Contacts of the helix formed by residues 257 - 278 (chain A) in PDB entry 1RS0
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 257 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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254A ASP 3.7 5.8 + - - -
256A ILE* 1.3 80.4 - - - +
258A ALA* 1.3 66.2 + - - -
259A SER* 3.6 2.2 - - - -
260A ASN 4.3 0.9 - - - -
261A PHE* 3.0 25.5 + - - +
319A TYR* 3.2 20.0 + - - -
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Residues in contact with ALA 258 (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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257A GLY* 1.3 71.2 - - - -
259A SER* 1.3 64.8 + - - +
261A PHE* 3.2 4.0 + - - +
262A THR* 3.0 27.4 + - - -
319A TYR* 3.7 29.8 - - + +
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Residues in contact with SER 259 (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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257A GLY 3.6 0.9 - - - -
258A ALA* 1.3 76.9 - - - +
260A ASN* 1.3 80.1 + - - +
262A THR* 3.1 9.5 + - - -
263A GLY* 2.8 23.9 + - - -
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Residues in contact with ASN 260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A ILE* 4.0 18.3 - - - +
257A GLY 3.8 2.0 + - - -
258A ALA 3.4 0.2 - - - -
259A SER* 1.3 89.4 + - - +
261A PHE* 1.3 61.7 + - - +
263A GLY* 3.7 3.8 - - - +
264A ALA* 2.9 28.9 + - - +
405A VAL* 3.9 21.9 - - + +
406A GLY* 3.7 22.1 - - - -
407A PRO* 4.3 7.3 - - - +
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Residues in contact with PHE 261 (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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250A LEU* 3.6 27.6 - - + -
251A ASP 3.6 16.8 - - - -
252A GLY* 3.8 14.8 - - - -
256A ILE* 3.9 7.8 - - + +
257A GLY 3.0 21.9 + - - +
258A ALA 3.5 2.7 - - - +
259A SER 3.2 0.2 - - - -
260A ASN* 1.3 77.3 - - - +
262A THR* 1.3 68.6 + - - +
264A ALA* 3.2 14.5 + - - +
265A LYS* 3.2 32.6 + - + +
288A THR* 4.4 10.1 - - + -
317A ILE* 3.8 22.0 - - + -
318A ASN 4.8 0.4 - - - -
319A TYR* 3.3 53.4 - + + -
322A HIS* 6.2 2.5 - - + -
325A LYS* 5.9 0.2 - - - -
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Residues in contact with THR 262 (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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258A ALA 3.0 14.8 + - - -
259A SER* 3.2 11.7 - - - -
261A PHE* 1.3 83.5 - - - +
263A GLY* 1.3 64.5 + - - +
265A LYS* 3.0 27.9 + - - +
266A LYS* 3.2 16.4 + - + +
319A TYR* 5.8 0.9 - - - +
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Residues in contact with GLY 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A SER 2.8 14.6 + - - -
260A ASN* 3.3 5.1 + - - -
262A THR* 1.3 78.5 - - - +
264A ALA* 1.3 60.6 + - - +
266A LYS* 3.2 22.7 - - - +
267A VAL* 3.4 13.1 + - - +
430A VAL* 5.3 3.3 - - - +
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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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250A LEU* 3.7 26.7 - - + -
260A ASN 2.9 14.1 + - - +
261A PHE* 3.3 11.0 - - - +
262A THR 3.1 0.2 - - - -
263A GLY* 1.3 75.0 - - - +
265A LYS* 1.3 64.5 + - - +
267A VAL* 3.1 16.0 + - - +
268A LEU* 3.2 15.7 + - - +
362A MET* 3.7 23.4 - - + +
