Contacts of the helix formed by residues 261 - 281 (chain A) in PDB entry 2XVS
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 ARG 261 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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0A MET* 1.3 75.6 - - - +
262A GLN* 1.3 62.0 + - - +
263A ARG* 3.5 3.6 - - + +
264A GLU* 3.0 33.4 + - + +
265A GLN* 3.0 27.6 + - - +
399A LYS* 5.9 1.8 - - - +
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Residues in contact with GLN 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A ARG* 1.3 72.3 - - - +
263A ARG* 1.3 67.9 + - - +
265A GLN* 3.3 8.4 + - - +
266A GLN* 3.1 26.4 + - - +
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Residues in contact with ARG 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A ARG* 3.5 2.0 - - + +
262A GLN* 1.3 78.0 - - - +
264A GLU* 1.3 64.0 + - - +
266A GLN* 3.3 18.2 + - - +
267A LEU* 3.1 21.9 + - + +
349A GLU* 2.8 43.2 + - - +
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Residues in contact with GLU 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0A MET* 3.5 13.8 - - + -
261A ARG* 3.0 53.2 + - - +
263A ARG* 1.3 79.5 - - - +
265A GLN* 1.3 65.4 + - - +
267A LEU* 3.3 6.5 + - - +
268A LEU* 2.9 29.5 + - + +
398A HIS* 2.7 42.8 + - + +
399A LYS* 3.6 19.7 + - - -
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Residues in contact with GLN 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0A MET* 4.2 33.4 - - + +
261A ARG 3.0 18.4 + - - +
262A GLN* 3.3 8.5 + - - +
264A GLU* 1.3 78.2 - - - +
266A GLN* 1.3 58.7 + - - +
268A LEU* 3.3 2.3 + - - +
269A GLU* 3.0 50.7 + - + +
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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
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262A GLN 3.1 16.2 + - - +
263A ARG* 3.3 25.6 + - - +
265A GLN* 1.3 73.0 - - - +
267A LEU* 1.3 75.3 + - - +
269A GLU* 3.4 14.8 + - - +
270A PHE* 3.0 23.0 + - - +
347A THR* 3.4 12.0 - - - +
348A GLU* 3.0 63.6 + - + +
349A GLU* 4.1 25.3 + - - +
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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 ARG* 3.1 19.4 + - + +
264A GLU* 3.7 7.2 - - - +
266A GLN* 1.3 86.7 - - - +
268A LEU* 1.3 65.8 + - + +
270A PHE* 3.2 23.7 + - + +
271A LEU* 3.0 47.3 + - + +
347A THR* 4.3 11.4 - - + -
396A ILE* 6.1 1.8 - - + -
398A HIS* 6.3 0.9 - - + -
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Residues in contact with LEU 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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0A MET* 3.6 32.1 - - + -
264A GLU* 2.9 21.7 + - + +
265A GLN* 3.8 4.3 - - - +
267A LEU* 1.3 83.6 - - + +
269A GLU* 1.3 59.2 + - - +
271A LEU* 3.2 4.2 + - + +
272A ASP* 2.9 35.5 + - - +
396A ILE* 5.5 2.0 - - + -
398A HIS* 4.2 32.5 - - + +
399A LYS* 4.1 19.7 - - + -
401A LYS* 4.3 9.0 - - + -
403A TYR* 3.4 34.2 + - + +
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Residues in contact with GLU 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 GLN* 3.0 42.1 + - + +
266A GLN* 3.6 20.1 - - - +
268A LEU* 1.3 76.3 - - - +
270A PHE* 1.3 56.1 + - - +
272A ASP* 3.3 11.7 + - - +
273A ARG* 3.0 36.7 + - - +
348A GLU* 4.6 6.6 - - - +
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Residues in contact with PHE 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 GLN 3.0 12.6 + - - +
267A LEU* 3.3 15.9 - - + +
269A GLU* 1.3 72.5 - - - +
271A LEU* 1.3 82.0 + - + +
273A ARG* 3.2 9.4 + - - +
274A LEU* 2.8 37.9 + - + +
345A LEU* 3.7 28.0 - - + -
346A THR* 3.7 23.6 - - - +
347A THR* 3.5 33.2 - - + -
352A PRO* 4.5 7.6 - - + -
354A THR* 3.4 30.5 - - + -
368A MET* 4.1 15.0 - - + -
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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* 3.0 39.6 + - + +
268A LEU* 3.7 7.9 - - + +
270A PHE* 1.3 94.3 - - + +
272A ASP* 1.3 60.2 + - - +
274A LEU* 4.3 5.6 - - + -
275A THR* 2.8 37.7 + - + +
368A MET* 5.0 1.8 - - + -
396A ILE* 3.9 26.0 - - + -
403A TYR* 3.7 35.2 - - + -
405A PHE* 3.7 27.1 - - + -
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Residues in contact with ASP 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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268A LEU* 2.9 19.5 + - - +
