Contacts of the helix formed by residues 256 - 277 (chain A) in PDB entry 3RAW
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 PRO 256 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254A PRO 3.6 4.9 - - - +
255A TYR* 1.3 85.2 - - + +
257A LEU* 1.3 68.5 + - - +
258A PRO* 3.3 10.3 - - + -
259A HIS* 2.9 49.3 + - + +
260A VAL 2.9 10.2 + - - -
309A LYS 5.7 4.5 - - - +
310A SER* 4.8 8.5 - - - +
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Residues in contact with LEU 257 (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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255A TYR 3.7 1.2 + - - -
256A PRO* 1.3 70.2 - - - +
258A PRO* 1.3 70.8 - - + +
260A VAL* 3.1 8.9 + - + +
261A ARG* 2.8 31.5 + - - +
368A TYR* 3.8 16.3 - - + -
441A GLU* 3.2 55.9 - - + +
442A HIS* 4.2 22.2 - - + +
445A LEU* 3.8 29.6 - - + -
471A PHE* 4.2 14.4 - - + -
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Residues in contact with PRO 258 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A PRO* 3.4 13.2 - - + -
257A LEU* 1.3 93.5 - - + +
259A HIS* 1.3 61.7 + - + +
261A ARG* 3.4 30.9 + - - +
262A HIS* 3.1 27.5 + - - +
441A GLU* 5.0 7.4 - - - +
479A GLU* 4.7 8.3 - - - +
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Residues in contact with HIS 259 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A TYR* 4.1 7.3 - - + -
256A PRO* 2.9 36.4 + - + +
258A PRO* 1.3 82.7 - - + +
260A VAL* 1.3 59.6 + - - +
262A HIS* 3.3 3.0 + - - +
263A MET* 2.9 49.8 + - + +
310A SER* 3.5 19.6 + - - -
311A VAL* 3.3 39.0 + - + +
314A THR* 3.4 21.2 - - + +
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Residues in contact with VAL 260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A TYR* 3.6 25.1 - - + +
256A PRO 2.9 19.0 + - - +
257A LEU* 3.4 11.7 - - + +
259A HIS* 1.3 75.3 - - - +
261A ARG* 1.3 58.7 + - - +
263A MET* 3.7 7.7 - - - +
264A ALA* 2.9 27.9 + - - +
364A LEU* 4.3 25.5 - - + +
367A TYR* 4.1 9.9 - - + -
368A TYR* 4.0 17.9 - - + -
445A LEU* 4.3 28.3 - - + -
471A PHE* 4.9 1.3 - - + -
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Residues in contact with ARG 261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A LEU* 2.8 27.9 + - - +
258A PRO* 3.6 34.6 + - - +
260A VAL* 1.3 73.4 - - - +
262A HIS* 1.3 58.3 + - - +
264A ALA 3.3 0.9 + - - -
265A TYR* 3.0 25.1 + - - +
441A GLU* 3.3 30.9 + - - +
471A PHE* 3.2 53.2 + - + -
472A PHE* 3.4 16.6 - - + +
474A GLY* 3.2 40.6 + - - -
475A LEU* 3.9 14.5 - - + +
479A GLU* 5.1 3.6 + - - -
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Residues in contact with HIS 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A PRO 3.1 14.4 + - - +
259A HIS* 3.9 3.6 - - - +
261A ARG* 1.3 79.7 - - - +
263A MET* 1.3 62.1 + - - +
265A TYR* 3.5 2.7 + + - +
266A GLN* 3.0 53.4 + - + +
314A THR* 2.6 37.1 + - - +
315A SER 4.0 0.7 - - - -
475A LEU* 3.8 10.1 - - + +
479A GLU* 3.6 48.6 + - + +
482A PHE* 5.7 1.2 - - - -
484A THR* 3.7 34.0 + - + -
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Residues in contact with MET 263 (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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243A THR* 4.6 2.0 - - - -
255A TYR* 3.7 26.7 - - + -
259A HIS* 2.9 47.8 + - + +
260A VAL* 3.7 7.4 - - - +
262A HIS* 1.3 72.4 - - - +
264A ALA* 1.3 66.5 + - - +
266A GLN* 3.4 8.6 + - - +
267A LEU* 3.0 28.8 + - - +
291A PHE* 3.9 24.5 - - - -
