Contacts of the helix formed by residues 260 - 274 (chain B) in PDB entry 3OX4
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 GLY 260 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201B GLU* 3.0 18.1 + - - -
259B LEU* 1.3 82.9 - - - +
261B TYR* 1.3 61.0 + - - -
262B VAL 3.4 0.3 + - - -
263B HIS 3.5 1.6 + - - -
264B ALA* 3.0 24.6 + - - +
362B CYS* 3.3 18.0 + - - +
366B ASN* 3.7 14.1 - - - -
367B PRO* 5.7 0.4 - - - -
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Residues in contact with TYR 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B GLU* 3.1 0.4 + - - -
260B GLY* 1.3 69.1 - - - -
262B VAL* 1.3 65.6 + - - +
263B HIS 3.3 0.2 - - - -
264B ALA* 3.7 5.8 - - + -
265B MET* 2.9 36.5 + - + +
288B VAL* 3.9 14.1 - - + -
291B TYR* 3.9 27.8 - + - -
358B LEU* 3.8 13.1 - - + +
363B ALA* 3.6 31.2 - - + -
366B ASN* 2.8 48.1 + - + +
368B ARG 3.7 7.6 - - - -
369B GLN* 3.7 10.1 + - - -
370B GLY 2.9 31.5 + - - -
375B VAL* 3.9 19.7 - - + -
378B LEU* 4.4 9.9 - - + -
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Residues in contact with VAL 262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B THR* 3.5 12.6 - - + -
201B GLU* 2.8 34.4 + - + +
261B TYR* 1.3 72.0 - - - +
263B HIS* 1.3 56.6 + - - +
265B MET* 3.9 0.6 - - - -
266B ALA* 2.9 30.3 + - - +
281B ASN* 3.2 36.6 - - - +
284B LEU* 3.9 7.0 - - + +
285B LEU* 3.9 25.4 - - + +
288B VAL* 3.4 33.2 - - + -
289B LEU* 5.2 2.5 - - + +
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Residues in contact with HIS 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194B ASP* 3.3 2.1 + - - -
197B THR* 3.4 16.8 - - + +
198B HIS* 3.1 20.9 + + - -
201B GLU* 2.8 28.2 + - - +
259B LEU* 3.4 26.4 - - + +
260B GLY 3.5 1.3 + - - +
261B TYR 3.3 0.2 - - - -
262B VAL* 1.3 73.8 - - - +
264B ALA* 1.3 67.8 + - - +
265B MET 3.1 0.4 - - - -
266B ALA* 4.2 1.1 - - - -
267B HIS* 2.8 37.8 + - - +
277B HIS* 3.5 19.2 + + - -
281B ASN* 3.0 24.7 + - - +
362B CYS* 4.0 11.7 - - - -
501B FE2 2.1 31.9 - - - -
1385B NAD 5.1 1.3 - + - -
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Residues in contact with ALA 264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260B GLY 3.0 17.8 + - - +
261B TYR* 3.6 13.9 - - + +
263B HIS* 1.3 78.7 - - - +
265B MET* 1.3 57.4 + - + +
268B GLN* 2.9 31.7 + - - +
357B ALA* 3.6 26.5 - - + +
360B ASP* 3.8 13.7 - - + -
362B CYS* 4.0 0.6 - - - +
363B ALA* 4.0 19.1 - - + +
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Residues in contact with MET 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261B TYR* 2.9 27.5 + - + +
264B ALA* 1.3 76.1 - - + +
266B ALA* 1.3 64.7 + - - +
267B HIS 3.2 0.4 - - - -
268B GLN* 3.1 19.1 + - - +
269B LEU* 3.4 5.9 + - - +
284B LEU* 3.7 17.3 - - + -
288B VAL* 4.1 10.5 - - - -
357B ALA* 4.1 10.5 - - + -
375B VAL* 4.0 7.9 - - + +
378B LEU* 3.5 36.3 - - + -
379B PHE* 3.5 74.0 - - + +
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Residues in contact with ALA 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262B VAL 2.9 23.5 + - - +
263B HIS 3.4 1.3 + - - +
265B MET* 1.3 68.3 - - - +
267B HIS* 1.3 62.7 + - + +
268B GLN 3.0 6.6 + - - -
269B LEU* 3.2 5.2 + - - +
270B GLY* 3.2 19.2 + - - -
277B HIS* 5.7 3.3 + - - +
280B CYS* 3.8 14.8 - - + +
281B ASN* 3.4 43.3 - - - +
284B LEU* 3.6 7.8 - - + +
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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
----------------------------------------------------------
151B ILE* 5.1 18.4 - - + +
160B LYS* 3.4 32.9 - - + +
259B LEU* 5.4 0.9 - - + -
263B HIS* 2.8 29.0 + + + +
