Contacts of the helix formed by residues 262 - 267 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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223B GLU* 5.5 2.3 - - - +
258B GLU* 2.7 34.0 + - + +
259B ALA* 2.9 16.6 - - - +
261B PHE* 1.3 76.3 + - - +
263B PRO* 1.3 62.3 - - - +
264B SER* 3.0 35.8 + - - +
265B PHE* 3.1 37.3 + - + +
311B ARG* 5.6 0.4 - - - +
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Residues in contact with PRO 263 (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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179B LEU* 4.3 14.1 - - + -
259B ALA 3.1 8.9 - - - +
260B LEU 4.2 1.8 - - - +
261B PHE 3.5 9.2 - - - +
262B GLN* 1.3 86.7 - - - +
264B SER* 1.3 59.7 + - - +
265B PHE 3.2 0.4 - - - -
266B LEU* 3.0 14.6 + - + +
267B GLY 2.9 22.3 + - - -
268B MET* 3.2 21.6 + - + +
270B SER* 3.1 28.9 - - - +
271B CYS* 3.6 3.4 - - - +
272B GLY* 3.5 22.2 - - - +
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Residues in contact with SER 264 (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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39A HIS* 5.3 1.7 - - - -
262B GLN* 3.8 21.8 + - - -
263B PRO* 1.3 76.9 - - - +
265B PHE* 1.3 69.8 + - - +
267B GLY* 3.0 16.0 + - - +
268B MET 4.1 7.5 + - - -
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Residues in contact with PHE 265 (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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187B TYR* 3.7 40.5 - - + +
190B LYS* 5.4 4.0 - - - -
222B PHE* 3.8 28.9 - + - -
255B ARG* 4.6 4.5 - - + -
258B GLU* 3.7 25.4 - - + -
259B ALA* 4.4 12.6 - - + -
262B GLN* 3.1 32.8 + - + +
264B SER* 1.3 82.1 - - - +
266B LEU* 1.3 61.2 + - - +
267B GLY* 4.6 0.2 - - - -
171C PRO* 5.8 3.8 - - - +
172C HIS* 5.5 1.7 + - - +
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Residues in contact with LEU 266 (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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179B LEU* 3.4 33.0 - - + -
183B ASP* 4.4 18.4 - - + +
184B LEU* 5.3 4.3 - - + -
187B TYR* 3.7 36.3 - - + +
190B LYS* 5.5 1.1 - - - +
259B ALA* 4.1 24.7 - - + +
263B PRO* 3.0 12.6 + - + +
265B PHE* 1.3 81.0 - - - +
267B GLY* 1.3 56.3 + - - +
268B MET* 3.6 20.4 - - + +
172C HIS* 3.2 28.6 - - - +
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Residues in contact with GLY 267 (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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38A ARG* 2.9 22.4 + - - -
39A HIS* 3.3 25.9 + - - -
263B PRO 2.9 3.6 + - - -
264B SER* 3.0 15.2 + - - -
265B PHE 4.5 0.2 - - - -
266B LEU* 1.3 80.1 - - - +
268B MET* 1.3 62.4 + - - +
171C PRO* 6.3 0.2 - - - -
172C HIS* 3.9 11.9 + - - -
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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