Contacts of the helix formed by residues 266 - 276 (chain A) in PDB entry 2CSX
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 VAL 266 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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166A LEU* 4.8 8.5 - - + -
173A LEU* 3.6 19.9 - - + +
177A TYR* 3.1 19.3 - - - +
193A ILE* 4.2 9.4 - - + -
196A PHE* 4.4 12.3 - - + -
197A VAL* 4.1 13.0 - - + -
262A ARG* 2.9 31.1 + - + +
265A THR* 1.3 80.4 - - - +
267A TYR* 1.3 84.4 + - + +
268A TRP 3.2 0.7 - - - -
269A PRO* 3.1 9.7 - - - +
270A ALA* 3.4 16.8 + - - +
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Residues in contact with TYR 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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166A LEU* 4.0 24.5 - - + -
196A PHE* 5.1 13.0 - + - -
204A LEU* 3.6 42.7 - - + +
230A TRP* 3.8 31.1 - + - -
234A LEU* 4.4 4.5 - - + -
262A ARG* 3.7 19.6 + - - -
263A PHE* 3.4 36.2 + + - +
266A VAL* 1.3 96.1 - - + +
268A TRP* 1.3 61.3 + - - +
270A ALA* 4.0 0.7 - - - +
271A PHE* 3.2 40.4 + - + -
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Residues in contact with TRP 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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234A LEU* 3.5 44.6 - - + +
235A PHE* 3.6 40.4 - + - -
237A TYR* 4.0 12.6 - + - -
238A ILE* 3.8 19.3 - - + -
249A TRP* 4.0 13.9 - + - -
254A HIS* 3.5 26.3 + + - -
263A PHE 2.9 13.4 + - - +
264A HIS* 3.3 28.0 - + - +
267A TYR* 1.3 75.9 - - - +
269A PRO* 1.3 70.1 - - + +
271A PHE* 3.3 6.6 + + - -
272A LEU* 3.2 32.3 + - + +
280A PRO* 3.5 21.3 - - + +
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Residues in contact with PRO 269 (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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173A LEU* 3.9 13.2 - - + -
176A LEU* 4.2 12.8 - - + -
183A PHE* 3.5 23.6 - - + -
264A HIS 3.5 0.9 - - - +
265A THR 3.2 26.7 - - - +
266A VAL 3.1 15.9 - - - +
268A TRP* 1.3 92.9 - - + +
270A ALA* 1.3 55.4 + - - +
272A LEU* 2.8 8.9 + - + +
273A MET* 2.6 39.3 + - + +
279A LEU* 4.5 13.9 - - + -
280A PRO* 5.5 0.9 - - + -
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Residues in contact with ALA 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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164A PHE* 3.6 13.0 - - + -
166A LEU* 3.8 24.2 - - + -
169A TYR* 3.9 22.9 - - + -
173A LEU* 4.0 5.7 - - + +
266A VAL 3.4 15.6 + - - +
267A TYR 4.0 2.0 - - - +
269A PRO* 1.3 78.4 - - - +
271A PHE* 1.3 65.6 + - - +
273A MET* 3.6 14.1 - - - +
274A SER* 3.0 16.8 + - - -
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Residues in contact with PHE 271 (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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164A PHE* 3.5 42.4 - + + -
204A LEU* 4.2 16.2 - - + -
206A VAL* 4.7 1.3 - - + -
230A TRP* 3.7 25.1 - - + -
231A PHE* 3.3 40.2 - + + -
234A LEU* 4.0 11.7 - - + -
235A PHE* 3.9 25.6 - + + -
267A TYR* 3.2 26.0 + - + -
268A TRP* 3.3 18.6 - + + +
269A PRO 3.0 0.4 - - - -
270A ALA* 1.3 78.5 - - - +
272A LEU* 1.3 62.6 + - - +
274A SER* 2.8 22.6 + - - -
275A LEU* 3.2 12.5 + - + +
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Residues in contact with LEU 272 (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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235A PHE* 4.2 5.4 - - + -
238A ILE* 3.5 29.8 - - + -
249A TRP* 4.0 9.2 - - + -
268A TRP* 3.2 48.2 + - + +
269A PRO* 2.8 11.1 + - + +
271A PHE* 1.3 76.3 - - - +
273A MET* 1.3 62.1 + - - +
275A LEU* 3.1 4.8 + - - +
276A GLY 2.9 19.4 + - - -
277A TYR* 3.0 36.2 + - + -
278A GLU 4.0 4.0 - - - +
279A LEU* 3.6 12.8 - - + -
280A PRO* 3.9 20.9 - - + -
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Residues in contact with MET 273 (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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169A TYR* 3.8 18.1 - - + -
172A LYS* 3.5 59.7 - - + +
173A LEU* 4.2 15.5 - - + +
176A LEU* 4.1 16.4 - - + -
269A PRO* 2.6 15.6 + - + +
270A ALA* 3.6 10.1 - - - +
271A PHE 3.2 0.2 - - - -
272A LEU* 1.3 74.0 - - - +
274A SER* 1.3 59.7 + - - +
276A GLY* 3.3 11.7 + - - -
277A TYR 4.9 2.2 - - - -
279A LEU* 4.0 31.1 - - + +
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Residues in contact with SER 274 (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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113A CYS* 3.6 11.9 - - - -
116A ARG* 2.8 30.0 + - - +
118A ASP* 3.3 16.6 - - - -
164A PHE* 3.6 16.0 - - - -
169A TYR* 2.7 31.2 + - - -
270A ALA 3.0 6.0 + - - -
271A PHE 2.8 19.7 + - - -
273A MET* 1.3 76.5 - - - +
275A LEU* 1.3 57.9 + - - +
276A GLY 3.2 0.2 - - - -
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Residues in contact with LEU 275 (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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109A VAL* 3.2 46.0 - - + +
112A GLU* 4.5 12.8 - - + +
113A CYS* 3.9 22.9 - - + +
116A ARG* 3.6 23.1 + - - +
231A PHE* 5.3 2.0 - - + -
235A PHE* 4.5 4.9 - - + -
271A PHE* 3.2 15.9 + - + +
272A LEU* 3.1 8.0 + - - +
274A SER* 1.3 87.9 + - - +
276A GLY* 1.3 60.9 + - - +
277A TYR* 3.5 47.0 + - + +
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Residues in contact with GLY 276 (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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116A ARG* 4.5 5.4 - - - -
272A LEU 2.9 4.9 + - - -
273A MET 3.3 7.7 + - - -
274A SER 3.2 4.9 + - - -
275A LEU* 1.3 79.3 - - - +
277A TYR* 1.3 65.9 + - - +
278A GLU 4.2 0.3 + - - -
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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