265B MET 3.2 0.2 - - - -
266B ALA* 1.3 76.8 - - - +
268B GLN* 1.3 63.4 + - - +
270B GLY* 5.5 0.2 - - - -
271B GLY* 3.1 19.6 + - - -
277B HIS* 3.5 37.0 - + - -
360B ASP* 3.2 28.2 + - - +
362B CYS* 3.8 23.6 - - - -
1385B NAD 5.0 6.9 + - - -
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Residues in contact with GLN 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B LYS* 5.7 2.0 - - - +
264B ALA 2.9 27.3 + - - +
265B MET* 3.3 7.9 - - - +
266B ALA 3.0 0.6 - - - -
267B HIS* 1.3 81.8 + - - +
269B LEU* 1.3 65.3 + - - +
270B GLY 3.1 1.8 - - - -
271B GLY* 3.5 2.5 - - - +
272B TYR* 3.1 29.3 + - - +
353B LEU* 3.6 41.5 - - + +
356B HIS* 3.1 30.5 + - + +
357B ALA* 3.8 9.6 - - + -
360B ASP* 3.4 19.6 + - - -
379B PHE* 5.0 0.2 - - + -
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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 MET 3.4 1.7 + - - +
266B ALA 3.2 6.8 + - - +
268B GLN* 1.3 77.5 - - - +
270B GLY* 1.3 58.4 + - - +
273B TYR* 2.8 64.2 + - + +
274B ASN 3.8 0.2 + - - -
275B LEU* 4.0 5.9 + - + +
280B CYS* 3.7 25.1 - - + +
284B LEU* 3.9 22.2 - - + -
340B LEU* 3.5 29.8 - - + -
343B LEU* 6.0 0.2 - - + -
345B ALA* 4.0 14.1 - - + -
353B LEU* 4.2 15.0 - - + -
379B PHE* 4.0 15.9 - - + -
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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
----------------------------------------------------------
71B ASN* 3.6 13.4 - - - +
160B LYS* 5.6 0.4 - - - -
266B ALA 3.2 10.0 + - - -
267B HIS* 4.4 0.4 - - - -
268B GLN 3.1 0.4 - - - -
269B LEU* 1.3 76.2 - - - +
271B GLY* 1.3 56.1 + - - +
272B TYR 2.8 5.5 + - - -
274B ASN* 2.8 32.7 + - - +
275B LEU* 3.5 26.9 - - - -
277B HIS* 5.9 1.3 - - - -
280B CYS* 4.1 2.8 - - - -
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Residues in contact with GLY 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B ASN* 5.0 3.4 - - - -
153B THR* 5.5 8.7 - - - +
158B HIS* 5.2 16.8 + - - +
160B LYS* 4.2 18.1 - - - +
267B HIS 3.1 20.1 + - - -
268B GLN* 3.3 3.3 + - - -
270B GLY* 1.3 72.5 - - - +
272B TYR* 1.3 60.3 + - - +
274B ASN* 5.5 2.9 - - - -
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Residues in contact with TYR 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B HIS* 6.3 0.4 - - + -
268B GLN 3.1 15.5 - - - +
269B LEU 4.1 0.4 - - - +
270B GLY 2.8 4.6 + - - -
271B GLY* 1.3 80.5 - - - +
273B TYR* 1.3 93.8 + + + +
274B ASN* 3.1 13.8 + - - -
349B ASP* 2.9 29.1 + - + -
352B LEU* 3.9 27.8 - - + +
353B LEU* 4.3 15.9 - - + -
356B HIS* 6.2 2.2 - + - -
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Residues in contact with TYR 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269B LEU* 2.8 46.6 + - + +
272B TYR* 1.3 98.8 - + - +
274B ASN* 1.3 73.0 + - - +
275B LEU* 3.1 24.3 + - + +
343B LEU 5.3 0.4 - - - +
344B GLY 4.0 15.7 - - - +
345B ALA* 3.5 17.7 - - + -
346B LYS* 2.9 25.4 + - + -
349B ASP* 2.6 39.2 + - + +
353B LEU* 4.2 9.2 - - + +
185C LYS* 5.7 7.4 - - - +
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Residues in contact with ASN 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B PRO* 5.6 1.4 - - - +
71B ASN* 4.4 11.8 - - - +
158B HIS* 6.3 0.8 - - - -
270B GLY 2.8 18.8 + - - +
271B GLY* 5.5 2.0 - - - -
272B TYR 3.1 11.8 + - - -
273B TYR* 1.3 80.8 - - - +
275B LEU* 1.3 62.1 + - - +
276B PRO* 4.5 1.6 - - - +
184C PRO* 5.3 11.4 - - + +
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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
------------------------------------------------------------
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