Contacts of the strand formed by residues 95 - 101 (chain B) in PDB entry 2W93
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 VAL 95 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55B ALA 5.2 1.6 - - - +
58B ALA* 3.9 7.6 - - + -
59B ASP* 3.9 17.7 - - - +
68B SER* 3.3 21.5 - - - +
70B ILE* 3.8 28.5 - - + -
85B ILE* 4.1 13.0 - - + -
88B SER* 3.6 27.4 - - - +
93B VAL* 3.0 13.6 + - + +
94B GLY* 1.3 74.8 - - - -
96B LEU* 1.3 61.4 + - - +
97B HIS* 3.6 1.6 + - - +
156B THR* 3.5 3.7 - - - +
162B PRO* 3.0 30.2 - - + +
163B VAL 3.1 4.3 + - - -
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Residues in contact with LEU 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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10B LEU* 4.4 8.3 - - + -
14B LEU* 4.3 9.4 - - + -
67B MET* 4.3 5.6 - - + -
68B SER 2.9 18.8 + - - +
69B CYS* 3.2 12.0 - - - -
70B ILE 2.9 27.9 + - - +
95B VAL* 1.3 71.0 - - - +
97B HIS* 1.3 60.5 + - - +
98B VAL* 3.8 22.0 - - + -
152B CYS* 3.9 26.2 - - + +
153B ILE* 4.0 24.2 - - + -
156B THR* 3.7 18.2 - - - +
163B VAL* 3.8 15.3 - - + +
165B LEU* 4.2 15.7 - - + -
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Residues in contact with HIS 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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70B ILE* 3.5 19.3 - - + -
72B THR* 2.8 35.8 + - + +
78B GLU* 3.8 29.8 - - + -
81B ALA* 4.1 11.1 - - + +
82B LEU* 4.5 6.4 - - + +
85B ILE* 3.8 32.9 - - + +
95B VAL 3.6 1.9 + - - +
96B LEU* 1.3 70.5 - - - +
98B VAL* 1.3 66.7 + - - +
99B VAL* 3.7 9.1 + - + +
129B SER* 4.7 0.6 + - - -
163B VAL 2.8 16.7 + - - +
164B TYR* 3.5 14.4 - + + -
165B LEU 2.8 25.9 + - - +
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Residues in contact with VAL 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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10B LEU* 4.2 10.3 - - + -
33B LEU* 4.0 26.9 - - + -
69B CYS* 3.9 12.8 - - - -
70B ILE 2.8 7.3 + - - +
71B ILE* 3.1 14.9 - - + +
72B THR 2.9 25.1 + - - +
96B LEU* 3.8 30.1 - - + -
97B HIS* 1.3 74.0 - - - +
99B VAL* 1.3 65.8 + - - +
165B LEU* 3.2 20.9 - - + +
167B LEU* 4.1 18.4 - - + -
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Residues in contact with VAL 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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72B THR* 3.5 4.9 - - - +
73B THR 3.8 4.7 - - - -
74B PHE* 3.6 23.8 - - - +
78B GLU* 3.7 24.7 - - + +
97B HIS* 3.7 22.7 - - + +
98B VAL* 1.3 79.4 - - - +
100B GLY* 1.3 67.0 + - - +
101B VAL* 3.5 8.2 + - + +
164B TYR* 3.6 36.6 - - + +
165B LEU 2.8 9.8 + - - +
166B GLY* 3.5 2.9 - - - -
167B LEU 2.9 27.2 + - - -
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Residues in contact with GLY 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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29B PHE* 3.1 31.2 - - - +
30B ASN* 4.2 6.1 - - - +
33B LEU* 5.4 3.6 - - - -
71B ILE* 5.0 1.0 - - - +
72B THR 2.9 14.3 + - - -
73B THR* 3.8 0.5 - - - -
74B PHE* 2.9 26.5 + - - +
98B VAL* 4.2 1.8 - - - +
99B VAL* 1.3 71.7 - - - +
101B VAL* 1.3 57.2 + - - +
167B LEU* 3.5 10.3 - - - -
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Residues in contact with VAL 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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29B PHE* 3.8 5.1 + - - +
74B PHE* 3.9 17.9 - - + -
99B VAL* 3.6 21.1 - - + +
100B GLY* 1.3 78.5 - - - +
102B PRO* 1.3 82.0 - - + +
107B GLN* 3.9 7.2 - - - +
138B MET* 3.9 36.1 - - + -
164B TYR* 4.9 2.2 - - - +
166B GLY* 4.5 0.4 - - - -
167B LEU 3.1 6.6 + - - +
168B PRO* 3.3 25.7 - - + +
169B ALA* 3.0 25.1 + - - +
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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