Contacts of the helix formed by residues 171 - 176 (chain B) in PDB entry 2B3T
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 VAL 171 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B ASP 3.6 2.2 + - - -
109B ARG 3.6 10.4 + - - +
110B ASN* 4.0 4.0 - - - +
111B ALA* 3.3 31.6 - - + +
144B TRP* 3.7 41.7 - - + -
166B ILE* 4.4 10.1 - - + -
167B SER* 4.1 3.6 - - - -
168B GLY 3.3 28.5 - - - +
169B ASP 3.3 0.2 - - - -
170B GLY* 1.3 74.7 - - - +
172B TYR* 1.3 60.2 + - - +
174B ARG* 2.6 33.1 + - - +
175B LEU* 3.2 12.5 + - + +
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Residues in contact with TYR 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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106B ASP* 3.9 20.4 - - + +
107B ASP* 5.0 1.8 - - - -
109B ARG 3.2 14.4 + - - +
110B ASN 4.2 4.7 - - - +
111B ALA* 4.1 3.4 - - + -
171B VAL* 1.3 82.0 - - - +
173B GLY* 1.3 58.0 + - - +
174B ARG 2.6 12.5 + - - -
175B LEU* 4.6 1.1 - - - +
176B LYS* 3.0 55.3 + - + +
205B VAL* 2.9 28.4 + - + -
206B MET* 3.0 28.9 - - - -
207B PRO* 3.1 27.7 - - + +
283B MET* 5.0 10.1 - - - +
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Residues in contact with GLY 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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107B ASP* 2.8 55.3 + - - +
170B GLY* 5.0 0.7 - - - -
171B VAL 3.1 0.2 + - - -
172B TYR* 1.3 73.0 - - - +
174B ARG* 1.3 58.5 + - - +
176B LYS* 3.4 22.8 - - - +
177B PHE* 4.6 0.9 - - - -
345B ILE* 4.4 12.8 - - - +
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Residues in contact with ARG 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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138B TYR* 3.0 25.8 + - - +
142B ARG* 3.2 29.2 - - - +
144B TRP* 3.8 15.5 - - + -
170B GLY 3.4 14.3 + - - +
171B VAL 2.6 13.2 + - - +
172B TYR 2.6 6.3 + - - -
173B GLY* 1.3 74.3 - - - +
175B LEU* 1.3 58.0 + - + +
176B LYS* 3.7 1.8 - - - -
177B PHE* 5.3 1.6 - - - -
338B ASP* 3.1 19.4 + - - -
341B ILE* 3.2 51.8 - - - +
342B GLU* 3.6 25.3 + - - +
345B ILE* 5.6 5.0 - - - +
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Residues in contact with LEU 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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111B ALA* 5.8 0.9 - - + -
113B LEU* 4.0 12.8 - - + -
135B TYR* 5.5 4.7 - - + -
138B TYR* 3.5 35.0 - - + -
139B ALA* 6.3 0.2 - - + -
144B TRP* 4.1 17.9 - - + -
166B ILE* 3.6 31.6 - - + -
171B VAL* 3.2 12.4 + - + +
172B TYR* 3.1 2.5 + - - +
174B ARG* 1.3 83.3 - - - +
176B LYS* 1.3 58.1 + - - +
177B PHE 3.2 3.1 - - - -
178B GLU* 2.7 41.3 + - + +
205B VAL* 3.6 17.4 - - + +
337B LEU* 5.0 9.0 - - + -
341B ILE* 4.4 9.9 - - + -
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Residues in contact with LYS 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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104B ASP* 3.7 12.9 + - - -
107B ASP* 2.9 24.9 + - - -
172B TYR* 3.0 45.5 + - + +
173B GLY* 3.4 20.0 - - - -
175B LEU* 1.3 75.9 - - - +
177B PHE* 1.3 94.8 + - + +
179B SER* 2.6 40.8 + - - -
205B VAL* 3.7 14.5 - - - +
345B ILE* 5.0 2.9 - - - +
348B HIS* 5.0 8.5 + - - -
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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