Contacts of the helix formed by residues 263 - 275 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260B ASP* 3.5 28.4 + - + +
262B HIS* 1.3 76.0 - - - +
264B VAL* 1.3 62.6 - - - +
265B GLN* 3.2 14.8 - - - +
266B GLU* 3.0 37.2 + - + +
267B LEU* 2.9 25.2 + - - +
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Residues in contact with VAL 264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B LEU* 3.7 30.7 - - + -
31B PRO* 3.8 25.8 - - + -
34B THR* 4.4 6.3 - - + +
60B ASP* 3.3 31.6 - - + +
63B THR* 3.8 22.7 - - + -
64B ALA* 3.8 8.5 - - + +
262B HIS 3.3 6.4 + - - +
263B ASN* 1.3 73.0 - - - +
265B GLN* 1.3 59.0 + - - +
267B LEU* 3.1 10.4 + - - +
268B VAL* 3.0 29.0 + - - +
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Residues in contact with GLN 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B ARG* 3.6 34.0 - - + +
28B GLU* 3.3 33.5 + - - +
30B LEU* 5.3 0.4 - - + -
31B PRO* 3.6 25.6 - - + +
263B ASN* 3.2 10.1 - - - +
264B VAL* 1.3 77.7 - - + +
266B GLU* 1.3 67.9 + - - +
268B VAL* 3.2 9.5 + - - +
269B TRP* 3.2 21.8 + - - +
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Residues in contact with GLU 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259B VAL* 4.0 11.7 - - - +
260B ASP* 3.6 33.3 + - - +
263B ASN* 3.0 28.9 - - - +
265B GLN* 1.3 78.8 - - - +
267B LEU* 1.3 57.4 + - - +
269B TRP* 3.6 10.8 - - + +
270B LEU* 3.1 47.9 + - + +
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Residues in contact with LEU 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B ASP* 4.0 6.5 - - + +
61B ILE* 3.9 32.8 - - + +
64B ALA* 3.6 12.1 - - + -
259B VAL* 4.5 8.3 - - + -
260B ASP 4.1 11.9 - - - +
261B GLY* 3.6 26.7 - - - +
263B ASN 2.9 22.0 + - - +
264B VAL* 3.4 8.3 - - - +
265B GLN 3.1 0.2 - - - -
266B GLU* 1.3 77.1 - - - +
268B VAL* 1.3 64.6 + - - +
270B LEU* 3.9 5.0 - - + +
271B LEU* 3.1 30.1 + - - +
283B LEU* 4.7 6.5 - - + +
285B ILE* 3.8 28.3 - - + -
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Residues in contact with VAL 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B ARG* 3.7 22.2 - - + +
30B LEU* 4.0 24.9 - - + -
64B ALA* 4.0 18.2 - - - -
67B TYR* 4.1 15.0 - - + -
68B VAL* 3.9 14.4 - - + -
264B VAL 3.0 17.8 + - - +
265B GLN* 3.2 8.3 + - - +
267B LEU* 1.3 71.0 - - - +
269B TRP* 1.3 69.4 + - - +
271B LEU* 3.0 3.8 + - - +
272B GLU* 2.9 50.4 + - - +
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Residues in contact with TRP 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B ARG* 5.3 4.0 - - - +
265B GLN 3.2 9.2 + - - +
266B GLU* 3.6 15.3 - - + +
268B VAL* 1.3 80.7 - - - +
270B LEU* 1.3 90.2 + - + +
272B GLU* 4.6 2.0 - - - -
273B ARG* 2.9 75.1 + - + +
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Residues in contact with LEU 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256B VAL* 4.6 19.1 - - + -
259B VAL* 3.8 35.9 - - + -
266B GLU* 3.1 35.7 + - + +
267B LEU* 3.9 6.5 - - + +
269B TRP* 1.3 102.8 - - + +
271B LEU* 1.3 58.0 + - - +
273B ARG* 3.0 6.1 + - + +
274B LEU* 2.8 45.6 + - + +
283B LEU* 4.5 9.4 - - + -
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Residues in contact with LEU 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B ILE* 5.0 4.7 - - + -
64B ALA* 3.6 36.8 - - + +
65B LEU* 3.6 24.9 - - + +
68B VAL* 3.9 14.6 - - + -
69B LEU* 5.7 0.9 - - + -
177B LEU* 3.5 31.2 - - + -
179B VAL* 4.9 2.9 - - + -
267B LEU 3.1 22.3 + - - +
268B VAL 3.0 5.3 + - - +
270B LEU* 1.3 74.8 - - - +
272B GLU* 1.3 63.9 + - - +
274B LEU* 4.4 3.8 - - + +
275B VAL* 2.9 33.6 + - + +
283B LEU* 4.0 20.6 - - + -
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Residues in contact with GLU 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B ARG* 2.6 44.9 + - - -
67B TYR* 5.2 1.2 - - - -
68B VAL* 4.0 22.1 - - + +
268B VAL* 2.9 24.0 + - - +
269B TRP* 3.6 1.1 - - - +
271B LEU* 1.3 76.8 - - - +
273B ARG* 1.3 88.3 + - - +
275B VAL* 4.0 6.4 + - - +
276B ASP* 4.2 16.8 - - - +
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Residues in contact with ARG 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B ARG* 6.0 0.2 - - - +
269B TRP* 2.9 80.5 + - + +
270B LEU* 3.0 8.9 + - + +
272B GLU* 1.3 109.9 + - - +
274B LEU* 1.3 66.1 + - + +
275B VAL 3.3 1.4 + - - -
276B ASP* 4.3 5.2 + - - +
277B LEU* 3.6 18.2 - - - +
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Residues in contact with LEU 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177B LEU* 4.0 22.9 - - + +
256B VAL* 3.7 31.0 - - + -
270B LEU* 2.8 29.9 + - + +
271B LEU* 3.3 4.9 + - - +
273B ARG* 1.3 79.7 - - + +
275B VAL* 1.3 62.9 + - - +
277B LEU* 3.2 37.2 + - + +
281B THR* 4.7 8.5 + - + -
283B LEU* 3.9 44.6 - - + -
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Residues in contact with VAL 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B VAL* 5.0 6.5 - - + -
69B LEU* 3.6 25.6 - - + -
147B HIS* 3.1 51.2 - - + +
175B LYS* 5.1 5.4 - - - +
177B LEU* 4.2 28.5 - - + -
271B LEU* 2.9 21.2 + - + +
272B GLU* 4.0 3.8 + - - +
273B ARG 3.3 1.6 - - - -
274B LEU* 1.3 78.3 - - - +
276B ASP* 1.3 68.1 + - - +
277B LEU 3.3 4.7 + - - +
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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