Contacts of the helix formed by residues 264 - 278 (chain B) in PDB entry 1OJ7
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 TRP 264 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198B HIS* 3.8 17.5 - + - -
201B GLU* 2.7 39.1 + - + -
202B GLN* 4.0 14.4 - - + -
252B LEU* 3.7 35.9 - - + -
262B GLN* 2.9 37.8 + - + +
263B ASP* 1.3 75.6 - - - +
265B ALA* 1.3 57.1 + - - +
266B THR 3.3 2.0 - - - -
267B HIS* 3.1 46.5 + + + +
268B MET* 2.9 40.2 + - + +
368B LEU* 6.0 0.2 - - - -
1388B NZQ 5.1 1.3 - - + -
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Residues in contact with ALA 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263B ASP* 3.1 19.6 + - - +
264B TRP* 1.3 74.3 - - - +
266B THR* 1.3 67.1 + - - +
268B MET* 3.8 4.4 - - - +
269B LEU* 3.0 30.0 + - + +
292B LEU* 3.7 9.4 - - + -
368B LEU* 3.9 23.6 - - + -
369B GLY 3.9 1.3 - - - +
374B ILE* 3.5 28.5 - - + -
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Residues in contact with THR 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B VAL* 4.3 3.6 - - + -
201B GLU* 3.3 16.4 + - - +
263B ASP* 4.6 0.5 + - - -
264B TRP 3.3 0.2 - - - -
265B ALA* 1.3 77.8 - - - +
267B HIS* 1.3 58.2 + - - +
269B LEU* 3.9 1.4 - - - +
270B GLY* 2.9 26.9 + - - -
285B LEU* 4.0 24.7 - - + +
288B VAL* 3.9 14.5 - - + +
289B LEU* 3.5 50.0 - - + +
292B LEU* 3.6 17.8 - - - +
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Residues in contact with HIS 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B VAL* 3.6 22.2 - - + -
198B HIS* 3.3 17.0 - + - -
201B GLU* 2.8 27.0 + - + +
264B TRP* 3.1 28.0 + + + +
266B THR* 1.3 76.2 - - - +
268B MET* 1.3 69.1 + - + +
270B GLY* 3.2 0.7 + - - -
271B HIS* 2.8 41.8 + + - +
281B HIS* 3.2 14.8 + + - -
285B LEU* 3.6 14.3 - - + +
1388B NZQ 2.8 10.4 + - + -
1389B ZN 2.1 37.1 - - - -
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Residues in contact with MET 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B ALA* 5.2 10.3 - - + +
264B TRP* 2.9 28.6 + - + +
265B ALA 3.2 3.8 + - - +
267B HIS* 1.3 85.0 - - + +
269B LEU* 1.3 62.6 + - - +
271B HIS* 3.5 38.7 + - + +
272B GLU* 3.6 18.9 + - - +
360B LEU* 4.1 2.7 - - - +
365B MET* 3.6 32.5 - - + +
368B LEU* 3.9 34.3 - - + -
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Residues in contact with LEU 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265B ALA* 3.0 19.5 + - + +
266B THR 4.0 2.7 - - - +
268B MET* 1.3 75.3 - - - +
270B GLY* 1.3 61.7 + - - +
272B GLU 3.5 6.6 + - - -
273B LEU* 3.5 6.4 + - - +
288B VAL* 4.0 14.4 - - + -
292B LEU* 4.6 3.4 - - + -
360B LEU* 3.6 22.7 - - + -
368B LEU* 3.8 13.9 - - + -
374B ILE* 5.3 1.3 - - + -
379B SER* 3.5 27.1 - - - +
382B ILE* 3.8 42.6 - - + -
383B TYR* 2.6 39.5 + - + +
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Residues in contact with GLY 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266B THR 2.9 18.7 + - - -
267B HIS* 3.6 1.8 - - - -
269B LEU* 1.3 77.5 - - - +
271B HIS* 1.3 64.7 - - - +
273B LEU* 3.0 11.7 + - - -
274B THR* 3.1 10.0 + - - -
284B THR* 3.2 41.4 + - - +
285B LEU* 5.1 0.4 - - - -
288B VAL* 4.5 2.9 - - - -
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Residues in contact with HIS 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B VAL* 4.0 24.0 - - + +
160B LYS* 3.9 44.6 + - + +
161B GLN* 5.1 1.8 - - - -
162B ALA* 4.8 5.6 - - + -
267B HIS* 2.8 28.0 + + + +
268B MET* 3.6 36.8 - - + +
269B LEU 3.4 0.2 - - - -