405A VAL* 4.5 9.2 - - + -
430A VAL* 5.5 2.2 - - - -
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Residues in contact with LYS 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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250A LEU* 3.8 15.2 - - + +
261A PHE* 3.2 25.8 + - + +
262A THR* 3.0 25.6 + - - +
264A ALA* 1.3 77.0 - - - +
266A LYS* 1.3 52.3 + - - +
268A LEU* 3.0 12.2 + - - +
269A VAL* 2.7 40.8 + - + +
314A LEU* 3.2 39.4 + - + +
315A ASN* 3.6 16.6 + - - +
317A ILE* 2.8 32.6 + - + +
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Residues in contact with LYS 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 THR* 3.2 12.4 + - + +
263A GLY* 3.2 18.2 - - - +
264A ALA 3.1 0.6 - - - -
265A LYS* 1.3 75.9 - - - +
267A VAL* 1.3 60.6 + - + +
269A VAL* 3.2 11.0 + - + +
270A ASN* 2.9 60.6 + - - +
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Residues in contact with VAL 267 (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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263A GLY 3.6 14.4 - - - +
264A ALA 3.1 8.2 + - - +
266A LYS* 1.3 76.1 - - + +
268A LEU* 1.3 59.7 + - + +
270A ASN* 3.3 9.2 + - - +
271A LEU* 2.9 30.1 + - + +
362A MET* 4.0 14.4 - - + -
403A PHE* 4.3 16.6 - - + -
430A VAL* 3.9 26.2 - - + -
436A LEU* 4.2 22.7 - - + -
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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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248A LEU* 4.1 41.3 - - + -
249A VAL 5.5 0.2 - - - +
250A LEU* 4.4 25.1 - - + -
264A ALA 3.4 11.7 - - - +
265A LYS* 3.0 9.8 + - - +
267A VAL* 1.3 81.1 - - + +
269A VAL* 1.3 59.4 + - - +
271A LEU* 3.3 9.5 + - + +
272A ILE* 3.0 31.5 + - - +
286A LEU* 4.9 1.6 - - + -
314A LEU* 3.7 21.1 - - + -
360A ILE* 4.2 14.4 - - + +
362A MET* 3.4 28.7 - - + -
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Residues in contact with VAL 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 LYS* 2.7 26.8 + - + +
266A LYS* 3.5 13.2 - - + +
268A LEU* 1.3 74.5 - - - +
270A ASN* 1.3 71.4 + - - +
272A ILE* 3.4 7.0 + - - +
273A GLU* 3.0 23.6 + - + +
311A THR* 4.5 19.7 + - + -
314A LEU* 3.5 21.3 - - + -
315A ASN* 3.8 24.5 - - - +
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Residues in contact with ASN 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 LYS* 2.9 44.1 + - - +
267A VAL* 3.6 6.8 - - - +
269A VAL* 1.3 82.5 - - - +
271A LEU* 1.3 60.3 + - - +
273A GLU* 3.2 8.3 + - - +
274A LYS* 2.8 31.2 + - - +
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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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246A ILE* 5.3 2.9 - - + -
248A LEU* 4.9 8.3 - - + -
267A VAL* 2.9 19.2 + - + +
268A LEU* 3.6 13.5 - - + +
269A VAL 3.2 0.2 - - - -
270A ASN* 1.3 72.6 - - - +
272A ILE* 1.3 68.6 + - + +
274A LYS* 3.1 3.6 + - - +
275A VAL* 2.8 39.5 + - + +
284A TYR* 5.6 2.0 - - + +
360A ILE* 3.2 35.4 - - + -
403A PHE* 5.2 8.1 - - + -
439A VAL* 6.2 0.9 - - + -
440A PHE* 4.0 28.3 - - + -
443A MET* 4.6 15.5 - - + -
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Residues in contact with ILE 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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248A LEU* 4.0 16.8 - - + -
