Contacts of the strand formed by residues 119 - 122 (chain B) in PDB entry 2WAL
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 CYS 119 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41B ALA* 3.8 0.9 - - - -
42B GLY* 2.8 41.6 + - - -
43B VAL* 4.0 10.3 - - + +
46B SER* 3.6 25.1 - - - -
60B CYS* 3.9 13.9 - - - -
61B VAL 3.3 4.9 - - - -
62B LEU* 3.6 21.8 - - + -
81B ILE* 4.1 11.4 - - + -
117B LEU* 3.5 2.7 - - - +
118B HIS* 1.3 81.8 - - - +
120B ILE* 1.3 74.0 - - - +
121B LEU* 4.7 0.4 - - - -
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Residues in contact with ILE 120 (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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30B LEU* 3.8 23.6 - - + -
39B LEU* 4.0 22.2 - - + +
40B THR 3.5 6.3 - - - +
41B ALA* 5.3 1.8 - - + -
59B PHE 3.7 0.2 - - - +
60B CYS* 3.1 7.3 - - - -
61B VAL* 2.8 47.0 + - + +
101B LEU* 4.1 18.8 - - + -
105B VAL* 4.3 8.5 - - + -
117B LEU* 3.8 25.1 - - + -
119B CYS* 1.3 81.0 - - - +
121B LEU* 1.3 68.4 + - - +
122B ILE* 3.6 23.4 + - + +
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Residues in contact with LEU 121 (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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39B LEU* 2.9 27.7 + - - -
40B THR* 3.0 23.1 + - - +
46B SER* 3.3 50.9 + - - +
49B VAL* 3.5 23.3 - - + -
50B LEU* 4.2 20.6 - - + -
57B VAL* 4.1 18.6 - - + -
59B PHE 3.4 0.7 - - - -
60B CYS* 4.0 29.8 - - + -
85B CYS* 5.2 0.4 - - - -
119B CYS* 4.7 0.4 - - - -
120B ILE* 1.3 73.9 - - - +
122B ILE* 1.3 61.0 + - - +
123B SER* 4.2 5.5 + - - +
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Residues in contact with ILE 122 (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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26B LEU* 6.4 0.2 - - + -
29B LEU* 4.6 19.1 - - + +
30B LEU* 5.0 9.9 - - + -
33B ALA* 4.6 16.4 - - + -
38B CYS* 5.1 1.6 - - + -
39B LEU* 4.3 6.1 - - + +
57B VAL* 3.4 3.8 - - - +
58B ALA* 2.6 39.9 + - + -
59B PHE* 2.7 40.3 + - + +
61B VAL* 5.5 1.6 - - + -
120B ILE* 3.6 23.6 - - + +
121B LEU* 1.3 78.5 - - - +
123B SER* 1.3 66.4 + - - +
130B TRP* 4.0 26.5 - - + -
135B LEU* 5.9 1.6 - - + -
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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