Contacts of the helix formed by residues 259 - 276 (chain B) in PDB entry 2OCP
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 GLU 259 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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255B ASP* 3.2 24.6 + - - +
256B PHE* 3.8 2.3 + - - +
258B GLU* 1.3 85.3 - - - +
260B VAL* 1.3 54.9 + - - +
261B THR* 2.8 21.6 + - - +
262B LYS* 3.0 23.2 + - + +
263B GLN* 3.3 13.0 + - - +
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Residues in contact with VAL 260 (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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258B GLU 2.9 10.9 + - - +
259B GLU* 1.3 68.8 - - - +
261B THR* 1.3 60.4 + - - +
263B GLN* 3.9 21.1 - - - +
264B GLU* 3.2 42.4 + - + +
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Residues in contact with THR 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259B GLU* 2.8 8.8 + - - +
260B VAL* 1.3 81.5 - - - +
262B LYS* 1.3 62.8 + - - +
264B GLU* 3.5 8.7 + - - +
265B ASP* 3.1 23.1 + - + +
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Residues in contact with LYS 262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251B ASP* 3.1 28.6 + - - +
252B VAL* 4.4 3.4 - - - +
254B ASP* 3.7 40.3 + - + +
255B ASP 5.4 0.2 - - - +
256B PHE* 3.8 19.5 - - + -
259B GLU* 3.0 15.6 + - + +
261B THR* 1.3 77.8 - - - +
263B GLN* 1.3 59.9 + - - +
265B ASP* 3.1 12.4 + - + +
266B LEU* 2.8 45.4 + - + +
269B GLU* 5.7 0.2 + - - -
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Residues in contact with GLN 263 (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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53B THR* 6.0 1.4 - - - +
57B LEU* 3.9 33.8 - - + +
60B LYS* 5.8 2.1 + - - -
256B PHE* 3.1 30.4 + - + +
257B SER* 3.4 16.8 + - - +
258B GLU* 4.3 3.9 - - - +
259B GLU 3.3 8.9 + - - +
260B VAL* 3.9 27.2 - - - +
261B THR 3.3 0.4 - - - -
262B LYS* 1.3 77.2 - - - +
264B GLU* 1.3 63.5 + - + +
266B LEU* 3.1 7.2 + - - +
267B MET* 3.0 30.4 + - - +
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Residues in contact with GLU 264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260B VAL* 3.2 36.4 + - + +
261B THR* 3.8 7.4 - - - +
262B LYS 3.3 0.4 - - - -
263B GLN* 1.3 80.3 - - + +
265B ASP* 1.3 60.5 + - - +
267B MET* 3.9 6.8 + - - +
268B ARG* 3.3 34.4 + - - +
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Residues in contact with ASP 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261B THR* 3.1 17.2 + - + +
262B LYS* 3.2 20.7 + - + +
264B GLU* 1.3 78.3 - - - +
266B LEU* 1.3 63.6 + - + +
268B ARG* 3.0 31.8 + - - +
269B GLU* 3.4 30.2 + - - +
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Residues in contact with LEU 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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54B PHE* 4.6 15.5 - - + -
57B LEU* 4.9 2.5 - - + -
250B LEU* 4.2 26.6 - - + +
251B ASP 4.9 3.1 - - - +
252B VAL* 4.1 8.1 - - + -
256B PHE* 3.8 40.6 - - + -
262B LYS* 2.8 39.4 + - + +
263B GLN* 3.1 6.9 + - - +
265B ASP* 1.3 75.7 - - + +
267B MET* 1.3 66.4 + - - +
268B ARG 2.9 3.8 - - - -
269B GLU* 2.8 33.1 + - - +
270B VAL* 2.9 16.0 + - - +
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Residues in contact with MET 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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54B PHE* 4.8 9.6 - - - -
57B LEU* 3.2 46.2 - - + +
58B LEU* 3.3 34.3 - - + -
61B THR* 3.1 39.0 - - + +
62B TYR* 2.9 31.1 + - + +
263B GLN 3.0 11.3 + - - +
264B GLU* 4.3 6.3 - - - +
266B LEU* 1.3 76.2 - - - +
268B ARG* 1.3 57.4 + - - +
270B VAL* 3.6 5.1 - - - +
271B ASN 2.9 16.1 + - - -
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Residues in contact with ARG 268 (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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261B THR 5.8 0.2 + - - -