268A LEU 3.0 19.3 + - - +
269A VAL* 3.6 5.2 - - - +
271A LEU* 1.3 75.5 - - + +
273A GLU* 1.3 58.8 + - - +
275A VAL* 3.8 1.4 - - - +
276A ALA* 3.0 28.2 + - - +
284A TYR* 3.6 33.2 + - + +
307A ALA* 3.9 24.9 - - + +
310A VAL* 4.1 16.4 - - + -
311A THR* 3.6 24.5 - - - +
314A LEU* 3.8 22.7 - - + -
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Residues in contact with GLU 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 VAL* 3.0 20.4 + - + +
270A ASN* 3.5 9.2 - - - +
271A LEU 3.1 0.2 - - - -
272A ILE* 1.3 79.2 - - - +
274A LYS* 1.3 58.2 + - - +
276A ALA* 3.5 2.5 + - - +
277A SER* 3.0 23.6 + - - -
311A THR* 5.5 0.2 + - - -
583A ARG* 2.8 40.2 + - - +
683A ARG* 3.6 12.0 + - - -
684A SER* 2.8 23.6 + - - +
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Residues in contact with LYS 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 ASN 2.8 20.1 + - - +
271A LEU* 3.9 2.9 - - - +
273A GLU* 1.3 72.2 - - - +
275A VAL* 1.3 67.1 + - - +
277A SER* 2.8 25.8 + - - +
278A TYR* 3.3 24.6 + - + -
440A PHE* 3.4 43.3 - - + -
441A TYR* 3.6 27.1 + - - -
456A VAL 5.0 1.8 + - - -
458A GLU* 3.3 30.0 + - - +
684A SER* 5.2 2.0 - - - -
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Residues in contact with VAL 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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246A ILE* 4.6 9.4 - - + -
271A LEU* 2.8 45.6 + - + +
272A ILE 3.8 0.4 - - - +
274A LYS* 1.3 71.3 - - - +
276A ALA* 1.3 64.1 + - - +
278A TYR* 3.2 17.8 + - - +
280A VAL* 3.6 27.7 + - + +
282A PRO* 4.0 16.6 - - + -
284A TYR* 3.7 22.9 - - - +
440A PHE* 4.0 12.8 - - + -
443A MET* 4.7 2.2 - - + -
444A ILE* 4.2 17.3 - - + -
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Residues in contact with ALA 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 ILE 3.0 18.4 + - - +
273A GLU* 3.7 2.2 - - - +
275A VAL* 1.3 73.0 - - - +
277A SER* 1.3 56.7 + - - +
278A TYR 3.0 4.9 - - - -
279A GLY* 2.8 22.7 + - - -
280A VAL 3.8 13.0 + - - +
307A ALA* 4.1 19.5 - - + -
583A ARG* 3.7 34.0 + - - +
685A ARG* 5.2 0.5 + - - -
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Residues in contact with SER 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 GLU 3.0 8.9 + - - -
274A LYS* 2.8 24.6 + - - +
276A ALA* 1.3 75.8 - - - +
278A TYR* 1.3 65.2 + - - +
279A GLY 3.2 1.1 - - - -
455A MET* 3.7 4.3 - - - +
583A ARG* 3.3 15.2 - - - +
683A ARG 3.6 4.0 - - - -
684A SER* 3.4 36.5 + - - -
685A ARG* 3.0 33.9 + - - +
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Residues in contact with TYR 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 LYS* 3.3 26.6 + - - +
275A VAL 3.2 11.5 + - - +
276A ALA 3.0 1.4 - - - -
277A SER* 1.3 86.1 + - - +
279A GLY* 1.3 61.9 + - - +
280A VAL* 3.2 14.2 + - + +
440A PHE* 3.7 23.3 - + - -
441A TYR* 3.8 12.8 + - - -
444A ILE* 3.8 20.2 - - + -
446A GLU* 3.5 37.9 + - - -
448A GLN 5.2 0.2 - - - +
449A SER* 2.6 40.6 + - - +
452A LEU* 3.4 8.8 - - - +
455A MET* 3.5 24.9 - - + +
456A VAL 4.1 15.6 + - - -
457A TRP* 4.5 2.8 - - - -
568A ARG* 5.3 0.9 + - - -
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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
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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