Contacts of the helix formed by residues 90 - 101 (chain B) in PDB entry 1O0W
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 90 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86B SER 3.2 12.3 + - - -
87B ALA* 2.7 23.5 + - - -
88B ALA 3.3 0.6 - - - -
89B ALA* 1.3 80.1 - - - +
91B GLU* 1.3 64.3 + - - +
92B GLU* 3.8 8.8 + - - +
93B VAL* 3.2 15.8 + - - +
94B LEU* 3.0 25.1 + - - +
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Residues in contact with GLU 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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89B ALA 3.9 0.4 + - - -
90B SER* 1.3 74.2 - - - +
92B GLU* 1.3 58.8 + - - +
94B LEU* 3.3 2.6 + - - +
95B ALA* 2.8 30.5 + - - +
122B ASP* 3.8 21.2 - - + +
123B SER* 3.2 33.3 - - - -
126B ALA* 3.9 24.1 - - + +
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Residues in contact with GLU 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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90B SER* 3.2 9.3 - - - +
91B GLU* 1.3 81.9 - - - +
93B VAL* 1.3 64.5 + - + +
95B ALA* 3.8 4.3 - - - +
96B MET* 3.2 21.7 + - - +
122B ASP* 5.0 10.1 - - - +
166B LEU 5.5 3.4 - - - +
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Residues in contact with VAL 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B ALA* 3.4 20.9 - - + +
88B ALA* 3.4 23.6 - - - +
90B SER* 3.2 8.0 + - - +
92B GLU* 1.3 78.9 - - + +
94B LEU* 1.3 64.8 + - - +
96B MET* 3.0 13.7 + - + +
97B VAL* 2.9 30.3 + - + +
153B PHE* 4.5 4.5 - - + -
156B TYR* 4.1 26.7 - - + -
160B ILE* 4.5 4.5 - - + -
166B LEU* 3.9 24.0 - - + -
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Residues in contact with LEU 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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61B LEU* 3.6 24.2 - - + -
88B ALA 4.3 8.5 - - - +
89B ALA 3.5 15.9 - - - +
90B SER 3.0 19.6 + - - +
91B GLU* 5.0 0.4 - - - -
93B VAL* 1.3 75.2 - - - +
95B ALA* 1.3 57.0 + - - +
97B VAL* 3.4 5.2 + - - +
98B SER* 2.9 32.4 + - - -
126B ALA* 3.7 23.3 - - + +
129B PHE* 4.1 17.2 - - + +
130B GLU* 3.3 37.0 - - + +
153B PHE* 4.2 19.1 - - + -
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Residues in contact with ALA 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 GLU 2.8 21.1 + - - +
92B GLU 3.8 3.4 - - - +
94B LEU* 1.3 73.8 - - - +
96B MET* 1.3 58.6 + - - +
98B SER* 3.2 7.5 + - - -
99B ARG* 2.9 55.5 + - - +
122B ASP* 3.9 31.2 - - - +
125B LEU* 4.5 6.4 - - + +
126B ALA* 4.3 1.9 - - - +
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Residues in contact with MET 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 GLU 3.2 13.3 + - - +
93B VAL* 3.0 20.3 + - + +
95B ALA* 1.3 76.0 - - - +
97B VAL* 1.3 62.4 + - + +
99B ARG* 3.3 11.9 + - - +
100B LYS* 3.0 43.6 + - + +
156B TYR* 3.6 40.2 - - + -
166B LEU* 4.0 17.7 - - + -
167B PHE* 3.9 33.9 - - - +
168B ASP* 4.2 10.3 - - + +
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Residues in contact with VAL 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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93B VAL* 2.9 16.7 + - + +
94B LEU* 3.6 9.4 - - - +
96B MET* 1.3 74.1 - - + +
98B SER* 1.3 64.9 + - - +
100B LYS* 3.1 19.1 + - - +
101B MET* 3.2 16.1 + - + +
129B PHE* 3.5 35.0 - - + -
149B PHE* 5.0 2.0 - - + -
152B GLU* 4.0 18.6 - - - +
153B PHE* 4.1 15.0 - - + -
156B TYR* 3.5 33.0 - - + +
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Residues in contact with SER 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 LEU 2.9 18.8 + - - -
95B ALA 3.2 5.1 + - - -
97B VAL* 1.3 75.8 - - - +
99B ARG* 1.3 63.3 + - - +
101B MET* 3.1 8.4 + - - +
103B LEU* 3.0 44.0 + - - +
125B LEU* 3.1 37.7 + - - -
129B PHE* 3.1 17.8 - - - +
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Residues in contact with ARG 99 (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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95B ALA* 2.9 37.5 + - - +
96B MET* 3.6 9.0 - - - +
98B SER* 1.3 77.3 - - - +
100B LYS* 1.3 62.5 + - + +
102B ASN* 2.9 21.8 + - - +
103B LEU 4.8 0.2 - - - +
104B GLY 5.8 1.3 - - - +
120B ASP* 2.9 27.9 + - - +
122B ASP* 2.7 30.9 + - - -
125B LEU* 3.4 21.6 - - + +
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Residues in contact with LYS 100 (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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96B MET* 3.0 40.5 + - + +
97B VAL* 3.1 8.3 + - - +
99B ARG* 1.3 77.2 - - + +
101B MET* 1.3 57.5 + - + +
102B ASN* 3.4 10.0 + - - -
152B GLU* 3.5 10.8 - - - +
156B TYR* 2.4 45.5 + - - +
168B ASP* 6.2 3.8 - - - +
221B LYS* 6.0 1.6 - - - +
225B LYS* 2.5 39.2 - - - +
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Residues in contact with MET 101 (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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12B PHE* 4.2 8.7 - - + -
16B THR* 4.1 31.0 - - + +
18B ILE* 4.3 11.0 - - + -
97B VAL* 3.2 12.1 + - + +
98B SER* 3.1 9.0 + - - +
100B LYS* 1.3 75.4 - - + +
102B ASN* 1.3 73.2 + - - +
103B LEU* 3.0 10.6 + - + +
106B PHE* 4.2 9.0 - - - -
129B PHE* 3.9 33.0 - - + -
132B LEU* 3.6 25.6 - - + -
149B PHE* 4.3 13.0 - - + -
152B GLU* 6.0 1.1 - - - +
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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