Contacts of the helix formed by residues 251 - 272 (chain A) in PDB entry 5Y7G
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 ASN 251 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213A ARG* 5.8 3.6 - - - +
217A ASP* 3.1 28.8 + - - +
249A TYR* 3.7 5.5 - - - +
250A ALA* 1.3 80.9 - - - +
252A PRO* 1.3 77.6 - - - +
253A TRP* 2.9 47.0 + - - +
254A LEU* 3.4 30.1 + - + +
255A GLU* 3.1 18.0 + - - +
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Residues in contact with PRO 252 (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 ALA 3.4 5.6 - - - +
251A ASN* 1.3 98.1 - - - +
253A TRP* 1.3 56.3 + - - +
255A GLU* 3.4 7.1 + - + +
256A GLY* 2.9 24.1 + - - -
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Residues in contact with TRP 253 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A GLY* 3.2 28.3 - - - -
182A ASN* 3.9 6.7 + - - -
211A GLY* 3.4 26.5 - - - -
212A PHE* 3.6 33.4 - + - -
217A ASP* 6.2 1.1 - - + -
221A TYR* 4.5 12.1 - + - -
251A ASN* 2.9 20.1 + - - +
252A PRO* 1.3 76.2 - - - +
254A LEU* 1.3 64.3 + - + +
256A GLY* 3.2 3.5 + - - +
257A ARG* 2.9 55.1 + - + +
411A PHE* 5.4 5.2 - + - -
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Residues in contact with LEU 254 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A PHE* 5.6 2.5 - - + -
216A ALA 4.6 0.4 - - - +
217A ASP* 3.7 25.8 - - + +
220A ALA* 3.7 22.7 - - + -
221A TYR* 3.8 41.3 - - + +
224A LEU* 4.1 6.1 - - + +
249A TYR* 3.9 22.4 - - + -
251A ASN* 3.4 32.2 + - + +
252A PRO 3.3 0.2 - - - -
253A TRP* 1.3 80.2 - - + +
255A GLU* 1.3 57.3 + - - +
257A ARG* 2.7 25.3 + - + +
258A ARG* 2.7 15.1 + - - +
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Residues in contact with GLU 255 (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 PRO* 3.3 17.5 - - + +
249A TYR* 3.1 24.7 + - - +
251A ASN 3.1 17.5 + - - +
252A PRO* 3.4 7.2 + - + +
254A LEU* 1.3 74.2 - - - +
256A GLY* 1.3 57.9 + - - +
258A ARG* 2.6 40.4 + - - -
259A VAL* 2.8 55.6 + - + +
286A SER* 4.4 6.0 + - - +
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Residues in contact with GLY 256 (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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252A PRO 2.9 15.9 + - - -
253A TRP* 3.2 6.0 + - - -
254A LEU 3.0 0.6 - - - -
255A GLU* 1.3 77.0 - - - +
257A ARG* 1.3 64.8 + - - +
259A VAL* 4.1 4.4 - - - +
260A LYS* 3.0 25.3 + - - +
287A HIS* 4.9 1.4 - - - -
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Residues in contact with ARG 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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182A ASN* 3.8 16.5 - - - +
221A TYR* 3.2 37.9 + - + -
224A LEU* 3.6 25.4 - - + -
253A TRP* 2.9 41.9 + - + +
254A LEU* 2.7 16.2 + - - +
256A GLY* 1.3 74.9 - - - +
258A ARG* 1.3 55.5 + - - +
260A LYS* 3.3 15.9 + - - +
261A LEU* 2.9 27.3 + - + +
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Residues in contact with ARG 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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224A LEU* 3.4 18.3 - - + +
244A LEU* 5.5 4.2 - - + +
245A PRO* 3.2 35.5 + - + -
246A GLY* 4.3 6.1 + - - -
247A GLU 4.3 3.4 + - - -
248A PRO* 3.6 23.3 - - - +
249A TYR* 3.6 39.3 - - + +
254A LEU 2.7 11.2 + - - +
255A GLU* 2.6 39.4 + - - +
257A ARG* 1.3 69.3 - - - +
259A VAL* 1.3 69.9 + - - +
261A LEU* 3.0 3.5 + - - +
262A LEU* 3.0 43.8 + - + +
284A GLN* 4.2 18.8 + - - +
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Residues in contact with VAL 259 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A GLU* 2.8 44.7 + - - +
256A GLY* 4.2 4.5 - - - +
258A ARG* 1.3 78.5 - - - +
260A LYS* 1.3 65.7 + - - +
262A LEU* 3.4 4.3 + - - -
263A PHE 3.1 10.7 + - - -
284A GLN 4.5 4.9 - - - +
285A SER* 2.8 24.3 + - - +
286A SER* 3.1 33.7 - - - +
287A HIS* 3.1 38.1 - - + +
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Residues in contact with LYS 260 (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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256A GLY 3.0 18.2 + - - +
257A ARG* 3.6 16.7 - - - +
259A VAL* 1.3 75.1 - - - +
261A LEU* 1.3 67.2 + - - +
263A PHE* 2.8 14.1 + - + +
264A GLN* 3.0 38.8 + - + +
287A HIS* 3.4 38.8 - - + +
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Residues in contact with LEU 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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224A LEU* 4.4 14.1 - - + +
227A CYS* 3.9 20.9 - - + -
228A ARG* 4.1 22.2 - - + +
231A PHE* 5.6 0.4 - - + -
244A LEU* 4.0 11.9 - - + -
257A ARG 2.9 14.6 + - - +
258A ARG* 3.0 10.7 + - - +
260A LYS* 1.3 74.7 - - - +
262A LEU* 1.3 64.6 + - - +
264A GLN* 2.9 27.7 + - + +
265A PHE* 3.0 53.5 + - + -