314A THR* 4.0 22.4 - - + +
316A ILE* 3.8 15.2 - - + +
367A TYR* 4.1 31.9 - - + +
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Residues in contact with ALA 264 (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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260A VAL 2.9 19.0 + - - +
261A ARG* 3.3 6.5 + - - +
263A MET* 1.3 75.3 - - - +
265A TYR* 1.3 65.9 + - - +
267A LEU* 3.3 4.5 + - - +
268A CYS* 2.9 30.8 + - - -
360A ILE* 5.7 0.2 - - - -
364A LEU* 3.5 38.3 - - + +
471A PHE* 4.5 3.8 - - + -
472A PHE* 3.9 14.6 - - + -
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Residues in contact with TYR 265 (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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261A ARG 3.0 15.9 + - - +
262A HIS* 3.7 9.2 - + - +
263A MET 3.3 0.2 - - - -
264A ALA* 1.3 77.7 - - - +
266A GLN* 1.3 58.5 + - - +
268A CYS* 3.3 3.9 + - - +
269A HIS* 3.0 27.8 + - + +
467A LEU* 3.8 24.7 - - + -
472A PHE* 3.5 23.5 - + + -
475A LEU* 3.5 27.8 - - + -
479A GLU 3.6 14.6 - - - -
480A ARG* 2.7 49.8 + - + +
482A PHE* 3.4 35.3 - + - -
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Residues in contact with GLN 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A LEU* 3.8 25.4 - - + +
262A HIS* 3.0 48.9 + - + +
263A MET* 3.7 4.4 - - - +
265A TYR* 1.3 78.6 - - + +
267A LEU* 1.3 59.2 + - - +
269A HIS* 3.4 4.9 + - - +
270A ALA* 2.9 30.5 + - - +
314A THR 2.9 24.4 + - - -
315A SER* 3.3 6.9 - - - -
316A ILE* 2.8 43.0 + - + +
317A ARG* 4.8 1.2 + - - -
482A PHE* 4.6 11.1 - - + -
484A THR* 5.3 0.6 + - - -
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Residues in contact with LEU 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A MET 3.0 19.4 + - - +
264A ALA 3.8 4.3 - - - +
265A TYR 3.3 0.2 - - - -
266A GLN* 1.3 77.1 - - - +
268A CYS* 1.3 63.7 + - - +
270A ALA* 3.4 3.3 + - - -
271A LEU* 2.9 37.3 + - + +
284A LEU* 5.2 4.0 - - + -
289A ILE* 3.5 39.7 - - + -
316A ILE* 4.1 10.3 - - + -
318A VAL* 4.1 17.9 - - + -
360A ILE* 4.3 32.8 - - + -
363A ILE* 4.3 15.9 - - + -
364A LEU* 4.4 10.1 - - + -
367A TYR* 4.4 6.3 - - + -
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Residues in contact with CYS 268 (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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264A ALA* 2.9 25.2 + - - +
265A TYR* 3.6 0.9 - - - +
267A LEU* 1.3 78.1 - - - +
269A HIS* 1.3 56.6 + - - +
272A ARG* 2.8 33.4 + - - +
360A ILE* 4.7 4.7 - - - -
452A MET* 3.6 31.2 - - - -
463A LEU* 3.8 22.6 - - + +
466A ALA* 4.1 10.3 - - - -
467A LEU* 3.5 27.1 - - + -
472A PHE* 4.4 8.5 - - - -
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Residues in contact with HIS 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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216A LYS* 2.9 41.4 + - - -
217A PHE* 3.4 25.6 - + - -
218A LEU* 3.7 15.3 - - + -
265A TYR* 3.0 17.3 + - + +
266A GLN 3.6 2.7 - - - +
268A CYS* 1.3 75.0 - - - +
270A ALA* 1.3 64.7 + - - +
272A ARG* 3.4 12.7 + - - +
273A PHE* 3.2 22.3 + - - +
467A LEU* 3.9 16.2 - - + +
482A PHE* 3.3 46.6 - + + -
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Residues in contact with ALA 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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217A PHE* 3.1 29.0 - - - +
218A LEU* 4.2 7.0 - - + +
219A CYS* 4.8 2.6 - - - -
266A GLN 2.9 17.4 + - - +
267A LEU 3.9 2.0 - - - +
