Contacts of the helix formed by residues 87 - 98 (chain B) in PDB entry 1W6T
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 87 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84B VAL 4.5 0.2 + - - -
85B ARG 2.9 9.4 + - - +
86B ASP* 1.3 72.0 - - - +
88B GLN* 1.3 61.8 + - + +
90B ILE* 3.3 7.3 + - - +
91B ASP* 2.9 46.2 + - - +
115B SER* 3.0 40.1 + - - +
118B VAL* 3.6 9.6 - - - +
119B ALA* 3.3 35.7 + - + +
133B TYR* 4.3 16.2 + - + +
134B LEU* 6.0 2.7 - - + -
350B LEU* 4.0 11.8 - - + +
351B THR* 4.2 3.8 - - - +
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Residues in contact with GLN 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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86B ASP 3.3 0.8 - - - -
87B GLN* 1.3 82.2 - - + +
89B ALA* 1.3 52.7 + - - +
91B ASP* 3.2 1.9 + - - +
92B ARG* 2.8 45.5 + - + +
351B THR* 3.4 32.4 - - + +
355B GLU* 5.0 3.6 - - - +
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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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82B TYR* 4.0 21.1 + - + -
86B ASP* 3.3 20.9 + - + +
88B GLN* 1.3 77.9 - - - +
90B ILE* 1.3 58.2 + - - +
92B ARG* 3.8 6.3 - - - +
93B ALA* 2.8 30.9 + - - +
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Residues in contact with ILE 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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4B ILE* 3.7 15.5 - - + -
79B ILE* 3.9 22.4 - - + +
82B TYR* 3.7 24.5 - - + -
83B ASP 3.6 22.2 - - - +
86B ASP 3.0 21.7 + - - +
87B GLN* 3.7 4.7 - - - +
89B ALA* 1.3 74.8 - - - +
91B ASP* 1.3 67.1 + - - +
93B ALA* 3.2 7.8 + - - +
94B MET* 3.0 37.5 + - + +
114B VAL* 4.8 0.4 - - + -
115B SER* 5.7 0.2 - - - -
118B VAL* 3.7 35.7 - - + -
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Residues in contact with ASP 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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87B GLN* 2.9 30.1 + - - +
88B GLN 3.6 1.3 - - - +
90B ILE* 1.3 76.0 - - - +
92B ARG* 1.3 64.4 + - + +
94B MET* 3.2 15.6 + - - +
95B ILE* 3.0 29.5 + - + +
115B SER* 2.6 30.5 + - - -
349B THR* 3.6 14.6 - - - +
351B THR* 2.6 48.4 + - - +
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Residues in contact with ARG 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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88B GLN* 2.8 31.9 + - + +
89B ALA* 3.8 7.0 - - - +
91B ASP* 1.3 71.3 - - + +
93B ALA* 1.3 57.3 + - - +
95B ILE* 3.3 30.4 + - - +
96B ALA* 2.9 30.1 + - - +
351B THR* 3.7 16.9 - - - +
352B GLU* 4.5 8.8 + - - +
355B GLU* 2.7 40.6 + - - -
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Residues in contact with ALA 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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78B ALA* 5.7 2.0 - - + +
79B ILE* 4.1 15.0 - - + -
82B TYR* 3.5 20.9 - - + +
89B ALA 2.8 20.1 + - - +
90B ILE 3.2 5.8 + - - +
92B ARG* 1.3 76.2 - - - +
94B MET* 1.3 57.2 + - - +
96B ALA* 3.4 5.8 + - - +
97B LEU* 2.9 30.6 + - - +
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Residues in contact with MET 94 (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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75B ILE* 3.8 23.6 - - + -
79B ILE* 4.2 8.3 - - + -
90B ILE* 3.0 21.7 + - + +
91B ASP* 3.5 30.1 - - - +
93B ALA* 1.3 73.1 - - - +
95B ILE* 1.3 59.0 + - - +
97B LEU* 3.2 9.5 + - + +
98B ASP* 3.0 31.0 + - - +
106B LEU* 4.0 3.6 - - + +
111B ILE* 3.5 47.7 - - + +
114B VAL* 3.6 32.8 - - + -
115B SER* 3.8 9.2 - - - +
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Residues in contact with ILE 95 (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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91B ASP* 3.0 22.5 + - + +
92B ARG* 3.5 30.3 - - - +
94B MET* 1.3 76.6 - - + +
96B ALA* 1.3 58.0 + - - +
98B ASP* 3.5 5.1 + - - +
99B GLY* 2.9 25.3 + - - -
100B THR 4.6 5.7 + - - +
103B LYS* 4.0 24.2 - - + +
111B ILE* 5.0 2.2 - - + -
349B THR* 4.0 9.2 - - + +
351B THR* 6.2 0.2 - - - -
352B GLU* 3.6 33.0 - - + +
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Residues in contact with ALA 96 (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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92B ARG 2.9 16.0 + - - +
93B ALA* 3.8 5.8 - - - +
95B ILE* 1.3 75.8 - - - +
97B LEU* 1.3 66.6 + - - +
99B GLY* 3.2 15.3 + - - +
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Residues in contact with LEU 97 (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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74B ILE* 3.9 33.0 - - + +
75B ILE* 4.1 12.8 - - + -
77B GLU* 4.6 1.3 - - - +
78B ALA* 3.7 25.1 - - + -
79B ILE* 6.1 0.2 - - + -
93B ALA 2.9 18.4 + - - +
94B MET* 3.2 8.0 + - + +
96B ALA* 1.3 76.5 - - - +
98B ASP* 1.3 63.2 + - - +
105B LYS* 3.8 13.7 + - - -
106B LEU* 4.2 12.0 - - + +
1434B 2PE 3.8 24.2 - - - +
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Residues in contact with ASP 98 (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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94B MET 3.0 16.5 + - - +
95B ILE* 3.8 3.8 - - - +
97B LEU* 1.3 75.1 - - - +
99B GLY* 1.3 61.0 + - - +
100B THR* 2.5 48.8 + - - +
103B LYS* 3.1 17.3 - - + +
105B LYS* 2.8 41.1 + - - +
106B LEU* 2.9 43.7 + - + +
111B ILE* 4.1 8.1 - - + -
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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