Contacts of the strand formed by residues 13 - 18 (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 ILE 13 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8F LEU 3.9 20.9 - - - +
9F ARG* 5.8 0.7 - - - -
11F CYS* 3.9 6.7 - - - +
12F LYS* 1.3 76.8 - - - +
14F ILE* 1.3 63.6 + - - +
15F PHE* 3.8 28.0 - - + -
83F MET* 4.0 24.0 - - + -
93F PHE* 3.7 8.1 - - + -
95F ILE* 4.0 12.1 - - + -
108F PHE* 4.2 14.4 - - + -
112F ILE* 4.4 1.1 - - + -
113F GLY* 4.2 9.2 - - - -
114F ASP 4.0 12.8 - - - +
115F PRO* 3.4 15.4 - - + +
116F GLN* 2.9 34.6 + - - +
117F LEU 3.6 2.8 + - - -
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Residues in contact with ILE 14 (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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12F LYS* 5.2 8.5 - - + -
13F ILE* 1.3 79.2 - - - +
15F PHE* 1.3 66.9 + - - +
16F ILE 3.9 0.2 + - - -
37F PHE* 3.7 41.1 - - + -
93F PHE 2.8 15.6 + - - +
94F LEU* 3.5 11.0 - - + +
95F ILE* 2.7 32.6 + - - +
116F GLN* 6.0 0.9 - - + -
117F LEU* 3.3 26.7 - - + +
119F ILE* 3.6 29.8 - - + -
193F ILE* 4.4 15.7 - - + -
196F ILE* 5.9 5.4 - - + -
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Residues in contact with PHE 15 (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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13F ILE* 3.8 19.9 + - + -
14F ILE* 1.3 80.3 - - - +
16F ILE* 1.3 55.4 + - - +
17F ILE* 4.3 2.7 - - + -
95F ILE* 3.3 30.7 - - + -
98F TYR* 3.6 13.9 - + - +
99F PRO* 3.7 21.5 - - + -
105F GLY* 5.5 0.2 - - - -
108F PHE* 3.6 32.3 - + - -
115F PRO* 3.6 24.5 - - + -
117F LEU 2.9 10.7 + - - +
118F VAL* 3.3 15.4 - - + -
119F ILE 2.8 30.7 + - - -
163F VAL* 6.0 0.2 - - + -
167F TYR* 3.4 30.5 - + - -
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Residues in contact with ILE 16 (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* 1.3 74.3 - - - +
17F ILE* 1.3 68.3 + - - +
24F LYS* 3.7 12.7 - - + +
27F GLN* 5.0 0.9 - - + -
28F CYS* 3.8 28.9 - - - -
31F LEU* 4.4 17.9 - - + -
94F LEU* 3.7 24.7 - - + -
95F ILE 2.9 16.4 + - - +
96F ASP* 3.6 8.9 - - + +
97F GLY 2.9 26.5 + - - -
119F ILE* 3.4 26.7 - - + +
121F MET* 4.0 22.0 - - - -
189F LEU* 4.4 5.8 - - + -
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Residues in contact with ILE 17 (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* 5.1 2.0 - - + -
16F ILE* 1.3 78.2 - - - +
18F GLY* 1.3 61.2 + - - +
24F LYS* 3.9 4.5 - - - +
97F GLY* 3.7 10.1 - - - -
98F TYR 3.6 35.9 - - - +
99F PRO* 4.1 11.9 - - + +
100F ARG* 6.0 1.3 - - - -
118F VAL* 4.9 10.8 - - + -
119F ILE 2.9 11.8 + - - +
120F CYS* 4.6 5.6 - - - -
121F MET* 2.8 29.1 + - - +
156F TYR* 3.6 23.3 - - + +
160F SER* 4.3 12.6 - - - -
163F VAL* 5.1 10.5 - - + -
164F ILE* 4.4 15.7 - - + -
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Residues in contact with GLY 18 (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* 1.3 78.7 - - - +
19F GLY* 1.3 67.8 + - - +
20F PRO* 4.6 0.5 - - - +
22F SER* 3.6 11.7 - - - -
24F LYS* 3.5 22.9 + - - +
121F MET* 3.8 9.4 - - - -
156F TYR* 3.3 19.9 - - - -
1199F SO4 4.8 0.2 + - - -
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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