Contacts of the helix formed by residues 249 - 265 (chain C) in PDB entry 6GYS
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 GLU 249 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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227B ALA* 4.7 12.4 - - - +
81C LYS* 3.9 25.4 + - - +
214C ARG* 5.4 7.4 + - - +
245C PHE* 2.8 29.5 + - + +
248C ASP* 1.3 86.3 - - + +
250C PRO* 1.3 61.5 - - - +
251C LEU* 3.3 3.1 + - - +
252C LEU* 3.7 26.4 + - + +
253C ALA* 2.8 27.2 + - - +
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Residues in contact with PRO 250 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78C TYR 5.1 2.7 - - - +
79C LYS* 4.7 16.8 - - - +
80C THR 4.5 4.7 - - - +
81C LYS* 3.8 38.6 - - + +
246C PRO* 3.3 22.0 - - + +
247C TYR* 4.5 4.5 - - - +
248C ASP 3.9 5.6 - - - +
249C GLU* 1.3 86.9 - - - +
251C LEU* 1.3 64.3 + - + +
253C ALA* 3.6 5.0 - - + +
254C ASN* 2.9 39.2 + - - +
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Residues in contact with LEU 251 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B MET 3.3 4.0 - - - +
227B ALA* 3.4 27.6 - - + +
229B PRO* 3.7 13.2 - - + -
262B HIS* 5.1 0.7 + - - -
266B ASN* 5.9 1.8 - - - +
79C LYS 5.9 0.4 - - - +
80C THR* 5.6 0.9 - - - -
81C LYS* 3.9 39.5 - - + +
83C ARG* 3.3 37.7 - - - +
249C GLU* 3.3 1.3 - - - +
250C PRO* 1.3 83.0 - - + +
252C LEU* 1.3 60.6 + - - +
254C ASN* 3.2 11.1 + - - +
255C SER* 2.9 30.1 + - - -
307C ARG* 5.5 18.8 - - + -
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Residues in contact with LEU 252 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224B ASP* 6.5 0.2 - - + -
226B MET* 3.3 37.6 + - + -
227B ALA* 3.9 15.9 - - + +
217C LEU* 4.1 15.3 - - + -
221C LYS* 5.7 9.2 - - - +
245C PHE* 3.9 21.8 - - + -
249C GLU* 3.5 26.9 + - + +
250C PRO 3.4 0.4 - - - -
251C LEU* 1.3 78.0 - - - +
253C ALA* 1.3 58.2 + - - +
255C SER* 3.2 0.9 + - - -
256C LEU* 2.9 47.7 + - + +
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Residues in contact with ALA 253 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237C TYR* 2.8 33.5 + - - +
245C PHE* 3.9 21.7 - - + -
246C PRO* 4.2 9.2 - - + -
249C GLU 2.8 18.5 + - - +
250C PRO* 3.6 8.5 - - + +
251C LEU 3.2 0.2 - - - -
252C LEU* 1.3 75.3 - - - +
254C ASN* 1.3 59.8 + - - +
256C LEU 3.4 0.3 + - - -
257C LEU* 2.8 17.7 + - - +
303C GLN* 3.8 14.8 - - - +
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Residues in contact with ASN 254 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262B HIS* 3.8 13.6 - - + +
79C LYS 5.9 0.2 + - - -
250C PRO* 2.9 29.0 + - - +
251C LEU* 3.6 7.9 - - - +
253C ALA* 1.3 71.8 - - - +
255C SER* 1.3 61.6 + - - +
257C LEU* 3.3 7.1 + - - +
258C THR* 2.9 33.2 + - - -
303C GLN* 3.6 21.3 + - - +
307C ARG* 3.0 41.6 + - - +
308C LYS* 3.9 17.3 - - + +
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Residues in contact with SER 255 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225B PHE 4.8 0.2 + - - -
226B MET* 2.3 48.4 + - - -
229B PRO* 6.0 0.3 - - - +
259B GLN* 3.2 32.1 + - - +
262B HIS* 4.3 7.7 + - - -
251C LEU 2.9 7.3 + - - -
252C LEU 3.2 6.3 + - - -
254C ASN* 1.3 76.8 - - - +
256C LEU* 1.3 58.9 + - - +
258C THR* 3.2 3.0 + - - -
259C GLN* 2.9 24.9 + - - +
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Residues in contact with LEU 256 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B MET* 3.7 19.7 - - + -
217C LEU* 4.8 21.5 - - + -
220C LEU* 5.3 0.7 - - + -
225C PHE* 3.9 22.4 - - + -
233C LEU* 3.8 28.3 - - + -
237C TYR* 3.8 24.2 - - + -
245C PHE* 5.9 2.5 - - + -
252C LEU* 2.9 45.7 + - + +
253C ALA* 4.7 0.7 - - - -
255C SER* 1.3 74.4 - - - +
257C LEU* 1.3 60.3 + - - +
259C GLN* 3.3 4.0 + - + +
260C CYS* 2.8 33.7 + - - -
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Residues in contact with LEU 257 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237C TYR* 3.5 27.1 - - + +
253C ALA 2.8 19.4 + - - +
254C ASN* 3.4 8.3 - - - +
255C SER 3.2 0.2 - - - -
256C LEU* 1.3 77.0 - - - +
258C THR* 1.3 57.3 + - - +
260C CYS* 3.1 4.0 + - - +
261C ILE* 2.9 47.4 + - + +