270B GLY* 1.3 75.8 - - - +
272B GLU* 1.3 59.8 + - + +
274B THR* 3.2 5.6 + - - -
275B ALA* 2.9 28.9 + - - +
281B HIS* 3.6 23.4 - + - -
1388B NZQ 3.5 18.2 + - - -
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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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158B GLY 4.7 0.2 - - - +
160B LYS 4.8 8.2 + - - +
268B MET 3.6 7.5 - - - +
269B LEU 3.5 6.9 + - - +
270B GLY 3.2 0.6 - - - -
271B HIS* 1.3 80.0 - - - +
273B LEU* 1.3 58.2 + - - +
275B ALA* 3.4 9.9 + - - +
276B MET* 3.0 32.9 + - - +
356B LEU* 3.6 16.9 - - + +
359B LYS* 3.4 32.4 - - + +
360B LEU* 3.5 34.7 - - + +
363B HIS* 3.2 25.0 + - - +
365B MET* 5.0 4.5 - - - +
383B TYR* 3.8 7.2 - - - +
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Residues in contact with LEU 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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269B LEU 3.5 10.2 + - - +
270B GLY 3.0 7.4 + - - +
272B GLU* 1.3 78.4 - - - +
274B THR* 1.3 56.8 + - - +
277B HIS* 2.9 43.6 + - + +
278B GLY 3.6 0.7 + - - -
279B LEU* 4.1 7.5 + - + +
284B THR* 3.7 24.2 - - + +
287B ILE* 4.6 6.3 - - + -
288B VAL* 4.0 28.0 - - + -
343B LEU* 4.0 31.0 - - + -
348B LEU* 5.4 0.7 - - + -
356B LEU* 3.6 31.9 - - + -
383B TYR* 4.0 9.2 - - + -
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Residues in contact with THR 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B ASN* 3.5 35.0 - - + +
153B SER* 5.7 0.2 - - - +
160B LYS* 3.7 19.4 - - + -
270B GLY 3.1 7.6 + - - -
271B HIS* 3.2 7.6 + - - -
273B LEU* 1.3 77.3 - - - +
275B ALA* 1.3 59.6 + - - +
278B GLY* 2.8 25.6 + - - -
279B LEU 2.8 29.0 + - - +
281B HIS* 3.9 10.3 + - - +
284B THR* 3.2 14.6 + - - +
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Residues in contact with ALA 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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153B SER* 6.2 0.2 - - - -
158B GLY* 3.4 36.8 - - - +
159B ASP 4.3 0.9 - - - +
160B LYS* 4.1 18.6 - - + +
271B HIS 2.9 15.7 + - - +
272B GLU* 3.4 11.0 + - - +
274B THR* 1.3 78.6 - - - +
276B MET* 1.3 62.5 + - - +
278B GLY 4.8 0.3 + - - -
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Residues in contact with MET 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 GLU 3.0 16.7 + - - +
275B ALA* 1.3 79.4 - - - +
277B HIS* 1.3 73.9 + - + +
278B GLY 3.8 0.2 - - - -
352B SER* 4.0 13.5 - - - -
355B ALA* 3.7 43.3 - - + +
356B LEU* 3.6 28.3 - - + +
359B LYS* 4.3 16.8 - - + -
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Residues in contact with HIS 277 (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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273B LEU* 2.9 31.4 + - + +
276B MET* 1.3 98.4 + - + +
278B GLY* 1.3 63.0 + - - +
279B LEU* 3.3 12.3 + - + +
348B LEU* 3.6 49.1 - - + +
352B SER* 2.7 39.7 + - - -
356B LEU* 4.7 0.8 - - + +
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Residues in contact with GLY 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B ASN* 5.1 5.3 + - - -
274B THR* 2.8 19.4 + - - -
275B ALA 4.8 0.2 + - - -
276B MET 3.8 0.6 - - - -
277B HIS* 1.3 77.4 - - - +
279B LEU* 1.3 66.4 + - - +
280B ASP* 3.6 4.2 + - - +
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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
------------------------------------------------------------
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