Contacts of the helix formed by residues 258 - 279 (chain A) in PDB entry 2GC5
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 258 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238A GLN* 3.3 19.7 + - - +
257A VAL* 1.3 82.4 - - - +
259A ASP* 1.3 61.3 + - - +
260A TYR* 3.2 19.7 - - - -
261A GLN* 2.9 20.6 + - - +
262A GLN 3.7 0.9 + - - -
301A LEU* 5.6 0.2 - - - -
327A ALA* 5.5 5.6 - - - -
330A GLN* 6.1 0.4 - - - +
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Residues in contact with ASP 259 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238A GLN* 5.0 0.2 - - - +
258A GLY* 1.3 70.3 - - - -
260A TYR* 1.3 72.7 + - - +
262A GLN* 3.1 46.7 + - - +
263A ARG* 4.0 1.4 + - - +
323A GLY* 6.0 1.7 - - - -
330A GLN* 6.2 0.4 - - - +
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Residues in contact with TYR 260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A ASN* 6.3 2.7 - - + -
49A GLY* 6.0 0.9 - - - -
256A LEU* 6.0 0.2 - - - +
257A VAL 4.6 4.2 + - - -
258A GLY* 4.0 17.9 - - - -
259A ASP* 1.3 93.0 - - - +
261A GLN* 1.3 92.6 + - + +
262A GLN 3.2 0.2 - - - -
263A ARG* 3.4 26.3 + - - +
264A ASN* 3.3 33.0 + - - +
300A ARG* 4.8 6.6 + - - +
320A GLY* 6.3 3.8 - - - -
323A GLY* 6.1 2.5 - - - -
900A SO4 4.7 9.4 - - - -
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Residues in contact with GLN 261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A SER* 2.8 25.5 + - - -
238A GLN* 4.4 7.0 - - - +
254A VAL* 6.2 0.2 - - + -
256A LEU* 3.6 43.5 - - + +
257A VAL 4.0 6.5 - - - +
258A GLY* 2.9 14.7 + - - +
260A TYR* 1.3 107.3 + - + +
262A GLN* 1.3 63.6 + - - +
264A ASN* 2.9 33.2 + - - +
265A MET* 2.9 33.6 + - + +
300A ARG* 3.7 10.2 + - - -
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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
----------------------------------------------------------
222A PHE* 5.6 1.3 - - + -
228A VAL* 3.6 28.9 + - + +
231A ALA* 3.4 28.9 - - + +
238A GLN* 2.8 35.5 + - + +
240A PHE* 5.2 6.6 - - + -
258A GLY 3.7 1.0 + - - -
259A ASP* 3.1 28.6 + - - +
261A GLN* 1.3 78.1 - - - +
263A ARG* 1.3 57.1 + - - +
265A MET* 3.4 5.2 + - - +
266A ALA* 3.0 29.5 + - - +
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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
----------------------------------------------------------
48A ASN* 3.4 25.5 + - - +
49A GLY* 4.1 0.2 - - - -
164A THR* 4.0 7.9 + - - -
165A GLU* 3.7 28.5 + - - +
198A GLY* 4.3 10.3 - - - -
199A ASN* 4.7 2.7 - - - +
222A PHE* 3.7 40.1 - - + -
259A ASP 4.0 1.4 + - - +
260A TYR* 3.4 24.8 + - - +
261A GLN 3.3 0.4 - - - -
262A GLN* 1.3 75.7 - - - +
264A ASN* 1.3 88.0 + - - +
266A ALA* 3.2 2.9 + - - +
267A ILE* 2.9 48.2 + - + +
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Residues in contact with ASN 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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49A GLY* 3.5 30.2 + - - -
52A SER* 3.7 6.3 + - - -
53A ALA* 4.1 9.1 - - - +
164A THR* 4.4 2.0 - - - +
260A TYR* 3.3 17.3 + - - +
261A GLN* 2.9 35.7 + - - +
263A ARG* 1.3 106.7 + - - +
265A MET* 1.3 64.3 + - + +
267A ILE* 3.4 12.2 + - - +
268A ALA* 3.0 27.4 + - - +
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Residues in contact with MET 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A SER 3.9 6.7 - - - +
56A ALA* 3.7 22.4 - - + -
240A PHE* 4.1 17.9 - - + -
254A VAL* 4.0 31.4 - - + -
256A LEU* 3.8 21.1 - - + -
261A GLN* 2.9 30.8 + - - +
262A GLN* 3.8 5.4 - - - +
264A ASN* 1.3 77.6 - - + +
266A ALA* 1.3 61.0 + - - +
268A ALA* 3.2 4.7 + - - +
