Contacts of the helix formed by residues 263 - 275 (chain A) in PDB entry 2O1X
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 ASN 263 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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260A ASP* 3.4 30.2 + - + +
261A GLY 3.7 0.8 - - - -
262A HIS* 1.3 75.2 - - - +
264A VAL* 1.3 55.8 + - - +
265A GLN* 3.3 17.2 - - - +
266A GLU* 3.1 40.2 + - + +
267A LEU* 2.9 32.9 + - - +
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Residues in contact with VAL 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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30A LEU* 3.6 22.7 - - + -
31A PRO* 3.6 37.0 - - + -
34A THR* 3.8 15.7 - - + +
60A ASP* 3.7 23.1 - - + +
63A THR* 4.0 13.2 - - + -
64A ALA* 4.0 13.5 - - + +
262A HIS 3.2 7.6 + - - +
263A ASN* 1.3 72.0 - - - +
265A GLN* 1.3 66.0 + - - +
267A LEU* 3.2 8.7 + - - +
268A VAL* 3.1 25.3 + - - +
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Residues in contact with GLN 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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27A ARG* 3.4 37.1 - - - +
28A GLU* 3.7 28.7 + - - +
30A LEU* 5.3 1.3 - - - -
31A PRO* 4.0 21.2 - - + +
263A ASN* 3.2 12.1 - - - +
264A VAL* 1.3 82.7 - - - +
266A GLU* 1.3 60.9 + - + +
268A VAL* 3.7 6.4 + - - +
269A TRP* 3.4 18.9 + - - +
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Residues in contact with GLU 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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259A VAL* 3.8 24.6 - - - +
260A ASP* 4.7 5.8 + - - +
263A ASN* 3.1 30.9 + - - +
265A GLN* 1.3 77.2 - - + +
267A LEU* 1.3 60.8 + - - +
268A VAL 3.5 0.2 - - - -
269A TRP* 3.8 16.7 - - + +
270A LEU* 3.4 26.8 + - - +
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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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60A ASP* 4.3 4.0 - - + -
61A ILE* 4.1 28.0 - - + +
64A ALA* 3.7 16.2 - - + -
259A VAL* 4.3 10.8 - - + -
260A ASP 4.1 14.8 - - - +
261A GLY* 3.5 31.4 - - - +
263A ASN 2.9 22.3 + - - +
264A VAL 3.2 2.2 + - - +
266A GLU* 1.3 77.7 - - - +
268A VAL* 1.3 60.6 + - - +
270A LEU* 3.5 4.1 + - + +
271A LEU* 3.0 35.4 + - + +
283A LEU* 4.6 12.3 - - + -
285A ILE* 4.1 22.0 - - + -
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Residues in contact with VAL 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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27A ARG* 3.6 13.5 - - + +
30A LEU* 3.6 24.9 - - + -
64A ALA* 3.8 21.3 - - + +
67A TYR* 3.9 18.6 - - + -
68A VAL* 3.7 14.1 - - + -
264A VAL 3.1 17.2 + - - +
265A GLN* 3.8 5.8 - - - +
267A LEU* 1.3 73.8 - - - +
269A TRP* 1.3 67.9 - - - +
271A LEU* 3.1 1.7 + - - +
272A GLU* 2.9 48.2 + - - +
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Residues in contact with TRP 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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27A ARG* 5.1 6.3 - - - +
265A GLN 3.4 12.1 + - - +
266A GLU* 3.8 20.9 - - + +
267A LEU 3.3 0.2 - - - -
268A VAL* 1.3 82.0 - - - +
270A LEU* 1.3 89.3 + - + +
272A GLU* 3.4 18.3 + - - +
273A ARG* 3.5 52.7 + - + +
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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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256A VAL* 4.1 23.6 - - + -
259A VAL* 3.6 39.7 - - + -
266A GLU* 3.4 23.0 + - - +
267A LEU* 3.8 11.0 - - + +
268A VAL 3.2 0.8 - - - -
269A TRP* 1.3 100.8 - - + +
271A LEU* 1.3 64.1 + - - +
273A ARG* 2.9 15.5 + - - +
274A LEU* 3.0 34.2 + - + +
283A LEU* 4.5 12.3 - - + -
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Residues in contact with LEU 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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61A ILE* 5.0 4.5 - - + +
64A ALA* 3.4 39.9 - - + +
65A LEU* 3.8 22.4 - - + +
68A VAL* 3.8 17.3 - - + -
69A LEU* 6.2 0.9 - - + -
177A LEU* 3.5 31.0 - - + -
179A VAL* 4.8 2.2 - - + -
267A LEU* 3.0 26.6 + - + +
268A VAL 3.8 2.5 - - - +
270A LEU* 1.3 75.7 - - - +
272A GLU* 1.3 63.1 + - - +
273A ARG 3.1 1.0 + - - -
274A LEU* 4.4 5.2 - - + +
275A VAL* 3.1 31.3 + - + +
283A LEU* 4.3 20.9 - - + -
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Residues in contact with GLU 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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27A ARG* 2.3 42.2 + - - -
67A TYR* 4.6 1.9 - - - -
68A VAL* 4.1 19.3 - - + +
268A VAL* 2.9 28.2 + - - +
269A TRP* 3.5 9.2 - - - +
270A LEU 3.2 0.2 - - - -
271A LEU* 1.3 78.2 - - - +
273A ARG* 1.3 61.5 + - + +
275A VAL* 4.5 5.2 - - - +
276A ASP* 4.3 13.7 - - - +
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Residues in contact with ARG 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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269A TRP* 3.6 54.7 - - + +
270A LEU* 2.9 10.5 + - + +
272A GLU* 1.3 79.7 - - + +
274A LEU* 1.3 70.1 + - + +
275A VAL 3.4 0.6 + - - -
276A ASP* 4.5 4.9 + - - +
277A LEU* 3.8 17.3 - - - +
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Residues in contact with LEU 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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177A LEU* 4.5 13.4 - - + +
256A VAL* 4.2 21.8 - - + -
270A LEU* 3.0 35.5 + - + +
271A LEU* 3.2 5.8 + - + +
273A ARG* 1.3 83.4 - - + +
275A VAL* 1.3 65.5 + - + +
276A ASP 3.2 3.9 + - - -
277A LEU* 3.3 32.4 + - + +
281A THR* 4.3 21.8 + - + -
283A LEU* 4.1 39.5 - - + -
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Residues in contact with VAL 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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68A VAL* 4.5 8.7 - - + -
69A LEU* 3.5 30.7 - - + -
147A HIS* 3.2 47.6 - - + +
149A ALA* 5.9 0.7 - - + -
175A LYS* 5.2 6.4 - - - +
177A LEU* 4.4 28.0 - - + -
271A LEU* 3.1 19.3 + - + +
272A GLU 4.5 4.7 - - - +
273A ARG 3.4 0.6 - - - -
274A LEU* 1.3 80.3 - - - +
276A ASP* 1.3 67.8 + - - +
277A LEU 3.5 2.9 + - - +
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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