Contacts of the strand formed by residues 163 - 168 (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 163 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B VAL 3.1 5.3 + - - -
96B LEU* 3.8 4.0 - - + +
97B HIS* 2.8 30.3 + - - +
133B SER* 4.4 2.2 - - - -
134B GLU* 4.5 0.4 - - + -
135B THR* 3.4 28.9 - - + +
152B CYS* 3.7 33.0 - - + +
155B THR* 4.0 16.2 - - + -
156B THR* 3.2 38.1 - - - +
161B ARG 3.8 4.3 - - - +
162B PRO* 1.3 80.3 - - - +
164B TYR* 1.3 65.3 + - - +
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Residues in contact with TYR 164 (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 PHE* 5.9 0.2 - - - -
78B GLU* 2.5 34.6 + - - -
97B HIS* 3.5 13.5 - + + -
99B VAL* 3.6 26.5 - - + +
101B VAL* 4.9 2.1 - - - +
125B PHE* 4.7 0.2 - - - +
126B HIS* 3.6 44.0 + + + +
129B SER* 3.4 29.8 - - - -
133B SER* 3.9 9.3 + - - +
135B THR 3.2 4.2 + - - -
136B THR* 3.2 16.6 - - + -
137B ALA* 2.8 32.1 + - - +
138B MET* 4.1 12.4 - - + +
163B VAL* 1.3 77.2 - - - +
165B LEU* 1.3 61.4 + - - +
166B GLY* 4.0 12.6 - - - -
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Residues in contact with LEU 165 (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* 4.7 5.4 - - + -
96B LEU* 4.2 17.9 - - + -
97B HIS 2.8 13.1 + - - +
98B VAL* 3.2 20.5 - - + +
99B VAL 2.8 25.4 + - - -
137B ALA* 3.5 24.9 - - + -
139B ILE* 3.9 25.4 - - + -
148B GLU 4.8 0.9 - - - +
149B ILE* 4.0 30.3 - - + -
152B CYS* 3.8 15.7 - - + -
163B VAL 4.0 0.2 + - - -
164B TYR* 1.3 75.8 - - - +
166B GLY* 1.3 60.1 + - - +
167B LEU* 3.7 13.9 + - + -
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Residues in contact with GLY 166 (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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99B VAL 3.5 7.6 - - - -
101B VAL* 4.5 2.2 - - - -
137B ALA 2.8 16.4 + - - -
138B MET* 3.8 26.2 - - - -
139B ILE* 3.0 33.1 + - - +
164B TYR* 4.0 7.1 - - - -
165B LEU* 1.3 71.6 - - - +
167B LEU* 1.3 59.6 + - - -
168B PRO* 3.7 0.7 - - - +
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Residues in contact with LEU 167 (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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6B LEU* 4.4 20.9 - - + -
7B GLY* 5.6 1.3 - - - -
10B LEU* 4.5 11.9 - - + -
29B PHE 4.6 0.2 - - - +
33B LEU* 4.0 34.5 - - + -
98B VAL* 4.1 16.4 - - + -
99B VAL 2.9 13.6 + - - +
100B GLY* 3.5 6.2 - - - -
101B VAL* 3.1 19.3 + - - +
139B ILE* 3.6 29.2 - - + -
149B ILE* 4.7 11.0 - - + -
165B LEU* 3.7 10.3 + - + -
166B GLY* 1.3 72.8 - - - +
168B PRO* 1.4 70.9 - - + +
169B ALA* 3.4 1.6 + - - -
171B LEU* 6.0 1.1 - - + -
172B VAL* 4.2 12.9 - - + +
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Residues in contact with PRO 168 (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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101B VAL* 3.3 21.5 - - + +
102B PRO 3.8 10.8 - - - +
103B SER* 4.3 0.9 - - - -
104B ILE* 4.1 15.5 - - + -
107B GLN* 4.6 1.3 - - - +
138B MET* 4.9 1.8 - - - -
139B ILE* 3.1 34.5 - - + +
166B GLY 3.7 4.7 - - - +
167B LEU* 1.4 83.6 - - + +
169B ALA* 1.3 65.9 + - - +
170B ASN* 3.1 20.4 - - - +
171B LEU* 3.0 30.7 + - + +
172B VAL* 3.7 6.8 + - - +
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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