269A ILE* 2.9 35.3 + - - +
292A LEU* 3.8 17.0 - - + +
297A TRP* 3.8 18.2 - - + -
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Residues in contact with ALA 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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222A PHE* 3.8 14.8 - - + -
226A PHE* 3.5 19.2 - - + -
227A SER 4.8 0.7 - - - +
228A VAL* 3.6 20.8 - - + +
240A PHE* 5.2 0.6 - - - -
242A TYR* 3.6 18.7 - - + -
262A GLN 3.0 17.9 + - - +
263A ARG 3.2 4.2 + - - +
265A MET* 1.3 74.9 - - - +
267A ILE* 1.3 62.6 + - - +
269A ILE* 3.4 2.0 + - - -
270A GLN* 2.9 21.7 + - - +
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Residues in contact with ILE 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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53A ALA* 4.4 9.2 - - + -
57A ILE* 5.6 0.2 - - + -
162A VAL* 3.5 31.6 - - + -
164A THR* 3.9 20.9 - - + -
196A VAL* 3.9 7.1 - - + +
197A THR 4.2 5.2 - - - +
198A GLY* 3.7 27.4 - - - +
222A PHE* 4.9 0.2 - - + -
226A PHE* 3.8 22.9 - - + -
263A ARG* 2.9 34.2 + - + +
264A ASN* 3.5 9.4 - - - +
266A ALA* 1.3 76.5 - - - +
268A ALA* 1.3 55.4 + - - +
270A GLN* 3.5 1.4 + - - +
271A THR* 2.7 39.4 + - - +
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Residues in contact with ALA 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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53A ALA 3.8 2.9 - - - +
56A ALA* 3.4 34.3 - - + +
57A ILE* 3.5 28.9 - - + +
60A VAL* 5.6 3.1 - - + -
264A ASN 3.0 12.7 + - - +
265A MET 3.2 9.6 + - - +
267A ILE* 1.3 74.3 - - - +
269A ILE* 1.3 60.9 + - + +
271A THR 3.3 0.3 + - - -
272A ALA* 2.9 31.5 + - - +
292A LEU* 5.8 0.4 - - + -
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Residues in contact with ILE 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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60A VAL* 5.2 5.4 - - + -
240A PHE* 4.0 10.1 - - + -
242A TYR* 3.5 48.5 - - + -
249A ILE* 4.4 0.2 - - + -
252A LEU* 3.9 17.5 - - + -
265A MET 2.9 21.9 + - - +
268A ALA* 1.3 76.1 - - + +
270A GLN* 1.3 63.0 + - - +
271A THR 3.3 0.2 + - - -
272A ALA* 3.3 5.5 + - - +
273A LYS* 3.0 25.9 + - + +
288A ILE* 4.0 34.1 - - + -
292A LEU* 3.9 27.6 - - + -
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Residues in contact with GLN 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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196A VAL* 3.8 14.4 - - + -
220A LEU* 3.5 33.7 - - + +
225A ASP 4.4 2.9 - - - +
226A PHE* 3.6 34.9 - - + +
242A TYR* 3.3 21.6 + - - +
244A ASP* 3.8 14.8 + - - +
245A GLN* 5.3 2.1 + - - +
266A ALA 2.9 16.9 + - - +
267A ILE 3.9 3.1 - - - +
269A ILE* 1.3 75.8 - - - +
271A THR* 1.3 55.8 + - - +
273A LYS* 3.3 9.6 + - - +
274A VAL* 3.0 30.5 + - - +
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Residues in contact with THR 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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42A ILE* 3.8 16.2 - - + -
57A ILE* 3.7 21.0 - - + +
160A VAL* 3.8 12.0 - - + +
162A VAL* 3.4 34.9 - - + +
196A VAL* 3.5 17.9 - - - +
267A ILE* 2.7 23.3 + - - +
268A ALA 3.7 3.6 - - - -
270A GLN* 1.3 72.3 - - - +
272A ALA* 1.3 61.5 + - - +
274A VAL* 3.2 3.6 + - - +
275A TYR* 2.8 28.8 + - - +
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Residues in contact with ALA 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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57A ILE* 4.9 4.8 - - + +
60A VAL* 3.6 33.0 - - + -
61A LEU* 4.0 20.6 - - + +
268A ALA 2.9 17.2 + - - +
269A ILE* 3.6 4.7 - - - +
