Contacts of the helix formed by residues 262 - 267 (chain D) in PDB entry 6G2T
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 262 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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222D PHE* 6.4 0.2 - - + -
258D GLU* 2.7 37.1 + - + +
259D ALA* 3.0 16.7 + - - +
261D PHE* 1.3 78.9 + - - +
263D PRO* 1.3 62.1 - - - +
264D SER* 3.0 22.9 + - - +
265D PHE* 3.1 35.9 + - + +
274D HIS* 5.3 5.1 - - - -
275D GLU* 5.7 1.0 + - - -
311D ARG* 5.3 3.8 - - - +
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Residues in contact with PRO 263 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179D LEU* 4.4 12.3 - - + -
259D ALA 3.1 9.8 - - - +
260D LEU 4.2 1.6 - - - +
261D PHE 3.5 7.9 - - - +
262D GLN* 1.3 86.3 - - - +
264D SER* 1.3 60.9 + - - +
265D PHE 3.2 0.2 - - - -
266D LEU* 3.0 13.1 + - + +
267D GLY 2.9 22.0 + - - -
268D MET* 3.1 21.5 + - + +
270D SER* 3.1 29.8 - - - +
271D CYS* 3.5 3.6 - - - +
272D GLY* 3.4 22.2 - - - +
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Residues in contact with SER 264 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39C HIS* 5.6 0.7 - - - -
262D GLN* 3.0 15.1 + - - -
263D PRO* 1.3 79.8 - - - +
265D PHE* 1.3 69.1 + - - +
267D GLY* 3.0 15.7 + - - +
268D MET 4.1 7.1 + - - -
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Residues in contact with PHE 265 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187D TYR* 3.9 38.2 - - + +
190D LYS* 5.0 5.5 + - - -
222D PHE* 3.9 27.6 - + - -
255D ARG* 4.7 4.7 - - + -
258D GLU* 3.8 25.4 - - + -
259D ALA* 4.3 12.8 - - + -
262D GLN* 3.1 31.5 + - + +
264D SER* 1.3 81.6 - - - +
266D LEU* 1.3 61.5 + - - +
267D GLY 3.5 0.2 + - - -
171E PRO* 5.8 4.3 - - - +
172E HIS* 5.7 0.7 - - - +
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Residues in contact with LEU 266 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179D LEU* 3.5 32.8 - - + -
183D ASP* 4.5 17.0 - - + +
184D LEU* 5.4 5.4 - - + -
187D TYR* 3.6 36.1 - - + -
190D LYS* 6.1 1.1 - - - +
259D ALA* 4.0 23.3 - - + +
263D PRO* 3.0 11.0 + - + +
265D PHE* 1.3 81.0 - - - +
267D GLY* 1.3 58.9 + - - +
268D MET* 3.7 19.8 - - + +
172E HIS* 3.2 29.7 - - - +
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Residues in contact with GLY 267 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38C ARG* 2.8 24.8 + - - -
39C HIS* 3.5 24.0 + - - -
263D PRO 2.9 3.4 + - - -
264D SER* 3.0 15.6 + - - -
265D PHE 3.2 0.4 - - - -
266D LEU* 1.3 79.8 - - - +
268D MET* 1.3 62.6 + - - +
171E PRO* 6.1 0.4 - - - -
172E HIS* 3.9 11.8 + - - -
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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