with GLY 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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1A MET 3.9 12.2 + - - -
2A LEU 4.5 0.8 - - - -
4A ARG* 3.8 30.9 + - - +
78B ASP* 3.2 7.5 + - - -
79B GLN* 1.3 78.2 - - - +
81B THR* 1.3 56.2 + - - +
83B PHE* 3.2 5.3 + - - +
84B GLU* 3.0 32.3 + - - +
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Residues in contact with THR 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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48B ILE* 4.0 18.6 - - + -
51B LYS* 4.6 11.0 - - + -
77B VAL* 3.7 24.3 - - + +
78B ASP* 2.6 37.1 + - - -
80B GLY* 1.3 68.4 - - - +
82B LEU* 1.3 55.3 + - - +
84B GLU* 3.1 10.4 + - - +
85B LEU* 2.8 41.7 + - + +
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Residues in contact with LEU 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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6A PHE* 4.1 12.3 - - + -
75B LEU* 4.1 19.5 - - + +
77B VAL* 3.8 10.4 - - + +
78B ASP 3.0 12.2 + - - +
79B GLN* 3.2 12.5 + - - +
81B THR* 1.3 76.0 - - - +
83B PHE* 1.3 62.0 + - - +
85B LEU* 3.1 11.5 + - + +
86B ILE* 3.0 21.9 + - + +
101B THR* 4.0 33.2 - - + +
104B THR* 4.2 20.0 - - + -
105B VAL* 3.8 24.5 - - + -
108B MET* 4.3 12.6 - - - -
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Residues in contact with PHE 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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4A ARG* 3.5 37.0 - - + +
6A PHE* 3.5 29.7 - + + -
9A ALA* 3.5 31.0 - - + -
10A LEU* 4.1 21.8 - - + -
13A GLN* 4.0 15.0 - - - -
79B GLN 2.8 15.2 + - - +
80B GLY 3.3 8.7 - - - +
82B LEU* 1.3 72.2 - - - +
84B GLU* 1.3 63.4 + - - +
86B ILE* 2.8 25.6 + - + +
87B LEU* 2.9 44.6 + - + +
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Residues in contact with GLU 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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4A ARG* 3.8 18.2 + - - +
43B ASN 5.5 2.6 - - - +
45B ASN* 5.9 2.9 - - - +
48B ILE* 3.6 29.4 - - + +
80B GLY 3.0 17.9 + - - +
81B THR* 3.4 9.6 - - - +
83B PHE* 1.3 84.3 - - - +
85B LEU* 1.3 57.3 + - - +
87B LEU* 3.6 17.7 + - - +
88B ALA* 3.1 28.8 + - - +
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Residues in contact with LEU 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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48B ILE* 4.3 16.6 - - + -
51B LYS* 4.2 29.6 - - + -
52B VAL* 4.4 11.4 - - + -
74B PHE* 4.6 12.6 - - + +
75B LEU* 4.1 22.2 - - + -
77B VAL* 4.3 6.7 - - + -
81B THR* 2.8 28.3 + - + +
82B LEU* 3.2 17.0 - - - +
83B PHE 3.1 0.2 - - - -
84B GLU* 1.3 76.2 - - - +
86B ILE* 1.3 59.7 + - - +
88B ALA* 3.4 3.8 + - - +
89B ALA* 2.9 31.4 + - - +
97B LEU* 4.5 11.1 - - + +
101B THR* 4.1 11.9 - - + -
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Residues in contact with ILE 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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6A PHE* 3.9 29.8 - - + -
10A LEU* 4.2 14.4 - - + -
15A LEU* 6.2 0.4 - - + -
18A ILE* 3.7 29.4 - - + -
22A ILE* 4.7 8.7 - - + -
82B LEU* 3.0 18.9 + - + +
83B PHE* 2.8 11.8 + - + +
85B LEU* 1.3 68.3 - - - +
87B LEU* 1.3 67.3 + - - +
89B ALA* 3.3 6.6 + - - +
90B ASN* 3.0 23.0 + - + +
98B LEU* 3.8 8.4 - - + +
101B THR* 3.5 30.5 - - - +
102B CYS* 4.7 2.0 - - - +
105B VAL* 4.0 14.8 - - + -
