Contacts of the helix formed by residues 172 - 179 (chain B) in PDB entry 2BV1
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 ASP 172 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168B LEU* 3.2 19.0 + - + +
169B MET 3.4 1.2 + - - -
171B LYS* 1.3 79.1 - - + +
173B SER* 1.3 69.3 + - - +
174B TYR 3.4 0.7 - - - -
175B PRO* 3.4 9.6 - - - +
176B ARG* 3.2 48.1 + - - +
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Residues in contact with SER 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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86B PHE* 3.8 2.8 - - - -
89B PHE* 3.5 4.3 - - - -
90B LEU* 3.4 31.8 - - - +
93B GLU* 4.3 2.9 - - - -
95B SER* 4.7 2.9 - - - -
98B ASN* 5.5 2.4 + - - -
168B LEU 4.5 0.2 + - - -
169B MET* 3.4 25.7 + - - +
172B ASP* 1.3 82.6 - - - +
174B TYR* 1.3 58.5 + - - +
176B ARG* 3.3 18.8 + - - +
177B PHE* 2.8 30.5 + - - +
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Residues in contact with TYR 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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69B TRP 2.7 29.4 + - - -
70B SER 3.3 17.1 + - - -
72B SER* 3.2 12.6 + - - -
73B LEU* 3.4 39.9 - - + -
76B LEU* 3.8 27.4 - - + -
86B PHE* 4.0 8.7 - - + -
169B MET 2.8 27.2 + - - +
170B GLU* 3.8 17.0 - - + -
173B SER* 1.3 74.0 + - - +
175B PRO* 1.3 65.5 - - + +
177B PHE* 3.0 14.0 + + - +
178B LEU* 3.2 36.9 + - + +
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Residues in contact with PRO 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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170B GLU 3.3 24.7 - - - +
171B LYS* 3.8 13.9 - - - +
172B ASP 3.4 13.5 - - - +
174B TYR* 1.3 91.9 - - + +
176B ARG* 1.3 64.0 + - + +
178B LEU* 3.3 22.4 + - + +
179B LYS* 3.5 17.0 + - - +
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Residues in contact with ARG 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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89B PHE* 3.8 8.2 - - + -
93B GLU* 2.7 43.4 + - - -
172B ASP* 3.2 43.7 + - - +
173B SER* 3.3 14.5 + - - +
174B TYR 3.2 0.8 - - - -
175B PRO* 1.3 79.2 - - + +
177B PHE* 1.3 64.1 + - - +
179B LYS* 3.1 17.8 + - + +
180B SER* 3.2 12.0 + - - -
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Residues in contact with PHE 177 (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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69B TRP* 4.5 2.5 - + + -
76B LEU* 3.6 32.5 - - + -
85B VAL* 3.9 28.9 - - + -
86B PHE* 3.5 33.9 - + + -
89B PHE* 3.6 37.0 - + + -
173B SER 2.8 14.7 + - - +
174B TYR* 3.3 8.5 - + - +
176B ARG* 1.3 76.8 - - - +
178B LEU* 1.3 68.9 + - + +
180B SER* 2.5 31.8 + - - -
182B ILE* 4.2 4.0 - - + -
183B TYR* 3.2 42.5 - + + +
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Residues in contact with LEU 178 (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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69B TRP 4.1 2.5 - - - +
70B SER* 3.9 39.3 - - - +
174B TYR* 3.2 48.6 + - + +
175B PRO* 3.6 13.5 - - + +
176B ARG 3.3 0.4 - - - -
177B PHE* 1.3 85.4 - - + +
179B LYS* 1.3 61.4 + - + +
183B TYR* 3.3 33.9 - - + -
184B LEU* 3.4 13.7 - - - +
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Residues in contact with LYS 179 (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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175B PRO 3.7 13.2 - - - +
176B ARG* 3.1 11.7 + - + +
177B PHE 3.1 0.8 - - - -
178B LEU* 1.3 79.7 - - + +
180B SER* 1.3 63.6 + - - +
181B ASP* 5.1 1.0 - - - +
184B LEU* 3.5 16.1 - - + +
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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