Contacts of the strand formed by residues 191 - 195 (chain A) in PDB entry 3GYQ
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 GLN 191 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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189A GLY 3.6 2.5 + - - +
190A MET* 1.3 70.6 - - - +
192A LEU* 1.3 60.8 + - - +
193A MET* 3.5 24.8 + - - +
209A ASN* 3.2 28.2 + - - +
211A ASP* 3.7 20.3 - - + +
212A ARG 3.6 6.8 + - - +
213A LEU* 3.7 13.4 - - + -
214A ALA* 3.1 20.5 + - - -
233A SER* 3.1 23.0 + - - +
234A ALA* 4.8 4.6 - - - +
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Residues in contact with LEU 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A VAL* 5.6 1.3 - - + -
182A ILE* 6.4 0.4 - - - -
185A ILE* 4.1 27.1 - - + -
190A MET 3.6 3.8 + - - +
191A GLN* 1.3 72.4 - - - +
193A MET* 1.3 62.9 + - - +
194A THR* 4.7 0.4 - - - +
214A ALA* 3.1 30.7 - - + +
215A LEU 5.0 0.2 - - - -
216A LEU* 4.0 22.2 - - + -
228A PHE* 4.0 20.6 - - + +
231A ALA* 3.6 28.4 + - + +
232A SER* 3.4 29.5 - - - +
233A SER* 3.1 30.2 + - - -
234A ALA 3.7 2.9 + - - -
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Residues in contact with MET 193 (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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191A GLN* 3.5 30.5 - - - +
192A LEU* 1.3 82.6 - - - +
194A THR* 1.3 63.1 + - - +
195A LEU* 3.7 3.3 + - + +
201A ILE* 5.2 5.8 - - + -
206A LEU* 3.7 15.5 - - + -
209A ASN* 5.0 2.7 - - + +
213A LEU* 3.6 33.7 - - + -
214A ALA 2.9 12.2 + - - +
215A LEU* 3.6 11.9 - - + -
216A LEU* 2.8 26.9 + - - +
234A ALA* 3.6 22.4 - - + -
236A VAL* 3.5 30.5 - - + -
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Residues in contact with THR 194 (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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192A LEU* 4.7 0.2 - - - +
193A MET* 1.3 70.2 - - - +
195A LEU* 1.3 60.5 + - - +
196A LYS* 4.9 5.8 - - + -
216A LEU* 3.5 20.0 - - + +
224A PRO* 3.7 33.2 - - + -
228A PHE* 4.8 0.9 + - - +
229A GLU* 4.8 12.1 + - - +
232A SER* 2.9 31.2 + - - -
234A ALA 2.9 11.5 + - - -
235A SER* 3.0 10.7 - - - -
236A VAL 2.7 28.5 + - - -
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Residues in contact with LEU 195 (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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193A MET* 3.8 15.5 - - + +
194A THR* 1.3 75.6 - - - +
196A LYS* 1.3 62.7 + - - +
203A VAL* 4.8 1.3 - - + -
206A LEU* 5.1 1.3 - - + -
215A LEU* 4.2 18.4 - - + -
216A LEU 3.1 15.8 + - - +
217A PHE* 3.3 37.9 - - + -
224A PRO* 4.4 1.6 - - - +
236A VAL* 3.1 29.6 - - + +
238A ILE* 4.7 4.5 - - + -
252A SER 4.4 3.4 - - - +
256A ALA* 3.5 21.1 - - + -
270A SAM 2.5 47.3 + - + +
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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