Contacts of the strand formed by residues 170 - 176 (chain B) in PDB entry 3BWC
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 TYR 170 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98B ARG* 3.8 16.6 + - + -
99B VAL 3.5 34.3 - - - -
100B LEU* 3.6 33.7 - - + -
121B HIS* 5.7 0.4 - + - -
123B ASP* 2.5 36.1 + - - +
161B PHE* 3.4 16.0 - + - -
165B THR* 3.8 13.9 - - + +
169B THR* 1.3 98.3 - - + +
171B ASP* 1.3 61.3 + - - +
172B VAL 3.9 12.6 - - - +
173B VAL* 4.2 9.0 - - + -
199B ILE* 3.0 17.2 + - + +
200B LEU* 3.3 5.3 - - + -
201B LYS* 2.8 33.5 + - - +
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Residues in contact with ASP 171 (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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93B HIS* 3.2 35.3 + - + +
95B LYS 3.5 4.9 - - - +
96B PRO* 4.0 11.4 - - + -
97B GLU* 2.9 29.0 + - - +
98B ARG* 2.8 20.3 + - - +
169B THR 4.3 0.2 + - - -
170B TYR* 1.3 74.9 - - - +
172B VAL* 1.3 59.9 + - - +
200B LEU* 3.8 1.6 - - - -
201B LYS* 3.6 29.1 + - - +
203B ASP* 4.5 2.6 - - - +
204B GLY* 3.2 7.4 - - - -
205B ILE 3.0 23.4 + - - -
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Residues in contact with VAL 172 (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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89B SER* 4.0 21.3 - - - +
90B LEU* 4.2 9.6 - - + -
93B HIS* 4.0 19.1 - - + -
96B PRO* 4.1 20.4 - - + -
98B ARG 3.4 3.2 + - - -
99B VAL* 3.4 12.3 - - + +
100B LEU 2.8 26.7 + - - +
170B TYR* 3.9 2.0 - - - +
171B ASP* 1.3 85.8 - - - +
173B VAL* 1.3 69.5 + - - +
174B ILE* 3.9 22.9 - - + -
200B LEU* 3.9 0.2 - - - -
205B ILE* 3.2 18.4 - - + +
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Residues in contact with VAL 173 (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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100B LEU* 3.4 33.7 - - + +
102B ILE* 4.6 5.2 - - + -
170B TYR* 4.2 7.9 - - + -
172B VAL* 1.3 75.9 - - - +
174B ILE* 1.3 58.8 + - - +
175B ILE* 3.6 23.5 - - + +
196B VAL* 4.1 20.6 - - + -
199B ILE* 4.3 11.7 - - + -
200B LEU* 3.6 24.2 - - + -
205B ILE 3.0 7.7 + - - +
206B CYS* 3.4 1.7 - - - -
207B CYS* 2.7 33.4 + - - +
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Residues in contact with ILE 174 (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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85B LEU* 4.1 19.3 - - + +
86B GLY* 4.3 0.7 - - - -
89B SER* 3.7 18.6 - - - +
90B LEU* 4.2 4.7 - - + -
99B VAL* 4.4 5.2 - - + -
100B LEU 2.8 14.5 + - - +
101B ILE* 3.3 8.7 - - + +
102B ILE* 2.8 26.9 + - - +
109B VAL* 3.8 23.3 - - + -
113B VAL* 3.7 29.8 - - + -
172B VAL* 3.9 13.9 - - + -
173B VAL* 1.3 75.7 - - - +
175B ILE* 1.3 63.5 + - - +
176B ASP* 3.6 5.2 + - + +
207B CYS* 3.4 21.8 - - + -
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Residues in contact with ILE 175 (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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85B LEU* 4.8 1.7 - - - +
102B ILE* 3.8 14.6 - - + +
173B VAL* 3.6 29.4 - - + +
174B ILE* 1.3 71.9 - - - +
176B ASP* 1.3 58.3 + - - +
177B THR* 3.2 29.6 + - - +
192B PHE* 4.1 27.6 - - + -
193B TYR* 4.8 13.5 - - + +
196B VAL* 4.7 12.8 - - + -
206B CYS* 5.1 1.8 - - + -
207B CYS 2.6 25.6 + - - +
208B ASN* 3.5 15.4 - - + -
209B GLN* 3.3 22.3 + - - +
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Residues in contact with ASP 176 (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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81B TYR* 2.6 44.1 + - - -
82B HIS* 4.6 1.9 - - - -
85B LEU* 4.2 4.9 - - + -
101B ILE* 4.5 7.9 - - + -
102B ILE 2.7 15.3 + - - +
103B GLY 4.2 0.2 - - - -
104B GLY* 3.2 29.3 + - - +
106B ASP* 4.5 4.0 - - - +
109B VAL* 3.4 22.0 - - + +
174B ILE* 3.6 3.2 + - + -
175B ILE* 1.3 68.9 - - - +
177B THR* 1.3 69.3 + - - +
209B GLN* 3.3 2.9 - - - -
501B SAM 3.2 26.1 - - - +
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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