269A HIS* 1.3 77.9 - - - +
271A LEU* 1.3 65.6 + - + +
273A PHE* 3.4 6.2 - - - +
274A LEU* 3.3 23.5 + - - +
318A VAL* 3.8 28.5 - - + -
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Residues in contact with LEU 271 (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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267A LEU* 2.9 22.5 + - + +
270A ALA* 1.3 87.4 - - + +
272A ARG* 1.3 58.7 + - - +
274A LEU* 3.1 21.1 + - + +
275A HIS* 2.8 41.5 + - + +
281A HIS* 4.0 8.7 - - + -
284A LEU* 3.7 32.1 - - + -
318A VAL* 4.1 18.6 - - + -
356A ASP* 3.7 23.1 - - + +
360A ILE* 4.1 4.3 - - + -
463A LEU* 3.1 25.4 - - + -
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Residues in contact with ARG 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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217A PHE* 5.8 5.7 - - - -
268A CYS 2.8 19.3 + - - +
269A HIS* 3.9 13.2 + - - +
270A ALA 3.3 0.2 - - - -
271A LEU* 1.3 77.7 - - - +
273A PHE* 1.3 58.0 + - - +
275A HIS* 3.3 7.5 + - + +
276A GLU* 2.9 60.3 + - - +
463A LEU* 3.7 10.0 - - + +
464A ALA* 3.7 45.3 + - + +
467A LEU* 3.5 25.2 - - + +
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Residues in contact with PHE 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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208A ILE* 4.1 19.1 - - + -
211A LYS* 3.9 27.1 - - + -
212A ASP* 3.8 17.9 - - + -
217A PHE* 3.2 66.2 - + + -
219A CYS* 5.0 1.6 - - - -
269A HIS 3.2 2.8 + - - +
270A ALA 3.4 9.0 - - - +
272A ARG* 1.3 82.4 - - - +
274A LEU* 1.3 84.9 + - + +
276A GLU* 3.3 5.3 + - - +
277A ASN* 3.0 48.3 + - + -
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Residues in contact with LEU 274 (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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208A ILE* 4.0 24.7 - - + -
219A CYS* 4.1 9.6 - - - -
270A ALA 3.3 11.2 + - - +
271A LEU* 3.1 33.4 + - + +
273A PHE* 1.3 98.1 - - + +
275A HIS* 1.3 61.2 + - + +
277A ASN* 2.9 21.1 + - + +
279A LEU* 3.0 44.0 + - + +
280A THR* 5.9 0.4 - - - -
281A HIS* 5.1 6.7 - - + +
318A VAL* 5.4 0.7 - - + -
321A PHE* 3.8 24.5 - - + -
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Residues in contact with HIS 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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271A LEU* 2.8 25.6 + - + +
272A ARG* 3.5 7.4 - - + +
274A LEU* 1.3 77.9 - - + +
276A GLU* 1.3 60.1 + - + +
278A GLN* 3.1 17.7 + - - +
279A LEU 3.3 19.1 - - - -
353A GLN* 3.4 48.7 + - + +
356A ASP* 3.0 31.4 + - + +
357A VAL* 4.3 5.0 - - + +
463A LEU* 3.8 33.4 + - + +
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Residues in contact with GLU 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A ARG* 2.9 44.8 + - - +
273A PHE* 4.0 5.0 - - - +
274A LEU 3.2 0.2 - - - -
275A HIS* 1.3 76.7 - - + +
277A ASN* 1.3 63.3 + - - +
278A GLN* 3.0 16.6 - - - +
464A ALA* 4.3 13.2 - - - +
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Residues in contact with ASN 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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211A LYS* 3.7 24.2 - - + +
273A PHE* 3.0 48.9 + - + +
274A LEU* 2.9 10.7 + - + +
276A GLU* 1.3 82.7 - - - +
278A GLN* 1.3 78.5 + - - +
279A LEU* 3.2 12.7 + - + +
326A PHE* 4.1 11.8 - - + -
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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