264B GLU* 3.3 30.1 + - - +
265B ASP* 3.0 41.0 + - - +
266B LEU 2.9 0.6 - - - -
267B MET* 1.3 77.5 - - - +
269B GLU* 1.3 66.4 + - + +
271B ASN* 3.2 6.9 + - + +
272B THR* 3.0 31.6 + - - +
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Residues in contact with GLU 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248B LEU* 4.0 11.9 - - + +
249B VAL 4.4 7.4 - - - +
250B LEU* 4.0 22.8 - - + +
251B ASP 5.8 0.5 + - - -
262B LYS* 5.7 0.2 + - - -
265B ASP* 3.4 24.5 - - - +
266B LEU* 2.8 22.8 + - - +
268B ARG* 1.3 75.8 - - + +
270B VAL* 1.3 62.3 + - - +
272B THR* 3.4 6.8 + - - -
273B PHE* 2.9 24.9 + - - +
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Residues in contact with VAL 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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54B PHE* 3.7 30.1 - - + -
58B LEU* 4.0 10.1 - - + -
62B TYR* 4.8 2.7 - - + -
65B TRP* 3.7 31.4 - - + -
190B ILE* 4.5 9.0 - - + -
248B LEU* 3.7 20.2 - - + -
250B LEU* 4.0 5.6 - - + -
266B LEU 2.9 15.3 + - - +
267B MET* 3.6 12.1 - - - +
269B GLU* 1.3 75.9 - - - +
271B ASN* 1.3 58.6 + - - +
273B PHE* 3.0 2.8 + - - +
274B VAL* 2.8 37.7 + - + +
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Residues in contact with ASN 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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62B TYR* 2.9 37.2 - - - +
65B TRP* 4.8 6.3 - - - -
267B MET 2.9 11.0 + - - +
268B ARG* 3.6 6.1 - - - +
270B VAL* 1.3 78.4 - - - +
272B THR* 1.3 63.8 + - - +
274B VAL* 4.0 3.4 - - - +
275B LYS* 3.1 59.2 + - - +
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Residues in contact with THR 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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268B ARG* 3.0 22.1 + - - +
269B GLU* 3.7 7.5 - - - -
271B ASN* 1.3 77.6 - - - +
273B PHE* 1.3 64.7 + - - +
275B LYS* 4.9 2.0 - - - -
276B ASN* 3.5 33.6 + - - +
128E GLU* 5.8 4.9 - - + -
132E GLN* 4.6 11.5 - - - +
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Residues in contact with PHE 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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41B LEU* 3.6 30.3 - - + -
188B GLY* 4.6 0.7 - - - -
189B PHE 4.0 5.8 - - - -
190B ILE* 4.7 2.7 - - + -
246B PRO* 3.5 38.1 - - + -
247B VAL 4.1 4.3 - - - -
248B LEU* 3.5 57.9 - - + -
269B GLU 2.9 17.5 + - - +
270B VAL 3.4 4.3 - - - +
272B THR* 1.3 75.3 - - - +
274B VAL* 1.3 67.9 + - + +
276B ASN* 3.3 14.5 + - - +
277B LEU* 3.4 20.6 - - + +
132E GLN* 4.9 16.4 - - - +
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Residues in contact with VAL 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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39B ARG* 4.6 6.9 - - + +
41B LEU* 4.2 21.1 - - + -
65B TRP* 3.3 30.3 - - + -
137B VAL* 3.6 32.1 - - + -
190B ILE* 5.3 2.0 - - + -
270B VAL* 2.8 28.7 + - + +
271B ASN* 4.0 4.0 - - - +
273B PHE* 1.3 76.7 - - + +
275B LYS* 1.3 65.0 + - + +
276B ASN 3.2 1.0 + - - -
277B LEU* 3.2 28.1 + - + +
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Residues in contact with LYS 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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135B LYS* 3.8 39.2 - - + +
271B ASN* 3.1 50.2 + - - +
272B THR* 4.1 2.5 - - - +
274B VAL* 1.3 79.1 - - + +
276B ASN* 1.3 70.8 + - - +
277B LEU 3.2 6.5 + - - +
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Residues in contact with ASN 276 (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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272B THR* 3.5 19.3 + - - +
273B PHE 3.3 8.9 + - - +
274B VAL 3.2 1.4 - - - -
275B LYS* 1.3 87.5 + - - +
277B LEU* 1.3 63.3 + - - +
128E GLU* 3.3 26.1 + - - +
129E LYS* 4.1 32.0 - - - +
132E GLN* 2.7 38.2 - - + +
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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