Contacts of the strand formed by residues 160 - 165 (chain A) in PDB entry 1WCP
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 ALA 160 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43A CYS* 4.3 1.8 - - - -
44A VAL 3.5 12.6 - - - +
45A GLU* 4.8 0.4 - - - -
46A VAL* 3.9 5.0 - - - +
151A VAL* 3.6 5.4 - - - +
152A ALA* 3.2 36.0 + - - +
154A ASP 5.0 0.2 - - - +
155A PRO* 3.6 36.3 - - + -
156A VAL* 4.3 4.5 - - + -
158A GLN 3.3 11.4 - - - +
159A ARG* 1.3 75.1 - - - +
161A CYS* 1.3 63.7 + - - +
162A HIS* 4.9 0.7 - - - -
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Residues in contact with CYS 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A CYS* 2.8 24.9 - - - -
44A VAL* 3.1 22.5 + - + -
46A VAL* 3.7 21.1 - - + -
48A GLN* 4.8 3.1 - - - -
62A THR* 5.1 7.2 - - - -
65A ALA* 5.2 5.6 - - + -
66A ILE* 6.5 0.7 - - - -
149A ALA* 4.1 12.8 - - - -
150A TYR 3.2 20.4 - - - -
151A VAL* 3.7 23.8 - - + -
160A ALA* 1.3 76.3 - - - +
162A HIS* 1.3 62.8 + - - +
163A ILE* 3.6 5.6 - - + +
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Residues in contact with HIS 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A TYR* 3.1 29.2 + - + -
42A GLY 3.6 6.5 - - - -
43A CYS* 4.4 1.3 - - - -
117A LEU* 5.3 1.9 - - + +
130A HIS* 3.6 26.0 - + - -
149A ALA* 3.4 24.0 - - - +
150A TYR* 3.2 61.3 + + + -
152A ALA* 4.1 8.9 - - + +
155A PRO* 3.4 41.3 - - + +
161A CYS* 1.3 77.5 - - - +
163A ILE* 1.3 66.5 + - - +
164A LEU* 5.0 0.2 - - - -
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Residues in contact with ILE 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A TYR* 3.6 8.4 - - - -
41A MET* 2.9 37.7 + - + -
42A GLY 3.0 21.8 + - - +
43A CYS* 3.7 8.7 - - - +
44A VAL* 4.2 7.9 - - + +
65A ALA* 5.3 1.6 - - + +
66A ILE* 3.8 30.7 - - + -
69A VAL* 4.2 17.3 - - + -
147A TYR* 3.7 28.3 - - + -
148A VAL 3.8 7.0 - - - +
149A ALA* 4.8 2.0 - - + -
161A CYS* 3.6 15.9 - - + +
162A HIS* 1.3 82.5 - - - +
164A LEU* 1.3 69.2 + - - +
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Residues in contact with LEU 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A VAL* 4.2 17.9 - - + -
39A ARG 3.0 19.3 - - - +
40A TYR* 4.2 6.5 - - + -
41A MET* 4.0 2.7 - - - +
106A ILE* 5.6 0.9 - - + -
108A LEU* 4.1 27.4 - - + -
147A TYR* 3.4 14.6 - - - +
148A VAL* 3.4 54.4 + - + +
149A ALA* 4.5 5.6 - - - +
150A TYR* 4.8 17.3 - - + -
162A HIS* 5.0 0.4 - - + -
163A ILE* 1.3 81.7 - - - +
165A GLU* 1.3 63.7 + - - +
174A VAL* 5.5 5.8 - - + -
175A ILE* 4.9 5.4 - - + -
178A ILE* 5.6 4.9 - - + -
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Residues in contact with GLU 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A VAL* 3.7 20.3 - - - +
39A ARG* 2.9 32.2 + - - -
41A MET* 4.7 0.4 - - - -
77A LYS* 2.7 37.3 + - - -
146A GLU* 4.2 14.3 - - - +
147A TYR* 3.5 29.7 + - + +
148A VAL* 5.3 2.7 - - - -
164A LEU* 1.3 75.5 - - - +
166A CYS* 1.3 74.1 + - + +
167A PRO* 2.8 19.0 - - + +
170A LEU 4.3 3.3 - - - +
171A ALA* 4.8 3.0 - - - +
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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