269A GLU* 3.4 12.9 - - - +
271A LEU* 1.3 76.9 - - - +
273A ARG* 1.3 63.4 + - + +
275A THR* 3.2 7.5 + - - -
276A SER* 3.1 24.1 + - - -
401A LYS* 4.4 15.8 + - - +
403A TYR* 2.6 29.7 + - - -
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Residues in contact with ARG 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A GLU* 3.0 23.6 + - + +
270A PHE* 3.6 7.4 - - - +
272A ASP* 1.3 76.9 - - + +
274A LEU* 1.3 59.1 + - - +
276A SER* 3.3 5.4 + - - -
277A LEU* 2.8 46.0 + - + +
344A SER 5.0 2.6 + - - -
345A LEU* 3.9 41.4 - - + +
346A THR 4.0 13.1 + - - +
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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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270A PHE* 2.8 28.5 + - + +
271A LEU* 3.8 5.6 - - + +
273A ARG* 1.3 76.5 - - - +
275A THR* 1.3 58.1 + - + +
276A SER 3.3 0.2 + - - -
277A LEU* 3.3 4.0 + - - -
278A LEU* 2.9 45.6 + - + +
343A PHE* 3.8 27.6 - - + -
345A LEU* 4.0 11.4 - - + +
354A THR* 3.8 17.5 - - + -
366A ALA* 4.1 10.3 - - + -
368A MET* 3.6 30.7 - - + -
405A PHE* 3.9 21.5 - - + -
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Residues in contact with THR 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 28.9 + - - +
272A ASP* 3.2 12.1 + - - -
274A LEU* 1.3 73.0 - - + +
276A SER* 1.3 61.0 + - - +
278A LEU* 3.5 9.0 + - - +
279A GLU* 3.1 23.7 + - - +
403A TYR* 3.7 25.9 - - + -
404A SER 5.4 1.8 - - - +
405A PHE* 4.2 28.0 - - + -
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Residues in contact with SER 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 ASP 3.1 18.2 + - - -
273A ARG* 3.6 6.3 - - - -
274A LEU 3.2 0.2 - - - -
275A THR* 1.3 78.9 + - - +
277A LEU* 1.3 62.1 + - - +
279A GLU* 3.3 6.8 + - - +
280A SER* 3.1 25.2 + - - -
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Residues in contact with LEU 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 ARG* 2.8 38.5 + - + +
274A LEU 3.8 2.9 - - - +
276A SER* 1.3 72.7 - - - +
278A LEU* 1.3 59.2 + - - +
280A SER* 3.3 6.0 + - - +
281A LYS* 2.9 26.5 + - - -
282A GLY* 3.0 31.6 + - - +
283A LYS* 5.6 6.5 - - + -
343A PHE* 3.6 38.8 - - + -
344A SER 5.1 2.2 - - - +
345A LEU* 4.1 22.7 - - + -
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Residues in contact with LEU 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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274A LEU* 2.9 39.8 + - + +
275A THR* 3.8 7.6 - - - +
276A SER 3.3 0.2 - - - -
277A LEU* 1.3 76.2 - - - +
279A GLU* 1.3 63.3 + - - +
281A LYS* 3.3 11.6 + - - +
343A PHE* 3.8 19.5 - - + -
364A CYS* 3.7 35.4 + - - +
365A TYR 3.8 7.0 - - - -
366A ALA* 3.6 34.3 - - + +
405A PHE* 4.2 24.2 - - + -
406A SER 5.0 1.1 - - - +
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Residues in contact with GLU 279 (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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275A THR 3.1 17.8 + - - +
276A SER* 3.3 6.0 + - - +
277A LEU 3.3 0.2 - - - -
278A LEU* 1.3 79.0 - - - +
280A SER* 1.3 56.6 + - - +
281A LYS* 3.8 3.8 + - - +
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Residues in contact with SER 280 (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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276A SER* 3.1 18.6 + - - -
277A LEU* 3.3 11.8 + - - +
279A GLU* 1.3 75.5 - - - +
281A LYS* 1.3 68.0 + - - +
282A GLY* 3.5 0.9 + - - -
283A LYS* 3.0 42.4 + - - +
284A VAL 4.0 4.0 + - - +
289A LEU* 5.7 0.2 - - - +
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Residues in contact with LYS 281 (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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277A LEU 2.9 7.8 + - - -
278A LEU 3.3 6.1 + - - +
279A GLU 4.9 3.1 - - - +
280A SER* 1.3 77.9 - - - +
282A GLY* 1.3 55.9 + - - +
284A VAL* 3.1 28.2 + - - +
289A LEU* 4.0 30.5 - - + -
342A VAL* 3.7 19.4 - - + +
358A VAL* 4.2 11.2 - - + -
360A SER 4.6 1.4 + - - -
361A ASP* 3.0 21.2 + - - +
362A GLY 2.9 31.1 + - - -
363A PRO* 4.3 1.8 - - - -
364A CYS* 4.0 24.0 - - + +
1426A EDO 4.3 11.9 + - - -
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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