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Residues in contact with LEU 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A LEU* 4.2 17.3 - - + -
244A LEU* 3.8 25.1 - - + -
245A PRO 5.6 0.2 - - - +
258A ARG* 3.0 41.9 + - + +
259A VAL* 3.5 11.0 - - - +
261A LEU* 1.3 75.5 - - - +
263A PHE* 1.3 62.0 + - - +
265A PHE* 3.5 6.2 + - + +
266A ALA* 3.0 23.4 + - - +
281A LEU* 4.3 18.7 - - + +
284A GLN* 3.8 35.7 - - + +
285A SER* 3.9 8.7 - - - -
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Residues in contact with PHE 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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259A VAL 3.1 12.3 + - - +
260A LYS 2.8 11.2 + - - +
262A LEU* 1.3 77.5 - - - +
264A GLN* 1.3 62.5 + - + +
266A ALA* 3.1 8.1 + - - +
267A GLN* 2.9 57.2 + - + +
282A TYR* 3.9 11.3 - + - -
285A SER* 4.0 4.9 - - - +
287A HIS* 3.6 28.5 - + + -
288A PRO 3.9 9.6 - - - -
289A GLY 3.7 7.4 - - - -
290A ALA* 3.4 46.0 - - + -
293A ARG* 4.2 11.7 - - + -
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Residues in contact with GLN 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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231A PHE* 4.8 6.6 - - + -
260A LYS* 3.0 43.5 + - + +
261A LEU* 2.9 23.3 + - + +
263A PHE* 1.3 75.1 - - + +
265A PHE* 1.3 68.6 + - + +
267A GLN* 3.1 22.4 + - - +
268A HIS* 3.0 22.3 + - - +
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Residues in contact with PHE 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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227A CYS* 4.4 5.4 - - + -
228A ARG* 4.9 0.2 - - - -
231A PHE* 3.4 50.5 - + + -
237A LEU* 3.6 31.4 - - + +
240A LEU* 4.4 14.8 - - + -
241A LEU* 4.0 17.9 - - + -
244A LEU* 4.4 11.4 - - + -
261A LEU* 3.0 53.5 + - + -
262A LEU* 3.7 10.1 - - + +
264A GLN* 1.3 76.4 - - + +
266A ALA* 1.3 62.9 + - - +
268A HIS* 3.1 8.2 + - - +
269A CYS* 2.9 26.2 + - - -
281A LEU* 4.4 4.9 - - + -
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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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262A LEU 3.0 10.6 + - - +
263A PHE 3.1 8.3 + - - +
265A PHE* 1.3 75.8 - - - +
267A GLN* 1.3 57.2 + - - +
269A CYS* 3.2 5.6 + - - +
270A GLU* 3.0 28.4 + - - +
278A ALA* 4.0 2.4 - - - +
281A LEU* 3.5 33.5 - - + +
282A TYR* 3.5 35.3 + - + +
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Residues in contact with GLN 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 PHE* 2.9 45.8 + - + +
264A GLN* 3.1 20.3 + - - +
266A ALA* 1.3 73.0 - - - +
268A HIS* 1.3 66.5 + - - +
270A GLU* 3.0 5.8 + - - +
271A LYS* 3.0 34.3 + - + +
282A TYR* 3.4 18.2 - - - +
293A ARG* 5.2 4.1 - - + +
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Residues in contact with HIS 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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231A PHE* 3.7 40.1 - + + -
237A LEU* 4.3 11.9 - - + +
264A GLN 3.0 9.1 + - - +
265A PHE 3.4 7.4 + - - +
267A GLN* 1.3 75.8 - - - +
269A CYS* 1.3 68.5 + - - +
271A LYS* 3.3 10.5 + - + +
272A GLN* 3.2 39.1 + - + +
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Residues in contact with CYS 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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237A LEU* 4.0 11.7 - - - -
265A PHE 2.9 18.3 + - - -
266A ALA* 3.3 9.0 - - - +
268A HIS* 1.3 79.8 - - - +
270A GLU* 1.3 54.4 + - - +
272A GLN* 2.8 27.0 + - - +
273A ARG 3.2 8.0 + - - -
274A ASP* 3.2 31.3 + - + +
277A LEU* 3.7 18.4 - - - -
278A ALA* 4.2 6.7 - - + -
281A LEU* 3.6 23.3 - - - -
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Residues in contact with GLU 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 ALA 3.0 8.2 + - - +
267A GLN* 3.0 8.9 + - - +
269A CYS* 1.3 75.3 - - - +
271A LYS* 1.3 64.1 + - + +
273A ARG 3.3 8.4 + - - -
275A PHE* 3.6 13.1 - - + -
278A ALA* 3.9 3.4 - - + -
282A TYR* 2.5 31.3 + - + +
293A ARG* 2.2 51.6 + - - -
297A SER* 3.4 25.2 - - - +
300A ARG* 3.2 40.4 + - - +
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Residues in contact with LYS 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 GLN* 3.0 26.2 + - + +
268A HIS* 3.9 9.4 - - + +
269A CYS 3.2 0.4 - - - -
270A GLU* 1.3 79.5 - - + +
272A GLN* 1.3 69.5 + - - +
273A ARG* 3.3 7.4 + - - +
300A ARG* 5.1 2.2 - - - +
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Residues in contact with GLN 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 HIS* 3.2 35.4 + - + +
269A CYS* 2.8 10.8 + - - +
271A LYS* 1.3 87.1 + - - +
273A ARG* 1.3 69.2 + - - +
274A ASP* 3.2 6.9 + - + +
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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