Contacts of the helix formed by residues 262 - 275 (chain A) in PDB entry 6A08
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 PRO 262 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37A ALA* 3.5 45.1 - - + +
38A ASN* 3.3 20.9 - - - +
41A ALA* 4.1 17.0 - - + -
231A LEU* 4.3 0.2 - - - -
251A ASN* 3.6 2.9 - - - +
260A ALA 3.9 3.8 - - - +
261A VAL* 1.3 96.5 - - + +
263A GLY* 1.3 66.0 + - - +
264A ILE* 4.1 7.6 - - + -
265A GLU* 3.0 28.0 + - + +
266A MET* 3.6 4.5 + - - +
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Residues in contact with GLY 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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38A ASN* 4.5 2.2 + - - -
231A LEU* 3.6 12.1 - - - +
249A VAL* 3.3 36.1 - - - +
250A SER* 4.1 1.5 - - - +
251A ASN 4.5 6.7 - - - +
261A VAL 3.6 2.4 + - - -
262A PRO* 1.3 72.5 - - - +
264A ILE* 1.3 62.5 + - - +
266A MET 3.0 12.5 + - - -
267A LEU* 3.0 11.8 + - - +
282A VAL* 4.0 4.5 - - - -
283A ASP 4.9 4.1 + - - -
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Residues in contact with ILE 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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38A ASN* 4.7 2.9 - - - +
41A ALA* 3.3 37.0 - - + +
42A LEU* 4.0 31.2 - - + +
45A VAL* 4.9 4.9 - - + -
262A PRO* 4.1 5.8 - - + -
263A GLY* 1.3 75.8 - - - +
265A GLU* 1.3 63.8 + - + +
266A MET 3.6 0.2 + - - -
267A LEU* 3.7 27.1 + - + +
268A GLY 4.8 1.2 + - - -
282A VAL* 3.9 15.2 - - + +
283A ASP 5.0 2.0 + - - +
284A GLY 5.8 3.4 - - - +
286A ILE* 5.4 2.0 - - + -
295A ALA* 4.1 16.6 - - + -
298A LEU* 3.5 36.0 - - + +
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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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37A ALA* 5.1 1.0 - - - +
41A ALA* 3.6 30.6 - - + +
44A ARG* 3.8 24.0 + - - +
261A VAL* 3.8 14.9 - - + +
262A PRO* 3.0 27.7 + - + +
264A ILE* 1.3 77.1 - - - +
266A MET* 1.3 61.7 + - - +
268A GLY 5.1 1.5 + - - -
269A GLU* 3.4 14.6 - - - +
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Residues in contact with MET 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A LEU* 3.4 31.2 - - + +
232A ALA* 4.9 1.8 - - - -
233A VAL* 4.1 17.5 - - + +
249A VAL* 4.3 3.6 - - + -
261A VAL* 3.6 36.3 - - + -
262A PRO 3.6 3.6 + - - +
263A GLY 3.0 6.3 + - - +
265A GLU* 1.3 79.7 - - - +
267A LEU* 1.3 64.6 + - - +
268A GLY 3.4 2.0 - - - -
269A GLU* 3.3 33.5 + - - +
270A ILE* 3.0 30.6 + - + +
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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
----------------------------------------------------------
249A VAL* 4.4 9.0 - - + -
263A GLY 3.0 14.3 + - - +
264A ILE* 3.8 25.1 - - + +
265A GLU 3.5 1.6 - - - -
266A MET* 1.3 78.0 - - - +
268A GLY* 1.3 58.1 + - - +
270A ILE* 3.2 2.9 + - - +
271A VAL* 2.8 40.1 + - + +
280A VAL* 3.7 27.6 - - + -
282A VAL* 4.0 19.3 - - + -
295A ALA 3.6 24.5 - - - +
298A LEU* 3.7 20.0 - - + +
300A ALA* 4.0 14.8 - - + +
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Residues in contact with GLY 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 ILE 4.8 2.2 + - - -
265A GLU 5.1 1.2 + - - -
266A MET 3.4 0.6 - - - -
267A LEU* 1.3 78.5 - - - +
269A GLU* 1.3 62.4 + - - +
271A VAL* 3.4 2.7 + - - +
272A ALA* 3.1 23.9 + - - +
298A LEU* 3.7 24.1 + - - +
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Residues in contact with GLU 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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233A VAL* 4.0 18.6 - - + +
265A GLU 3.4 21.7 - - - +
266A MET* 3.3 29.2 + - - +
267A LEU 3.3 0.4 - - - -
268A GLY* 1.3 75.8 - - - +
270A ILE* 1.3 58.1 + - - +
272A ALA* 3.4 7.3 + - - +
273A ALA* 3.0 28.4 + - - +
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Residues in contact with ILE 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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230A ILE* 4.4 5.6 - - + +
231A LEU* 3.6 27.6 - - - +
232A ALA 4.5 4.0 - - - +
233A VAL* 4.2 22.0 - - + -
236A ALA* 3.6 19.3 - - + -
247A ILE* 3.7 16.4 - - + -
249A VAL* 3.8 33.2 - - + -
266A MET* 3.0 21.4 + - + +
267A LEU 3.7 3.6 - - - +
269A GLU* 1.3 75.6 - - - +
271A VAL* 1.3 65.8 + - - +
273A ALA* 3.1 5.8 + - - -
274A VAL* 3.0 26.3 + - + +
280A VAL* 4.1 6.5 - - + -
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Residues in contact with VAL 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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267A LEU* 2.8 33.3 + - + +
268A GLY* 3.8 4.5 - - - +
270A ILE* 1.3 76.0 - - - +
272A ALA* 1.3 65.3 + - - +
274A VAL* 3.5 10.6 + - + +
275A SER* 3.2 19.6 + - - -
276A GLY 4.6 1.0 + - - -
280A VAL* 3.9 14.4 - - + -
298A LEU 4.2 4.0 - - - +
299A GLY* 3.6 31.4 - - - +
348A ARG* 3.9 22.2 - - - +
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Residues in contact with ALA 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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268A GLY 3.1 14.4 + - - +
269A GLU* 3.6 8.7 - - - +
271A VAL* 1.3 78.9 - - - +
273A ALA* 1.3 61.5 + - - +
275A SER* 3.4 17.2 + - - +
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Residues in contact with ALA 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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233A VAL* 3.5 33.0 - - + +
236A ALA* 5.7 0.2 - - + -
237A ARG* 4.0 31.1 + - + +
269A GLU 3.0 12.9 + - - +
270A ILE* 3.1 5.1 + - - +
272A ALA* 1.3 77.8 - - - +
274A VAL* 1.3 62.9 + - + +
275A SER* 3.6 2.8 + - - -
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Residues in contact with VAL 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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236A ALA* 3.9 27.8 - - + +
237A ARG* 4.5 2.0 - - - +
240A VAL* 3.8 30.3 - - + +
247A ILE* 4.7 1.6 - - + -
270A ILE* 3.0 18.0 + - + +
271A VAL* 3.6 10.5 - - + +
273A ALA* 1.3 78.4 - - - +
275A SER* 1.3 73.7 + - - +
276A GLY 4.1 7.2 - - - +
277A GLY* 2.9 18.2 + - - +
278A CYS* 4.3 13.9 - - - +
280A VAL* 3.6 23.3 - - + -
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Residues in contact with SER 275 (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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271A VAL 3.2 11.5 + - - -
272A ALA* 3.7 14.1 - - - +
273A ALA 3.3 3.3 - - - -
274A VAL* 1.3 79.1 - - - +
276A GLY* 1.3 59.3 + - - +
277A GLY 3.4 0.5 + - - -
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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