Contacts of the helix formed by residues 262 - 274 (chain C) in PDB entry 4GQS
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 ASP 262 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136C MET* 3.7 18.6 - - + -
180C SER 4.4 1.6 - - - +
181C ILE 3.7 4.7 - - - +
182C ILE 3.2 11.7 - - - +
183C PHE* 2.7 38.7 - - - +
184C GLN* 3.0 2.9 + - - -
251C HIS* 2.9 22.8 + - - -
260C PRO* 3.5 1.8 - - - +
261C ARG* 1.3 83.9 - - - +
263C PHE* 1.3 66.4 + - - +
264C ILE 3.2 2.9 + - - -
265C ASP* 3.1 28.9 + - - +
266C CYS* 3.2 15.3 + - - -
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Residues in contact with PHE 263 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126C PHE* 3.7 28.8 - + - -
127C SER* 3.9 22.7 - - - -
130C THR* 3.6 24.7 - - + -
131C LEU* 4.6 13.5 - - + -
136C MET* 3.4 6.7 - - - -
181C ILE* 2.9 23.0 + - + +
182C ILE* 3.5 24.5 - - + -
262C ASP* 1.3 78.5 - - - +
264C ILE* 1.3 62.8 - - - +
266C CYS* 3.5 3.3 + - - +
267C PHE* 3.1 19.3 + + - +
287C LEU* 4.2 20.0 - - + -
290C THR* 4.1 17.5 - - + -
291C ALA* 5.1 3.8 - - + -
294C LEU* 3.9 22.4 - - + -
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Residues in contact with ILE 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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182C ILE* 3.3 26.4 + - + +
183C PHE* 3.9 23.6 - - + -
244C ILE* 5.4 0.7 - - + -
247C LYS 4.3 0.2 - - - +
248C VAL* 3.7 43.3 - - + +
251C HIS* 3.6 28.7 - - + +
262C ASP* 3.2 2.0 + - - +
263C PHE* 1.3 73.6 - - + +
265C ASP* 1.3 67.4 + - - +
267C PHE* 3.0 8.5 + - - +
268C LEU* 2.8 46.3 + - + +
287C LEU* 4.4 9.4 - - + -
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Residues in contact with ASP 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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251C HIS* 3.2 27.9 - - - +
255C MET* 3.8 15.9 - - - +
259C ASN 3.7 3.3 - - - +
260C PRO* 3.6 11.4 - - + +
261C ARG* 2.9 55.5 + - - +
262C ASP* 3.1 13.8 + - - +
264C ILE* 1.3 79.6 - - - +
266C CYS* 1.3 58.7 + - - +
268C LEU* 3.1 9.4 + - - +
269C ILE* 2.8 37.5 + - + +
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Residues in contact with CYS 266 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126C PHE* 3.7 16.4 - - + -
130C THR* 4.2 8.7 - - + +
135C GLY 4.9 2.7 - - - -
136C MET* 3.2 37.2 - - - -
260C PRO* 3.9 17.0 - - - -
262C ASP 3.2 11.5 + - - -
263C PHE 3.7 7.4 - - - +
264C ILE 3.3 0.2 - - - -
265C ASP* 1.3 77.6 - - - +
267C PHE* 1.3 58.2 + - - +
269C ILE* 3.3 11.8 + - - +
270C LYS* 2.8 28.2 + - - +
273C LYS* 5.1 2.6 + - - +
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Residues in contact with PHE 267 (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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123C ILE* 4.4 11.7 - - + -
126C PHE* 3.4 29.8 - + + -
263C PHE* 3.1 12.3 + + - +
264C ILE 3.0 9.1 + - - +
266C CYS* 1.3 76.2 - - - +
268C LEU* 1.3 58.5 + - - +
270C LYS* 2.7 24.6 + - - +
271C MET* 3.0 25.1 + - + +
282C PHE* 3.6 31.0 - + + -
283C THR 3.4 37.9 - - - -
286C ASN 4.7 1.6 - - - -
287C LEU* 3.3 57.2 - - + -
290C THR* 5.7 3.4 - - + -
