Contacts of the helix formed by residues 264 - 278 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198A HIS* 3.7 30.1 - + - -
201A GLU* 2.8 37.5 + - + +
202A GLN* 4.0 15.0 - - + -
252A LEU* 3.8 35.4 - - + -
262A GLN* 2.9 35.9 + - + +
263A ASP* 1.3 76.0 - - - +
265A ALA* 1.3 62.4 + - - +
266A THR 3.2 2.0 - - - -
267A HIS* 3.1 36.0 + + + +
268A MET* 2.9 38.0 + - + +
368A LEU* 5.9 0.2 - - - -
1388A NZQ 5.1 0.9 - - + -
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Residues in contact with ALA 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A ASP* 3.0 20.3 + - - +
264A TRP* 1.3 77.3 - - - +
266A THR* 1.3 62.8 + - - +
268A MET* 3.2 4.6 + - - +
269A LEU* 2.9 30.3 + - + +
292A LEU* 3.7 9.0 - - + -
368A LEU* 3.9 23.8 - - + -
369A GLY 3.9 1.6 - - - +
374A ILE* 3.7 27.6 - - + -
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Residues in contact with THR 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A VAL* 4.3 3.4 - - + -
201A GLU* 3.4 16.4 + - - +
263A ASP* 4.7 0.7 + - - -
264A TRP 3.2 0.4 - - - -
265A ALA* 1.3 78.9 - - - +
267A HIS* 1.3 59.7 + - - +
269A LEU* 3.5 1.9 + - - +
270A GLY* 2.9 25.8 + - - -
285A LEU* 4.0 21.7 - - + +
288A VAL* 3.9 15.4 - - + +
289A LEU* 3.5 52.4 - - + +
292A LEU* 3.6 18.5 - - - +
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Residues in contact with HIS 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A ASP* 3.5 0.4 + - - -
197A VAL* 3.6 17.0 - - + +
198A HIS* 3.3 22.4 - + - -
201A GLU* 2.7 23.7 + - + +
264A TRP* 3.1 29.5 + + + +
266A THR* 1.3 78.6 - - - +
268A MET* 1.3 69.6 + - + +
270A GLY* 3.3 0.9 + - - -
271A HIS* 2.9 39.0 + + - +
281A HIS* 3.3 22.2 + + - -
285A LEU* 3.6 22.6 - - + +
1388A NZQ 2.9 31.5 + - + -
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Residues in contact with MET 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A ALA* 5.5 7.0 - - + -
264A TRP* 2.9 32.8 + - + +
265A ALA 3.2 5.4 + - - +
267A HIS* 1.3 83.3 - - + +
269A LEU* 1.3 63.6 + - - +
271A HIS* 3.4 39.3 + - + +
272A GLU* 3.7 13.9 + - - +
360A LEU* 4.0 3.8 - - - +
365A MET* 3.5 34.4 - - + +
368A LEU* 3.8 34.3 - - + -
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Residues in contact with LEU 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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265A ALA* 2.9 22.2 + - + +
266A THR 4.0 2.7 - - - +
268A MET* 1.3 75.9 - - - +
270A GLY* 1.3 61.0 + - - +
272A GLU 3.4 7.6 + - - -
273A LEU* 3.6 5.5 + - - +
288A VAL* 3.8 24.7 - - + -
292A LEU* 4.0 14.8 - - + -
360A LEU* 3.5 23.1 - - + -
368A LEU* 4.0 9.4 - - + -
374A ILE* 5.1 1.1 - - + -
379A SER* 3.4 28.0 - - - +
382A ILE* 4.1 23.6 - - + -
383A TYR* 2.6 39.6 + - + +
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Residues in contact with GLY 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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266A THR 2.9 19.2 + - - -
267A HIS* 3.7 2.0 - - - -
269A LEU* 1.3 75.5 - - - +
271A HIS* 1.3 65.7 + - - +
273A LEU* 3.1 15.2 + - - -
274A THR* 3.1 10.8 + - - -
281A HIS* 5.6 0.4 - - - -
284A THR* 3.2 38.5 + - - +
285A LEU* 5.1 0.7 - - - -
288A VAL* 4.4 0.8 - - - +
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Residues in contact with HIS 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A VAL* 3.8 24.5 - - + +
160A LYS* 3.6 48.3 + - + +
161A GLN* 5.1 2.0 - - - -
162A ALA* 4.8 7.2 + - + -
267A HIS* 2.9 25.1 + + + +
268A MET* 3.7 35.9 - - + +
269A LEU 3.3 0.4 - - - -
