Contacts of the strand formed by residues 266 - 270 (chain A) in PDB entry 2GP0
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 266 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A VAL* 2.8 17.9 + - + +
144A TYR* 3.1 19.4 - - + +
145A ILE 2.9 19.6 + - - -
169A LEU* 3.7 39.0 - - + +
171A VAL* 4.1 12.6 - - + -
253A VAL* 4.1 17.5 - - + +
258A GLU* 5.8 4.0 - - - +
264A GLY 4.9 3.1 - - - +
265A PRO* 1.3 72.1 - - - +
267A VAL* 1.3 72.1 + - - +
268A VAL* 3.6 7.4 + - + -
280A PHE* 5.6 0.4 - - + -
284A ARG* 3.8 26.7 - - - +
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Residues in contact with VAL 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A ILE* 3.4 18.8 - - + +
147A THR* 3.9 16.6 - - + -
158A PHE* 3.9 28.3 - - + -
161A MET* 4.4 11.2 - - + -
162A VAL* 4.7 5.2 - - + -
167A VAL* 3.5 34.5 - - + -
169A LEU 3.1 11.8 + - - +
170A ILE* 3.4 12.1 - - + -
171A VAL* 2.7 32.2 + - - -
265A PRO 3.6 0.8 + - - -
266A ILE* 1.3 73.5 - - - +
268A VAL* 1.3 59.2 + - - +
269A HIS* 4.2 3.8 - - + -
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Residues in contact with VAL 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A TYR* 4.0 24.2 - - + -
145A ILE 2.9 8.7 + - - +
146A ALA* 3.4 2.8 - - - -
147A THR* 3.1 23.4 + - - +
171A VAL* 3.3 10.3 - - + +
173A LEU* 3.9 17.3 - - + -
266A ILE* 4.1 6.7 - - + +
267A VAL* 1.3 78.9 - - - +
269A HIS* 1.3 61.6 - - - +
277A THR* 3.6 29.8 + - + +
280A PHE* 3.8 36.6 - - + -
281A ILE* 4.0 6.1 - - + -
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Residues in contact with HIS 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A THR* 3.0 29.2 - - + +
148A GLN 3.9 3.4 - - - +
149A GLY* 3.5 21.7 - - - -
150A PRO* 4.5 0.2 - - + -
158A PHE* 4.2 13.5 - + - -
170A ILE* 3.7 17.7 - - + -
171A VAL 2.9 11.5 + - - +
172A MET* 3.4 32.3 - - + +
173A LEU* 2.9 30.0 + - - +
186A TYR* 2.6 42.0 + + - -
267A VAL* 4.3 1.8 - - + -
268A VAL* 1.3 74.3 - - - +
270A CYS* 1.3 64.5 + - - +
277A THR* 3.6 6.1 - - - -
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Residues in contact with CYS 270 (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 THR 3.6 1.4 + - - -
148A GLN* 3.2 0.5 - - - -
149A GLY* 2.8 19.7 + - - -
173A LEU* 3.4 20.4 - - + +
269A HIS* 1.3 77.8 - - - +
271A SER* 1.3 66.0 + - - +
273A GLY* 3.1 21.2 + - - -
274A ILE 3.9 0.4 - - - -
276A ARG* 3.9 14.6 - - + +
277A THR* 3.5 26.9 - - - +
436A PO4 3.1 35.7 - - - +
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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
------------------------------------------------------------
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