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Residues in contact with LEU 268 (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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248C VAL* 4.3 16.6 - - + +
251C HIS* 3.6 30.5 - - + +
252C GLN* 3.5 33.3 - - + +
255C MET* 4.0 16.5 - - + +
264C ILE* 2.8 42.6 + - + +
265C ASP* 3.5 9.2 - - - +
267C PHE* 1.3 73.1 - - - +
269C ILE* 1.3 61.8 + - - +
271C MET* 3.3 40.6 + - + +
272C GLU* 3.6 6.6 + - - +
284C ILE* 5.1 0.9 - - + -
287C LEU* 4.8 1.1 - - + -
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Residues in contact with ILE 269 (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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255C MET* 3.6 23.1 - - + -
256C ASP 4.4 4.0 - - - +
257C ILE* 3.7 32.8 - - + +
260C PRO* 3.5 33.4 - - + -
265C ASP* 2.8 31.4 + - + +
266C CYS* 3.4 10.3 - - - +
268C LEU* 1.3 75.2 - - - +
270C LYS* 1.3 63.7 + - - +
271C MET 3.3 0.3 + - - -
272C GLU* 3.4 8.0 + - - +
273C LYS* 3.1 50.2 + - + +
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Residues in contact with LYS 270 (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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126C PHE* 4.0 15.7 - - + +
266C CYS 2.8 13.7 + - - +
267C PHE* 2.7 18.6 + - - +
269C ILE* 1.3 73.1 - - - +
271C MET* 1.3 59.0 + - - -
273C LYS* 3.2 25.2 + - + +
274C GLU* 3.1 41.9 + - - +
282C PHE* 3.5 55.9 - - + +
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Residues in contact with MET 271 (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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252C GLN* 4.9 3.1 - - - +
267C PHE* 3.0 29.4 + - + +
268C LEU* 3.4 50.7 - - + +
269C ILE 3.2 0.2 - - - -
270C LYS* 1.3 77.4 - - - +
272C GLU* 1.3 52.4 + - - +
274C GLU* 3.2 3.9 + - - -
275C LYS* 2.7 39.6 + - - +
280C SER* 5.7 0.4 - - - -
282C PHE* 3.6 29.6 - - + +
283C THR* 4.2 1.3 - - - -
284C ILE* 3.9 35.2 - - + -
287C LEU* 4.5 1.1 - - + -
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Residues in contact with GLU 272 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255C MET* 5.4 2.4 - - - +
257C ILE* 4.2 23.5 - - - +
268C LEU 3.6 6.3 + - - +
269C ILE* 3.4 9.7 + - + +
271C MET* 1.3 78.2 - - - +
273C LYS* 1.3 65.5 + - + +
275C LYS* 3.1 49.3 + - + +
276C GLN 4.7 0.3 + - - -
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Residues in contact with LYS 273 (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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257C ILE* 6.1 0.7 - - - -
266C CYS 5.1 1.8 + - - -
269C ILE* 3.1 39.6 - - + +
270C LYS* 3.3 30.4 - - + +
271C MET 3.2 0.2 - - - -
272C GLU* 1.3 80.4 - - + +
274C GLU* 1.3 63.2 + - + +
275C LYS 3.7 0.3 + - - -
276C GLN* 4.9 3.3 + - - +
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Residues in contact with GLU 274 (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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270C LYS* 3.1 36.0 + - - +
271C MET* 3.3 3.4 - - - +
273C LYS* 1.3 80.6 - - - +
275C LYS* 1.3 58.0 + - - +
276C GLN 3.1 3.4 - - - +
277C ASN* 2.9 53.1 + - + +
280C SER* 3.7 19.7 - - - +
282C PHE* 5.5 1.8 - - + -
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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