270A GLY* 1.3 74.7 - - - +
272A GLU* 1.3 61.3 + - + +
274A THR* 3.2 5.6 + - - -
275A ALA* 3.0 29.0 + - - +
281A HIS* 4.0 16.1 - + - -
1388A NZQ 3.6 18.8 + - - -
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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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160A LYS 4.9 4.2 + - - +
268A MET 3.8 6.6 - - - +
269A LEU 3.4 0.4 + - - -
270A GLY 3.2 0.8 - - - -
271A HIS* 1.3 79.2 - - - +
273A LEU* 1.3 57.3 + - - +
275A ALA* 3.8 9.0 - - - +
276A MET* 3.0 25.1 + - - +
356A LEU* 3.4 26.4 - - + +
359A LYS* 3.4 28.0 - - + +
360A LEU* 3.5 32.8 - - + +
363A HIS* 2.7 38.2 + - - +
365A MET* 4.8 2.8 - - - +
383A TYR* 3.7 13.2 - - - +
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Residues in contact with LEU 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 LEU 3.6 7.8 + - - +
270A GLY 3.1 7.9 + - - +
272A GLU* 1.3 75.9 - - - +
274A THR* 1.3 58.7 + - - +
277A HIS* 2.9 46.6 + - + +
278A GLY 3.6 0.5 + - - -
279A LEU* 4.1 7.4 + - + +
284A THR* 3.7 24.0 - - + +
287A ILE* 4.7 6.1 - - + -
288A VAL* 3.9 28.0 - - + -
343A LEU* 3.8 31.4 - - + -
348A LEU* 5.1 1.8 - - + -
352A SER* 5.5 0.4 - - - +
356A LEU* 3.7 27.6 - - + -
383A TYR* 4.0 12.3 - - + -
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Residues in contact with THR 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A ASN* 3.5 36.6 - - + +
160A LYS* 3.7 17.1 - - + -
270A GLY 3.1 7.5 + - - -
271A HIS 3.2 7.4 + - - -
273A LEU* 1.3 76.5 - - - +
275A ALA* 1.3 62.1 + - - +
278A GLY* 2.8 27.8 + - - -
279A LEU 2.8 30.1 + - - +
281A HIS* 3.8 10.6 + - - +
284A THR* 3.3 15.0 + - - +
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Residues in contact with ALA 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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153A SER* 6.6 0.2 - - - -
158A GLY* 3.5 38.2 - - - +
159A ASP 4.4 0.7 - - - -
160A LYS* 3.9 20.8 - - + +
271A HIS 3.0 16.4 + - - +
272A GLU* 3.8 11.0 - - - +
273A LEU 3.3 0.2 - - - -
274A THR* 1.3 80.8 - - - +
276A MET* 1.3 59.5 + - + +
278A GLY 4.9 0.2 + - - -
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Residues in contact with MET 276 (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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272A GLU 3.0 16.6 + - - +
275A ALA* 1.3 78.8 - - - +
277A HIS* 1.3 79.0 + - + +
278A GLY 3.8 0.4 - - - -
352A SER* 4.2 5.8 - - - -
355A ALA* 3.7 38.8 - - - +
356A LEU* 3.8 22.9 - - + +
359A LYS* 4.0 15.9 - - + -
367B GLN* 3.7 38.6 - - - +
372B HIS* 4.3 9.4 + - + -
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Residues in contact with HIS 277 (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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273A LEU* 2.9 29.4 + - + +
276A MET* 1.3 92.9 + - + +
278A GLY* 1.3 64.4 + - - +
279A LEU* 3.3 10.7 + - + +
348A LEU* 3.3 48.5 - - + +
352A SER* 2.7 40.4 + - - -
356A LEU* 4.6 2.0 - - + +
372B HIS* 3.8 22.7 + + - -
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Residues in contact with GLY 278 (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 ASN* 5.3 3.8 + - - -
186A ARG* 5.7 1.0 + - - -
273A LEU 3.6 0.2 + - - -
274A THR* 2.8 19.4 + - - -
275A ALA 4.9 0.4 + - - -
276A MET 3.8 0.4 - - - -
277A HIS* 1.3 78.0 - - - +
279A LEU* 1.3 66.7 + - - +
280A ASP* 3.6 4.5 + - - +
125B LYS* 6.1 1.0 - - - -
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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