Contacts of the strand formed by residues 164 - 168 (chain A) in PDB entry 2G5T
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 LEU 164 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A LEU* 4.8 1.6 - - + -
134A ILE* 3.3 34.5 - - + -
148A ILE* 4.2 12.1 - - + -
155A VAL* 4.2 15.3 - - + -
156A THR 3.8 13.9 - - - +
157A TRP* 3.4 47.6 - - + -
162A HIS 4.2 2.0 - - - +
163A LYS* 1.3 73.9 - - - +
165A ALA* 1.3 62.2 + - - +
166A TYR* 5.1 5.4 - - + -
173A TYR 4.4 0.2 - - - -
174A VAL* 3.2 8.8 - - - +
175A LYS* 2.7 57.6 + - + +
178A PRO* 5.0 3.6 - - + -
216A TRP* 4.0 2.7 - - - -
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Residues in contact with ALA 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155A VAL* 3.5 2.3 - - - +
156A THR* 3.1 37.9 + - + +
164A LEU* 1.3 75.1 - - - +
166A TYR* 1.3 62.2 + - - +
172A ILE* 5.2 0.4 - - + -
173A TYR 3.3 8.5 - - - +
174A VAL* 4.9 0.9 - - + -
214A LEU* 4.4 10.2 - - + +
216A TRP* 3.7 27.8 - - + +
223A LEU* 4.1 20.4 - - + -
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Residues in contact with TYR 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A ARG 5.3 0.3 + - - -
148A ILE* 4.4 23.6 - - + -
149A PRO* 3.6 33.7 - - + +
152A THR* 4.2 2.0 - - + -
154A TRP 3.1 14.4 - - - +
155A VAL* 3.6 16.4 - - + -
164A LEU* 5.1 6.7 - - + -
165A ALA* 1.3 79.2 - - - +
167A VAL* 1.3 74.3 + - - +
168A TRP* 4.1 4.5 - - + -
171A ASP 3.8 0.2 - - - +
172A ILE* 3.5 3.9 - - - +
173A TYR* 2.9 72.3 + + + +
175A LYS* 4.3 14.1 + - + -
182A SER* 2.8 33.6 + - - -
214A LEU* 5.1 0.6 - - - +
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Residues in contact with VAL 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152A THR* 3.4 6.9 - - - +
153A GLN* 2.9 42.0 + - + +
154A TRP* 2.9 13.5 + - + +
166A TYR* 1.3 78.6 - - - +
168A TRP* 1.3 61.0 + - - +
170A ASN* 3.9 9.6 - - - -
171A ASP 3.1 14.4 - - - +
172A ILE* 4.3 3.6 - - + -
196A ASN 3.4 24.9 - - - +
197A GLY* 3.9 19.7 - - - +
198A ILE* 3.9 19.3 - - + -
214A LEU* 4.1 15.0 - - + -
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Residues in contact with TRP 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A PRO* 3.4 30.1 - - + +
150A ASN 2.9 28.9 + - - -
151A ASN* 3.6 20.5 + - - +
152A THR* 4.1 3.1 - - - +
153A GLN* 3.6 2.2 - - - +
166A TYR* 4.1 13.4 + - + -
167A VAL* 1.3 74.5 - - - +
169A ASN* 1.3 104.0 + - + +
170A ASN 3.1 0.2 - - - -
171A ASP* 2.9 18.3 + - - +
173A TYR* 3.8 40.7 + + + -
184A ARG* 5.6 3.4 - - - -
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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