Contacts of the strand formed by residues 117 - 122 (chain F) in PDB entry 2BWJ
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 117 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13F ILE 3.6 3.5 + - - +
14F ILE* 3.3 20.1 - - + +
15F PHE 2.9 24.6 + - - -
115F PRO* 4.0 1.8 - - - +
116F GLN* 1.3 81.8 - - - +
118F VAL* 1.3 73.2 + - - +
119F ILE* 4.0 20.2 - - + -
171F THR* 5.0 0.2 - - - -
172F GLN* 3.4 22.9 - - + +
174F HIS* 3.5 29.8 - - + +
192F ALA* 3.8 21.8 - - + +
193F ILE* 3.9 26.7 - - + -
196F ILE* 4.3 13.9 - - + -
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Residues in contact with VAL 118 (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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15F PHE* 3.3 23.6 - - + +
17F ILE* 4.9 8.7 - - + -
115F PRO* 4.3 7.2 - - + -
117F LEU* 1.3 78.2 - - - +
119F ILE* 1.3 65.7 - - - +
120F CYS* 4.1 9.4 - - - -
163F VAL* 5.7 2.5 - - + -
164F ILE* 5.6 2.2 - - + -
167F TYR* 3.9 22.7 - - + -
171F THR* 3.7 23.3 - - + -
172F GLN 2.9 11.3 + - - +
173F LEU* 3.2 27.3 - - + +
174F HIS 2.9 26.9 + - - -
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Residues in contact with ILE 119 (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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14F ILE* 3.6 23.3 - - + -
15F PHE 2.8 11.2 + - - +
16F ILE* 3.4 21.6 - - + -
17F ILE* 2.9 29.6 + - - +
31F LEU* 4.9 3.8 - - + -
94F LEU* 5.1 0.2 - - + -
117F LEU* 4.0 21.3 - - + -
118F VAL* 1.3 75.1 - - - +
120F CYS* 1.3 62.4 + - - +
121F MET* 4.3 8.5 - - + -
174F HIS 3.5 4.3 - - - +
176F ILE* 4.0 12.6 - - + -
189F LEU* 3.3 36.1 - - + +
192F ALA* 5.0 3.8 - - + -
193F ILE* 4.2 17.0 - - + -
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Residues in contact with CYS 120 (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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17F ILE* 3.5 8.1 - - + -
118F VAL* 4.1 5.6 - - - -
119F ILE* 1.3 78.5 - - - +
121F MET* 1.3 62.7 + - - +
122F ASP* 3.3 8.2 + - - +
156F TYR* 5.4 1.3 - - - +
164F ILE* 3.7 34.8 - - + -
173F LEU* 3.6 37.0 - - - -
174F HIS 2.9 8.7 + - - +
175F LYS* 3.4 11.8 - - + -
176F ILE 2.8 27.7 + - - -
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Residues in contact with MET 121 (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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16F ILE* 4.0 15.7 - - + -
17F ILE 2.8 17.0 + - - +
18F GLY* 3.8 12.8 - - - -
19F GLY 4.3 1.7 + - - -
22F SER* 3.3 40.0 - - - +
23F GLY 3.9 3.8 - - - -
24F LYS* 3.7 34.1 - - - +
27F GLN* 3.9 19.1 - - + -
119F ILE* 4.3 14.4 - - + -
120F CYS* 1.3 71.6 - - - +
122F ASP* 1.3 63.4 + - - +
123F CYS* 3.8 2.3 + - - +
156F TYR* 4.1 8.1 + - - -
176F ILE* 3.8 11.7 - - + -
178F ALA* 3.8 13.0 - - + -
185F VAL* 4.0 9.0 - - + -
189F LEU* 4.7 2.0 - - + -
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Residues in contact with ASP 122 (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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120F CYS* 3.3 9.6 + - - +
121F MET* 1.3 71.2 - - - +
123F CYS* 1.3 63.5 + - - +
164F ILE* 5.6 3.5 - - - +
175F LYS* 3.9 25.8 - - + +
176F ILE 2.8 19.2 + - - +
177F ASN* 3.8 7.9 - - - +
178F ALA* 2.7 30.1 + - - +
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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