Contacts of the strand formed by residues 132 - 137 (chain F) in PDB entry 2B8K
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 LEU 132 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1443A VAL* 3.8 21.8 - - + -
1444A MET 2.8 11.0 - - - +
1445A ILE* 4.1 11.9 - - + -
1446A ASP* 5.3 0.2 - - - +
1449A SER* 5.6 0.2 + - - -
93F ILE* 5.0 11.0 - - + -
96F THR* 3.9 13.5 - - + -
97F ARG* 4.8 2.7 - - - +
100F GLN* 4.3 13.0 - - - +
130F ILE* 2.9 21.3 + - + -
131F PRO* 1.3 101.0 - - + +
133F VAL* 1.3 68.9 + - - +
134F ILE* 5.8 0.7 - - - -
147F SER* 3.7 2.9 - - - -
148F VAL* 2.8 36.0 + - + +
18G PHE* 6.0 0.7 - - + -
61G ILE* 3.5 28.7 - - + -
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Residues in contact with VAL 133 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1443A VAL* 3.1 5.6 - - - -
1444A MET* 2.5 52.6 + - + +
1446A ASP* 3.5 30.7 - - + +
132F LEU* 1.3 82.1 - - - +
134F ILE* 1.3 62.8 + - - +
145F ASP* 4.0 15.7 - - + +
146F TRP 3.0 22.2 - - - +
147F SER* 4.4 7.0 - - - +
58G ARG* 3.6 34.5 - - - +
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Residues in contact with ILE 134 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1441A PHE* 3.9 21.1 - - + -
1442A ASP 3.3 4.0 - - - +
1443A VAL* 4.4 8.7 - - + -
85F MET* 4.4 0.7 - - + -
89F GLU* 2.9 57.0 - - + +
93F ILE* 3.2 38.4 - - + -
132F LEU 5.8 0.4 - - - -
133F VAL* 1.3 72.3 - - - +
135F ARG* 1.3 62.1 + - - +
136F ARG* 3.5 13.7 + - + +
144F GLU 3.6 0.5 - - - +
146F TRP* 2.8 31.2 + - - +
147F SER* 4.9 0.2 - - - +
148F VAL* 5.4 2.9 - - + +
151F LEU* 4.3 15.9 - - + -
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Residues in contact with ARG 135 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1441A PHE* 2.9 23.4 - - - +
1442A ASP* 2.7 21.6 + - + +
1444A MET* 3.2 34.9 - - + +
133F VAL 3.5 2.4 + - - -
134F ILE* 1.3 70.7 - - - +
136F ARG* 1.3 61.8 + - - +
137F TYR* 3.5 28.9 + - + -
143F PHE* 2.9 55.5 - - + -
144F GLU 3.5 3.8 - - - -
145F ASP* 2.7 31.8 + - - +
58G ARG* 4.5 11.1 - - - +
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Residues in contact with ARG 136 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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852A TYR* 3.4 32.5 - - + -
81F THR* 3.1 38.0 - - + +
82F THR* 2.9 22.3 + - - +
84F TYR 3.1 19.8 + - - -
86F THR* 3.7 5.7 - - - +
89F GLU* 2.7 40.7 + - - +
134F ILE* 3.9 9.8 - - + +
135F ARG* 1.3 72.0 - - - +
137F TYR* 1.3 66.8 + - - +
138F LEU* 3.5 5.9 + - - +
143F PHE* 3.1 6.4 - - - -
144F GLU* 2.7 34.7 + - + +
146F TRP* 3.4 24.7 - - - +
151F LEU* 3.8 8.8 - - - +
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Residues in contact with TYR 137 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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851A HIS* 5.5 3.1 + - - -
852A TYR* 3.6 18.2 + - - +
1440A ALA 4.3 10.2 + - - +
1441A PHE* 4.4 8.7 - - - -
1442A ASP* 3.3 30.0 + - + -
135F ARG* 3.5 41.4 + - + -
136F ARG* 1.3 73.5 - - - +
138F LEU* 1.3 64.8 + - - +
141F GLY* 3.7 19.5 - - - -
142F SER 3.6 4.3 - - - -
143F PHE* 3.9 15.2 - + + -
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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