271A THR* 1.3 76.3 - - - +
273A LYS* 1.3 56.7 + - - +
275A TYR* 3.2 5.9 + - - +
276A ALA* 2.9 30.8 + - - +
283A LEU* 3.8 8.8 - - + +
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Residues in contact with LYS 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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242A TYR* 4.1 14.2 - - + +
244A ASP* 2.8 36.8 + - - +
246A ASP* 3.1 31.7 + - - +
247A GLY 6.2 0.2 - - - -
249A ILE* 5.0 6.5 - - + +
269A ILE* 3.0 20.0 + - + +
270A GLN* 3.5 14.6 - - - +
272A ALA* 1.3 76.9 - - - +
274A VAL* 1.3 55.3 + - - +
276A ALA* 3.5 2.6 + - - +
277A LYS* 3.0 30.9 + - - +
283A LEU* 3.9 19.7 - - + +
288A ILE* 4.4 10.5 - - + -
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Residues in contact with VAL 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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160A VAL* 3.8 17.7 - - + -
194A PRO* 3.6 33.9 - - + -
196A VAL* 4.4 5.6 - - + -
218A GLN* 5.1 3.6 - - - +
220A LEU* 3.3 33.4 - - + -
270A GLN* 3.0 20.4 + - - +
271A THR 3.6 7.4 - - - +
273A LYS* 1.3 71.4 - - - +
275A TYR* 1.3 61.4 + - - +
277A LYS* 3.2 6.3 + - - +
278A GLN* 2.8 35.8 + - + +
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Residues in contact with TYR 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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40A ARG* 3.3 21.1 + - - -
42A ILE* 3.8 25.4 - - + -
61A LEU* 4.0 16.4 - - + -
66A LEU* 3.8 24.0 - - + +
138A ASP* 3.6 4.9 + - - +
139A VAL* 3.3 37.3 - - + +
159A VAL* 3.6 43.7 - - + -
160A VAL* 4.4 3.1 - - + -
271A THR 2.8 13.3 + - - +
272A ALA* 3.4 10.1 - - - +
274A VAL* 1.3 78.9 - - - +
276A ALA* 1.3 63.5 - - - +
278A GLN* 3.3 1.4 + - - +
279A THR* 2.9 46.2 + - + +
281A TRP* 5.4 1.3 - - + -
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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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61A LEU* 5.2 1.8 - - + -
272A ALA 2.9 15.7 + - - +
273A LYS* 3.7 4.9 - - - +
275A TYR* 1.3 81.7 - - + +
277A LYS* 1.3 57.0 + - - +
279A THR* 3.3 5.4 + - - -
280A GLU* 3.0 9.4 + - - -
281A TRP* 2.8 53.9 + - + +
283A LEU* 3.7 22.9 - - + -
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Residues in contact with LYS 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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245A GLN* 5.3 8.1 + - - -
246A ASP* 5.3 10.0 + - - +
273A LYS 3.0 18.5 + - - +
274A VAL* 3.6 6.3 - - - +
276A ALA* 1.3 76.0 - - - +
278A GLN* 1.3 68.7 + - + +
279A THR 3.3 0.9 + - - -
280A GLU* 3.3 21.8 + - - +
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Residues in contact with GLN 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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40A ARG* 5.3 0.9 + - - -
159A VAL* 3.7 23.9 + - + +
192A GLY 5.1 3.2 + - - -
193A ILE* 5.9 2.2 - - - +
194A PRO* 4.2 24.4 - - + +
218A GLN* 5.8 0.5 - - - +
274A VAL* 2.8 36.8 + - + +
275A TYR 3.7 0.2 - - - +
277A LYS* 1.3 77.7 - - + +
279A THR* 1.3 61.5 + - - +
280A GLU* 3.5 3.0 - - - +
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Residues in contact with THR 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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40A ARG* 3.6 45.2 + - - +
159A VAL* 4.1 9.9 - - + -
275A TYR* 2.9 44.2 + - + +
276A ALA 3.4 4.7 + - - -
277A LYS 3.2 0.2 - - - -
278A GLN* 1.3 79.3 - - - +
280A GLU* 1.3 74.4 + - - +
281A TRP* 3.3 15.9 + - - +
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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