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Residues in contact with LEU 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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10A LEU* 4.2 10.5 - - + -
13A GLN* 3.9 26.5 - - + +
15A LEU* 3.8 26.9 - - + +
43B ASN 6.0 1.8 - - - +
83B PHE* 2.9 49.7 + - + +
84B GLU* 3.7 22.7 - - - +
86B ILE* 1.3 77.0 - - - +
88B ALA* 1.3 51.3 + - - +
90B ASN* 3.3 5.5 + - - +
91B TYR* 2.9 35.3 + - - +
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Residues in contact with ALA 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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43B ASN 5.7 1.6 - - - +
44B VAL* 4.0 21.3 - - + -
48B ILE* 3.8 21.5 - - + -
52B VAL* 4.5 9.2 - - + -
84B GLU 3.1 18.9 + - - +
85B LEU 3.8 3.1 - - - +
86B ILE 3.2 0.2 - - - -
87B LEU* 1.3 73.1 - - - +
89B ALA* 1.3 56.9 + - - +
91B TYR* 3.3 6.4 + - - +
92B LEU* 2.8 43.0 + - + +
97B LEU* 5.5 0.2 - - - -
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Residues in contact with ALA 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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85B LEU 2.9 18.6 + - - +
86B ILE* 3.6 5.4 - - - +
88B ALA* 1.3 75.7 - - - +
90B ASN* 1.3 54.0 + - - +
92B LEU* 3.6 1.5 - - - -
93B ASP* 2.8 28.4 + - - -
94B ILE* 3.0 18.0 + - - +
97B LEU* 3.8 21.2 - - + +
98B LEU* 3.7 36.9 - - + +
101B THR* 4.9 0.2 - - - +
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Residues in contact with ASN 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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15A LEU* 3.7 32.0 - - + +
17A HIS* 3.9 7.8 + - - -
18A ILE* 3.3 25.3 - - + +
26B THR* 4.7 0.2 + - - -
86B ILE* 3.0 13.1 + - + +
87B LEU* 3.6 9.8 + - - +
89B ALA* 1.3 75.1 - - - +
91B TYR* 1.3 64.6 + - - +
93B ASP* 3.2 15.0 + - - +
98B LEU* 4.0 19.6 - - + +
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Residues in contact with TYR 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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26B THR* 2.6 37.6 + - + +
30B MET* 5.9 3.0 - - - -
40B PRO 4.8 1.4 + - - -
41B LEU* 4.2 23.3 - - + -
42B PRO* 3.5 23.0 - - - +
43B ASN* 3.3 45.5 + - + +
44B VAL* 3.7 19.3 - - + -
87B LEU 2.9 18.1 + - - +
88B ALA* 3.6 6.7 - - - +
90B ASN* 1.3 78.7 - - - +
92B LEU* 1.3 57.4 + - + +
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Residues in contact with LEU 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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24B SER* 2.6 26.4 + - - +
25B VAL 3.2 0.2 + - - -
26B THR* 3.0 20.0 + - + -
27B ILE* 4.0 18.4 - - + -
41B LEU* 3.7 32.5 - - + -
44B VAL* 4.6 9.2 - - + -
49B LEU* 4.9 8.7 - - + -
52B VAL* 4.0 31.4 - - + -
88B ALA* 2.8 24.2 + - + +
91B TYR* 1.3 86.7 - - + +
93B ASP* 1.3 67.3 + - - +
94B ILE* 3.7 14.8 - - + -
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Residues in contact with ASP 93 (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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23B GLN 3.8 1.4 - - - +
25B VAL* 3.1 51.1 + - + +
26B THR* 3.5 10.8 - - - +
89B ALA 2.8 9.5 + - - -
90B ASN* 3.2 12.7 + - - +
92B LEU* 1.3 83.1 - - - +
94B ILE* 1.3 54.6 + - - +
95B LYS* 4.1 9.2 + - - +
98B LEU* 6.5 0.4 - - - -
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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