296C LEU* 4.0 20.2 - - + +
299C CYS* 4.9 1.6 - - + -
300C ASP* 4.2 31.2 - - - +
303C GLN* 3.4 17.5 - - + +
308C LYS* 4.4 22.4 - - + -
310C ILE 5.1 1.1 - - - +
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Residues in contact with THR 258 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258B THR* 3.7 18.6 - - + +
259B GLN* 3.3 15.5 - - - +
262B HIS* 2.8 34.9 + - + -
310B ILE* 4.5 2.6 - - + +
254C ASN 2.9 10.8 + - - -
255C SER 3.4 9.2 - - - -
257C LEU* 1.3 76.7 - - - +
259C GLN* 1.3 55.1 + - - +
261C ILE* 3.3 8.3 + - - +
262C HIS* 2.9 28.8 + - - +
310C ILE* 3.7 27.8 - - + +
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Residues in contact with GLN 259 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B MET* 3.8 17.0 - - + -
255B SER* 3.4 40.8 + - - +
258B THR* 4.0 7.8 - - - +
259B GLN* 3.0 17.7 - - - +
225C PHE* 3.7 11.1 + - + -
226C MET* 3.4 26.1 - - - +
229C PRO* 6.0 1.2 - - - +
233C LEU* 3.9 15.0 - - + +
255C SER 2.9 17.4 + - - +
256C LEU* 3.5 9.6 - - - +
257C LEU 3.3 0.2 - - - -
258C THR* 1.3 75.3 - - - +
260C CYS* 1.3 54.0 + - - +
262C HIS* 3.4 7.2 + - - +
263C THR* 2.6 39.4 + - - -
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Residues in contact with CYS 260 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233C LEU* 4.0 13.9 - - - -
234C VAL* 3.6 33.3 - - + +
237C TYR* 3.6 33.4 - - - -
256C LEU 2.8 23.7 + - - +
257C LEU* 3.1 8.0 + - - +
259C GLN* 1.3 74.7 - - - +
261C ILE* 1.3 61.2 + - - +
263C THR* 3.2 1.6 + - - -
264C PHE* 2.8 31.3 + - - +
296C LEU* 4.4 15.9 - - + -
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Residues in contact with ILE 261 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310B ILE* 4.4 9.4 - - + -
257C LEU* 2.9 36.1 + - + +
258C THR* 4.0 4.9 - - - +
260C CYS* 1.3 75.5 - - - +
262C HIS* 1.3 57.1 - - - +
264C PHE* 3.9 5.1 - - + +
265C LYS* 2.9 45.2 + - + +
296C LEU* 4.3 8.7 - - + -
300C ASP* 3.7 23.8 - - + +
310C ILE* 4.5 22.7 - - + +
311C ALA 5.7 0.9 - - - +
312C LEU* 3.8 41.1 - - + -
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Residues in contact with HIS 262 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254B ASN* 3.8 15.6 - - + +
255B SER* 3.7 25.0 + - - -
258B THR* 3.3 37.4 + - + +
307B ARG 3.8 11.4 + - - -
308B LYS* 4.8 2.9 - - + -
309B PRO* 3.4 35.4 - - + +
310B ILE* 3.7 11.6 - - + +
229C PRO* 5.2 7.4 - - + +
258C THR 2.9 18.0 + - - +
259C GLN* 3.4 9.4 - - - +
261C ILE* 1.3 77.4 - - - +
263C THR* 1.3 61.7 + - - +
266C ASN* 3.1 34.2 + - - +
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Residues in contact with THR 263 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229C PRO* 3.6 21.8 - - + +
230C ASP* 3.6 44.6 - - - +
231C ILE* 4.2 4.7 - - + +
233C LEU* 4.0 9.2 - - - +
234C VAL* 4.4 7.9 - - + -
259C GLN* 2.6 24.4 + - - +
260C CYS 3.2 3.8 + - - -
262C HIS* 1.3 76.6 - - - +
264C PHE* 1.3 64.4 + - - +
266C ASN* 3.2 19.3 + - + +
267C PHE* 3.4 16.7 - - + -
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Residues in contact with PHE 264 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231C ILE* 4.5 19.7 - - + -
234C VAL* 4.7 1.5 - - + +
260C CYS 2.8 18.4 + - - +
261C ILE* 3.9 4.5 - - - +
263C THR* 1.3 78.7 - - - +
265C LYS* 1.3 79.0 + - + +
266C ASN 3.2 1.2 + - - -
267C PHE* 3.3 17.4 + - - +
268C HIS 4.0 2.3 + - - -
269C VAL* 4.4 14.5 + - + +
272C PHE* 3.7 18.6 - + - -
289C LEU* 3.9 36.8 - - + +
292C ILE* 5.3 5.8 - - + -
293C PHE* 3.4 41.5 - + + -
296C LEU* 4.5 16.6 - - + -
312C LEU* 5.0 6.1 - - + -
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Residues in contact with LYS 265 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309B PRO* 3.6 26.5 + - + +
310B ILE* 5.0 5.9 - - + +
261C ILE* 2.9 28.5 + - + +
264C PHE* 1.3 88.8 - - + +
266C ASN* 1.3 62.3 + - - +
267C PHE 3.1 2.2 - - - -
268C HIS* 3.1 34.4 + - - +
269C VAL 5.7 0.2 - - - +
311C ALA 5.3 1.6 + - - -
312C LEU* 3.6 30.8 - - - +
315C GLU* 3.9 20.4 + - - +
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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