Contacts of the helix formed by residues 262 - 270 (chain A) in PDB entry 3GBG
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 ALA 262 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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255A PHE* 3.8 3.1 - - - -
256A LYS* 3.8 9.8 - - + +
261A VAL* 1.3 73.9 - - - +
263A PRO* 1.3 77.3 - - + +
264A SER* 4.4 6.5 - - - +
265A GLU* 3.0 40.8 + - + +
266A TYR 3.0 10.6 + - - -
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Residues in contact with PRO 263 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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229A MET* 4.0 5.8 - - + +
236A ILE* 3.9 17.9 - - + -
251A PHE* 3.6 33.0 - - + -
252A SER* 4.0 25.1 - - - +
255A PHE* 3.5 40.4 - - + -
261A VAL 4.3 0.2 - - - +
262A ALA* 1.3 84.5 - - + +
264A SER* 1.3 62.5 + - - +
266A TYR* 3.1 4.5 + - - +
267A LEU* 3.0 22.9 + - - +
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Residues in contact with SER 264 (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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236A ILE* 3.8 22.1 - - - +
262A ALA* 4.4 5.7 - - - +
263A PRO* 1.3 80.0 - - - +
265A GLU* 1.3 70.4 + - - +
267A LEU* 3.4 7.8 + - - +
268A PHE* 3.1 22.7 + - - +
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Residues in contact with GLU 265 (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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256A LYS* 5.3 2.4 - - - -
261A VAL* 3.6 16.9 - - + +
262A ALA* 3.0 38.5 + - + +
264A SER* 1.3 83.7 + - - +
266A TYR* 1.3 65.6 + - - +
268A PHE* 3.3 11.0 + - - +
269A MET* 3.1 27.1 + - + +
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Residues in contact with TYR 266 (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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12A TYR* 2.6 43.1 + + - -
226A ILE* 3.4 36.1 - - + +
229A MET* 3.9 17.7 - - + -
230A LYS* 3.5 4.7 - - - -
255A PHE* 3.6 25.8 - + + -
259A MET* 4.0 21.3 - - + -
261A VAL* 4.1 5.3 - - + +
262A ALA 3.0 6.6 + - - +
263A PRO 3.1 6.5 + - - +
265A GLU* 1.3 72.1 - - - +
267A LEU* 1.3 68.9 + - - +
269A MET* 2.8 26.6 + - - +
270A LEU* 3.2 33.4 + - + +
5975A PAM 3.7 18.2 + - + -
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Residues in contact with LEU 267 (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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229A MET* 3.9 28.7 - - + +
233A GLU 3.5 20.6 - - - +
234A PHE* 3.5 39.9 - - + +
236A ILE* 4.3 9.9 - - + -
263A PRO 3.0 13.0 + - - +
264A SER* 3.5 11.7 - - - +
266A TYR* 1.3 78.7 - - - +
268A PHE* 1.3 58.6 + - - +
270A LEU* 2.9 35.1 + - + +
271A THR* 4.4 1.6 + - - -
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Residues in contact with PHE 268 (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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264A SER 3.1 14.0 + - - +
265A GLU* 3.4 13.0 - - - +
266A TYR 3.1 0.2 - - - -
267A LEU* 1.3 76.3 - - - +
269A MET* 1.3 68.7 + - + +
271A THR* 3.0 37.2 + - + -
272A GLY 4.6 0.2 + - - -
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Residues in contact with MET 269 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A VAL 4.3 8.0 - - - +
12A TYR* 4.2 26.5 - - + -
13A ARG* 4.7 4.7 - - + +
20A TYR* 3.2 35.9 - - + +
261A VAL* 5.2 7.9 - - + -
265A GLU* 3.1 18.6 - - + +
266A TYR* 2.8 15.9 + - - +
268A PHE* 1.3 78.8 - - + +
270A LEU* 1.3 57.2 + - - +
271A THR* 3.0 10.4 + - - -
272A GLY* 3.8 8.2 + - - +
5975A PAM 3.6 28.0 - - + -
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Residues in contact with LEU 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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10A ASN* 4.1 19.9 + - - +
12A TYR* 3.9 13.9 - - + +
229A MET* 3.4 46.4 - - + +
230A LYS* 4.0 9.4 - - + +
266A TYR* 3.3 42.2 - - + +
267A LEU* 2.9 20.1 + - + +
269A MET* 1.3 76.3 - - - +
271A THR* 1.3 61.2 + - - +
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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