Contacts of the strand formed by residues 142 - 149 (chain B) in PDB entry 2WA2
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 ASP 142 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73B GLU 5.1 0.2 - - - +
75B LYS* 3.5 41.2 + - - +
76B GLY* 3.4 8.3 - - - -
77B THR* 2.8 32.7 + - - +
140B GLN* 5.1 11.0 + - - +
141B ALA* 1.3 75.1 - - - +
143B THR* 1.3 60.2 + - - +
179B CYS* 3.3 8.8 - - - +
180B GLY 3.0 22.2 + - - -
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Residues in contact with THR 143 (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 VAL* 4.1 4.7 - - + -
73B GLU 3.3 18.6 + - - +
74B LEU* 3.8 25.1 - - + -
75B LYS* 2.8 30.0 + - - +
77B THR 3.1 3.5 + - - +
78B VAL* 3.4 14.7 - - + -
79B VAL* 2.9 29.1 + - - +
141B ALA* 4.0 1.0 - - - +
142B ASP* 1.3 79.5 + - - +
144B VAL* 1.3 64.9 + - - +
145B LEU* 3.9 14.1 - - + -
180B GLY 3.3 9.4 - - - +
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Residues in contact with VAL 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B VAL* 3.8 21.8 - - + -
81B LEU* 4.3 5.4 - - + -
141B ALA* 4.2 7.9 - - + -
143B THR* 1.3 75.2 - - - +
145B LEU* 1.3 63.5 + - - +
169B ILE* 3.8 28.7 - - + -
172B TRP* 4.1 29.4 - - + -
173B LEU* 4.5 5.2 - - + -
176B ASN* 4.5 3.8 - - - +
179B CYS* 4.1 18.4 - - - -
180B GLY 2.8 13.2 + - - +
181B PHE* 3.2 11.1 - - + +
182B CYS 3.0 24.8 + - - +
183B VAL* 4.3 1.3 - - + +
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Residues in contact with LEU 145 (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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63B LEU* 4.0 27.1 - - + -
72B VAL* 4.4 0.9 - - + -
74B LEU* 3.9 15.5 - - + -
78B VAL* 3.6 24.5 - - + -
79B VAL 2.8 15.9 + - - +
80B ASP* 4.2 10.1 - - + +
81B LEU* 2.9 28.8 + - - +
88B TRP* 3.8 21.1 - - + +
92B ALA* 4.4 6.7 - - + -
143B THR* 3.9 15.5 - - + -
144B VAL* 1.3 81.4 - - - +
146B CYS* 1.3 63.1 + - - +
182B CYS* 3.4 25.8 - - + +
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Residues in contact with CYS 146 (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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80B ASP* 4.9 0.4 - - - -
81B LEU* 3.4 22.0 - - + -
88B TRP* 3.9 3.0 - - - -
133B VAL* 5.5 0.7 - - - -
145B LEU* 1.3 77.0 - - - +
147B ASP* 1.3 57.6 + - - +
148B ILE* 3.8 24.5 - - - -
165B VAL* 3.8 24.0 - - - -
168B VAL* 6.5 0.4 - - - -
169B ILE* 3.6 25.4 - - + -
182B CYS 3.0 8.9 + - - +
183B VAL* 3.2 9.8 - - + +
184B LYS 2.7 32.2 + - - -
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Residues in contact with ASP 147 (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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59B GLY* 5.3 1.9 - - - -
62B LYS* 6.0 1.2 - - - +
80B ASP* 4.9 1.2 + - - +
81B LEU 3.4 7.1 + - - -
82B GLY 4.6 1.8 - - - +
88B TRP* 3.5 28.5 + - + -
146B CYS* 1.3 74.5 - - - +
148B ILE* 1.3 63.3 + - - +
149B GLY 3.8 0.9 + - - +
184B LYS* 3.3 22.2 + - - +
222B TYR* 3.0 24.4 + - - -
1267B SAM 2.9 61.6 + - + +
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Residues in contact with ILE 148 (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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81B LEU 3.7 3.1 - - - +
82B GLY* 3.6 26.2 - - - +
133B VAL* 3.4 32.5 - - + -
134B THR* 6.2 0.4 - - + -
146B CYS* 3.6 17.1 + - - -
147B ASP* 1.3 77.7 - - - +
149B GLY* 1.3 61.7 + - - +
165B VAL* 3.6 33.6 - - + +
184B LYS* 3.6 20.0 - - - +
186B LEU* 5.0 1.7 - - - +
1267B SAM 3.6 43.7 - - + +
1269B SO4 3.7 11.2 - - - +
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Residues in contact with GLY 149 (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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147B ASP 3.8 2.5 + - - +
148B ILE* 1.3 81.2 - - - +
150B GLU* 1.3 62.9 + - - +
151B SER 3.9 0.2 + - - -
161B ARG* 5.3 3.8 - - - -
165B VAL* 5.6 0.7 - - - -
184B LYS* 2.6 29.4 + - - -
186B LEU* 3.9 21.1 - - - -
1267B SAM 4.9 4.0 - - - +
1269B SO4 3.6 10.2 + - - -
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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