Contacts of the strand formed by residues 13 - 18 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8C LEU 3.9 21.3 - - - +
9C ARG* 5.8 0.4 - - - +
11C CYS* 3.2 8.5 + - + +
12C LYS* 1.3 76.6 - - - +
14C ILE* 1.3 67.3 + - - +
15C PHE* 3.7 28.7 - - + -
83C MET* 3.9 24.2 - - + -
93C PHE* 3.6 9.2 - - + +
95C ILE* 4.3 8.3 - - + -
108C PHE* 4.2 11.4 - - + -
112C ILE* 4.8 0.2 - - + -
113C GLY* 4.4 15.3 - - - -
114C ASP 4.3 10.1 - - - +
115C PRO* 3.4 15.1 - - + +
116C GLN* 2.5 35.7 + - - +
117C LEU 3.7 1.7 + - - -
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Residues in contact with ILE 14 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C LYS* 5.0 2.0 - - + -
13C ILE* 1.3 80.1 - - - +
15C PHE* 1.3 63.9 + - - +
16C ILE 4.1 0.2 + - - -
37C PHE* 3.8 38.4 - - + -
93C PHE 2.7 15.4 + - - +
94C LEU* 3.5 19.5 - - + +
95C ILE* 2.7 34.1 + - - +
117C LEU* 3.4 16.6 - - + +
119C ILE* 3.7 24.0 - - + -
193C ILE* 4.1 15.9 - - + -
197C PHE* 4.2 24.9 - - + -
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Residues in contact with PHE 15 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13C ILE* 3.7 20.6 - - + -
14C ILE* 1.3 83.0 - - - +
16C ILE* 1.3 56.8 + - - +
17C ILE* 5.1 0.9 - - + -
95C ILE* 3.2 20.2 - - + -
98C TYR* 3.6 35.2 - + - +
99C PRO* 3.9 12.3 - - + -
108C PHE* 3.6 34.8 - + - -
115C PRO* 3.7 22.2 - - + -
117C LEU 3.0 6.7 + - - +
118C VAL* 3.4 19.2 - - + -
119C ILE* 2.7 33.8 + - - +
167C TYR* 3.4 28.5 - + - -
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Residues in contact with ILE 16 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C PHE* 1.3 74.1 - - - +
17C ILE* 1.3 62.2 + - - +
24C LYS* 3.7 14.6 - - + +
27C GLN* 5.2 1.1 - - + -
28C CYS* 3.8 25.8 - - - -
31C LEU* 4.1 25.8 - - + -
94C LEU* 3.9 17.3 - - + -
95C ILE 2.9 5.4 + - - +
96C ASP* 3.7 20.4 - - - +
97C GLY* 2.8 28.8 + - - -
119C ILE* 3.4 29.8 - - + -
121C MET* 4.1 17.9 - - - -
189C LEU* 4.2 4.0 - - + -
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Residues in contact with ILE 17 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C PHE 5.1 0.2 - - - -
16C ILE* 1.3 76.2 - - - +
18C GLY* 1.3 62.1 + - - +
24C LYS* 3.8 4.7 - - - +
97C GLY* 3.8 6.5 - - - +
98C TYR 3.3 43.3 - - - +
99C PRO* 4.4 6.5 - - + +
118C VAL* 4.5 17.0 - - + -
119C ILE 2.8 12.4 + - - +
120C CYS* 3.6 5.6 - - + -
121C MET* 2.8 29.8 + - - +
156C TYR* 3.6 19.1 - - + +
160C SER* 4.0 19.3 - - - -
163C VAL* 4.7 11.9 - - + -
164C ILE* 4.4 11.7 - - + -
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Residues in contact with GLY 18 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C ILE* 1.3 79.6 - - - +
19C GLY* 1.3 65.4 + - - -
20C PRO* 4.7 0.2 - - - +
22C SER* 3.6 9.4 - - - -
24C LYS* 3.3 24.6 - - - +
121C MET* 3.9 12.3 - - - -
156C TYR* 3.3 18.6 - - - -
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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