Contacts of the helix formed by residues 260 - 268 (chain A) in PDB entry 2W3S
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 HIS 260 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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241A TYR* 4.7 4.2 - + - -
255A PHE* 6.0 2.5 - + - -
256A ALA* 2.8 29.6 + - + +
259A PRO* 1.3 86.2 + - + +
261A PRO* 1.4 66.9 - - - +
262A ALA* 3.0 4.8 + - + -
263A LEU* 3.0 13.4 + - + +
264A ALA 3.2 6.4 + - - -
301A MET* 3.5 41.3 - - + +
341A LEU* 4.3 14.0 - - + +
342A PRO* 2.9 29.7 + - + -
343A LYS 4.2 2.0 - - - -
344A SER* 3.6 8.4 + - - -
345A ALA* 3.5 34.4 + - + +
348A LEU* 5.1 1.7 - - + +
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Residues in contact with PRO 261 (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 ALA 3.1 7.5 - - - +
257A GLU* 4.3 10.5 - - - +
258A GLY 3.4 13.5 - - - +
259A PRO 3.4 5.2 - - - +
260A HIS* 1.4 86.0 - - - +
262A ALA* 1.3 53.0 + - + +
264A ALA* 3.0 8.2 + - + +
265A GLY* 2.7 32.6 + - - -
346A PRO* 6.4 3.1 - - + -
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Residues in contact with ALA 262 (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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260A HIS* 3.0 2.1 + - + -
261A PRO* 1.3 81.8 - - + +
263A LEU* 1.3 57.6 + - - +
265A GLY* 3.4 3.6 + - - +
266A LEU* 3.1 24.9 + - - +
345A ALA* 6.3 0.2 - - + -
348A LEU* 3.6 40.2 - - + +
349A ARG* 4.5 11.0 - - - +
350A CYS* 4.2 9.9 + - - +
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Residues in contact with LEU 263 (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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252A LEU* 4.3 18.6 - - + -
256A ALA* 4.2 14.4 - - + -
260A HIS* 3.0 15.8 + - + +
262A ALA* 1.3 78.9 - - - +
264A ALA* 1.3 50.7 + - - +
266A LEU* 3.0 9.3 + - + -
267A LEU* 2.7 57.2 + - + +
293A ASP 5.6 0.9 - - - +
294A GLY* 5.7 2.5 - - - +
297A ALA* 4.1 22.4 - - + -
298A LEU* 4.0 26.9 - - + -
301A MET* 4.1 15.3 - - + -
341A LEU* 4.4 8.7 - - + -
348A LEU* 4.8 4.9 - - + +
350A CYS* 4.9 4.0 - - - -
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Residues in contact with ALA 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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253A ARG* 3.4 43.0 + - + +
256A ALA* 3.8 6.2 - - + +
257A GLU* 3.7 31.3 - - + +
260A HIS 3.2 2.0 + - - -
261A PRO* 3.0 9.3 + - + +
263A LEU* 1.3 78.2 - - - +
265A GLY* 1.3 57.2 + - - +
267A LEU* 4.4 1.6 - - - +
268A ARG* 3.1 26.5 + - - +
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Residues in contact with GLY 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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261A PRO 2.7 16.6 + - - -
262A ALA* 3.6 6.5 - - - -
263A LEU 3.2 0.4 - - - -
264A ALA* 1.3 72.9 - - - +
266A LEU* 1.3 58.4 + - - +
268A ARG* 3.5 22.1 + - - +
269A ARG* 4.3 7.3 + - - +
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Residues in contact with LEU 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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262A ALA 3.1 5.0 + - - +
263A LEU* 3.0 12.3 + - + +
265A GLY* 1.3 73.8 - - - +
267A LEU* 1.3 61.8 + - + +
268A ARG 3.2 2.0 - - - -
269A ARG* 3.1 27.7 + - + +
270A PHE* 4.6 1.2 - - - +
293A ASP* 3.5 33.3 - - + +
297A ALA* 3.7 22.7 - - + -
350A CYS* 3.8 31.0 - - + +
352A LYS* 3.7 39.0 - - + +
365A CYS* 4.5 8.1 - - - -
367A CYS* 4.5 4.9 - - - -
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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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249A ILE* 3.6 28.0 - - + +
252A LEU* 3.6 28.3 - - + +
253A ARG* 3.3 45.1 - - + +
263A LEU* 2.7 40.6 + - + +
264A ALA 3.6 0.2 + - - -
266A LEU* 1.3 72.7 - - + +
268A ARG* 1.3 66.7 + - - +
270A PHE* 3.0 35.2 + - + +
276A ARG* 3.3 11.4 - - - -
293A ASP 5.4 5.8 - - - +
294A GLY* 5.6 4.5 - - - -
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Residues in contact with ARG 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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127A ASP* 3.1 48.9 + - - +
253A ARG* 3.4 29.1 - - - +
264A ALA 3.1 13.6 + - - +
265A GLY* 3.5 18.5 + - - +
267A LEU* 1.3 76.0 - - - +
269A ARG* 1.3 70.3 + - - +
276A ARG* 2.9 28.2 + - - -
358A ASP* 4.6 12.7 + - - -
458A LEU* 3.6 31.7 - - - +
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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