Contacts of the strand formed by residues 130 - 138 (chain B) in PDB entry 2W3M
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 HIS 130 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2B GLY 4.1 15.7 + - - +
3B SER* 2.9 32.0 + - - -
4B LEU* 3.3 20.8 + - - +
128B PRO 5.0 0.9 - - - +
129B GLY* 1.3 72.2 - - - -
131B LEU* 1.3 64.8 + - - +
132B LYS* 3.7 27.8 - - + +
183B GLU* 2.7 29.4 + - + +
184B LYS 3.4 20.6 - - - -
185B ASN* 3.5 26.6 + - - +
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Residues in contact with LEU 131 (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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4B LEU* 3.5 34.3 - - + +
6B CYS* 4.1 13.5 - - - -
124B ALA* 3.2 28.0 - - + +
127B HIS* 3.4 28.7 - - + +
128B PRO 4.8 1.8 - - - +
129B GLY 3.5 1.1 + - - +
130B HIS* 1.3 79.3 - - - +
132B LYS* 1.3 63.6 - - - +
133B LEU* 4.1 15.9 - - + -
156B TYR* 3.8 19.3 - - + +
183B GLU* 3.4 4.3 - - - +
184B LYS* 3.0 45.3 + - + +
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Residues in contact with LYS 132 (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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3B SER* 5.3 1.3 - - - -
4B LEU 3.3 6.7 + - - -
5B ASN* 3.3 22.1 + - - +
6B CYS 2.9 25.2 + - - +
111B MET* 5.3 7.6 - - - +
130B HIS* 3.7 25.1 - - + +
131B LEU* 1.3 74.0 - - - +
133B LEU* 1.3 66.0 + - - +
134B PHE* 3.8 24.2 - - + -
162B TYR* 2.7 43.7 + - + +
181B VAL* 4.4 6.1 - - + -
182B TYR 3.2 11.7 - - - +
183B GLU* 3.7 15.9 - - + +
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Residues in contact with LEU 133 (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 CYS* 3.5 22.0 - - + -
125B MET* 3.5 42.0 - - + -
131B LEU* 4.1 4.0 - - + -
132B LYS* 1.3 79.7 - - - +
134B PHE* 1.3 63.3 + - - +
135B VAL* 3.6 12.8 + - + -
148B PHE* 5.0 3.6 - - + -
151B ILE* 4.0 21.3 - - + -
156B TYR* 3.7 40.4 - - + +
180B GLU 3.7 0.2 - - - +
181B VAL* 3.4 4.9 - - - -
182B TYR* 2.9 41.1 + - + +
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Residues in contact with PHE 134 (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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5B ASN* 3.9 8.5 - - - -
6B CYS 2.8 14.8 + - - +
7B ILE* 3.3 18.3 - - + +
8B VAL* 3.0 28.1 + - - +
33B TYR* 3.5 26.2 - - + +
37B MET* 3.5 25.8 - - + -
111B MET* 6.4 0.2 - - + -
113B TRP* 3.6 28.9 - + - -
132B LYS* 3.8 38.6 - - + -
133B LEU* 1.3 72.7 - - - +
135B VAL* 1.3 59.9 + - - +
136B THR* 4.1 0.9 - - - -
162B TYR* 4.4 6.7 - + - -
165B VAL* 4.2 7.4 - - + -
180B GLU 3.5 3.6 - - - -
181B VAL* 3.8 29.2 - - + -
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Residues in contact with VAL 135 (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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8B VAL* 3.5 17.7 - - + -
10B VAL* 3.6 27.6 - - + -
33B TYR* 6.4 0.2 - - - -
133B LEU* 4.0 14.6 - - + -
134B PHE* 1.3 75.5 - - - +
136B THR* 1.3 60.5 + - - +
137B ARG* 3.6 26.6 + - - +
148B PHE* 4.6 6.3 - - + -
151B ILE* 4.1 10.8 - - + -
179B PHE* 4.9 0.7 - - - -
180B GLU* 2.9 38.3 + - - +
182B TYR* 4.0 28.5 - - + -
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Residues in contact with THR 136 (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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8B VAL 2.9 12.0 + - - -
9B ALA* 3.9 3.8 - - - -
10B VAL* 2.9 32.6 + - - +
30B GLU* 2.7 34.7 + - + +
33B TYR* 4.4 3.8 - - - -
134B PHE 4.1 0.4 + - - -
135B VAL* 1.3 69.4 - - - +
137B ARG* 1.3 61.1 + - - +
138B ILE* 3.5 9.4 + - + -
177B TYR* 3.6 32.3 - - + -
178B LYS 3.3 12.3 - - - +
179B PHE* 3.5 16.2 - - + +
1188B FOL 3.7 5.0 + - - -
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Residues in contact with ARG 137 (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 VAL* 3.8 20.7 - - - +
11B SER 5.5 1.9 + - - -
14B MET* 3.9 26.7 - - - +
135B VAL* 3.6 14.3 - - + +
136B THR* 1.3 69.8 - - - +
138B ILE* 1.3 62.7 + - - +
139B MET* 3.5 6.2 + - + +
148B PHE* 5.5 0.8 - - - -
151B ILE* 3.8 17.2 - - - +
177B TYR* 3.1 7.0 - - - -
178B LYS* 2.8 51.7 + - + -
180B GLU* 2.9 36.2 + - + +
182B TYR* 3.1 27.5 + - - -
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Residues in contact with ILE 138 (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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9B ALA* 4.7 3.4 - - + -
10B VAL 3.0 20.2 + - - +
11B SER* 3.6 4.7 - - - -
12B GLN* 3.2 22.3 + - - -
24B TRP* 4.3 26.7 - - + +
27B LEU* 3.7 28.5 - - + -
30B GLU* 5.0 1.6 - - + -
136B THR* 3.5 12.1 + - + +
137B ARG* 1.3 69.6 - - - +
139B MET* 1.3 59.8 + - - +
140B GLN 3.0 11.4 + - - +
142B PHE* 3.8 33.9 - - + -
175B ILE* 3.8 14.4 - - + -
176B LYS 3.9 2.2 - - - -
177B TYR* 3.7 17.0 - - + -
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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