Contacts of the helix formed by residues 283 - 299 (chain B) 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 THR 283 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B PHE* 4.2 9.6 - - + -
119B ARG* 6.2 0.2 - - - +
267B PHE* 3.6 2.9 - - - -
271B MET* 3.6 4.3 - - - -
280B SER 5.2 4.5 - - - +
281B GLU* 3.1 8.5 + - - +
282B PHE* 1.3 75.3 - - - +
284B ILE* 1.3 69.4 + - - +
285B GLU* 3.6 14.9 + - + +
286B ASN* 2.8 37.8 + - + +
287B LEU 3.0 9.0 + - - -
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Residues in contact with ILE 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B LEU* 3.8 28.9 - - + -
248B VAL* 4.7 13.7 - - + -
252B GLN* 5.1 9.6 - - - +
268B LEU* 4.3 13.5 - - + -
271B MET* 3.5 30.6 - - + +
283B THR* 1.3 75.4 + - - +
285B GLU* 1.3 63.0 + - - +
287B LEU* 3.0 14.9 + - - +
288B VAL* 3.1 17.0 + - + +
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Residues in contact with GLU 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B ARG* 2.8 36.4 + - - +
110B PHE* 3.5 31.6 - - + -
283B THR* 3.0 10.4 + - + +
284B ILE* 1.3 80.9 - - - +
286B ASN* 1.3 61.6 + - - +
287B LEU 3.1 1.4 + - - -
288B VAL* 3.4 6.0 + - - +
289B ILE* 3.1 32.6 + - + +
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Residues in contact with ASN 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B PHE* 3.0 34.5 - - - +
111B GLY 3.4 3.3 + - - -
119B ARG* 3.2 24.3 - - - +
123B ILE* 3.0 29.9 - - - +
267B PHE* 4.1 6.9 - - + -
281B GLU* 2.9 27.0 + - - +
283B THR* 2.8 21.2 + - + +
285B GLU* 1.3 74.3 - - - +
287B LEU* 1.3 58.7 + - - +
289B ILE* 4.1 1.8 - - - +
290B THR* 2.8 28.8 + - - -
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Residues in contact with LEU 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248B VAL* 3.4 42.0 - - + -
263B PHE* 4.5 16.4 - - + -
264B ILE* 4.4 14.1 - - + -
267B PHE* 3.2 52.5 - - + -
268B LEU* 3.8 11.9 - - + -
283B THR 3.0 3.8 + - - +
284B ILE* 3.0 14.3 + - - +
286B ASN* 1.3 76.5 - - - +
288B VAL* 1.3 67.0 + - - +
289B ILE 3.1 1.3 - - - -
290B THR* 3.1 3.6 + - - -
291B ALA* 2.9 26.5 + - + +
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Residues in contact with VAL 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241B GLU* 3.1 45.8 - - + +
244B ILE* 3.8 15.8 - - + +
245B LEU* 4.0 32.3 - - + -
248B VAL* 4.7 7.6 - - + -
284B ILE* 3.1 17.2 + - + +
285B GLU* 3.9 6.5 - - - +
287B LEU* 1.3 75.6 - - - +
289B ILE* 1.3 59.2 + - + +
291B ALA* 3.6 1.9 + - - +
292B ALA* 3.0 28.1 + - - +
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Residues in contact with ILE 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B ALA 4.6 3.8 - - - +
107B ASN* 4.0 29.4 - - + +
110B PHE* 3.4 24.0 - - + +
111B GLY* 3.3 29.2 - - - +
241B GLU* 3.1 30.7 - - + +
285B GLU* 3.1 23.7 + - + +
286B ASN 4.3 0.7 - - - +
287B LEU 3.1 0.6 - - - -
288B VAL* 1.3 78.1 - - + +
290B THR* 1.3 60.1 + - - +
292B ALA* 3.5 3.3 + - + +
293B ASP* 2.9 30.6 + - - +
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Residues in contact with THR 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B GLY* 3.9 12.9 - - - -
112B ILE* 4.3 17.0 - - + +
123B ILE* 3.3 23.8 - - + +
127B SER* 4.5 0.9 - - - +
263B PHE* 3.8 31.9 - - + -
267B PHE* 5.0 3.6 - - + -
286B ASN 2.8 20.8 + - - -
287B LEU* 3.1 6.6 + - - -
289B ILE* 1.3 79.0 - - - +
291B ALA* 1.3 65.0 + - - +
293B ASP* 3.1 5.5 + - - +
294B LEU* 2.9 30.7 + - + +
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Residues in contact with ALA 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B ILE* 3.8 30.3 - - + +
244B ILE* 3.8 23.8 - - + -
263B PHE* 5.3 3.6 - - + -
264B ILE* 6.3 0.4 - - + -
287B LEU* 2.9 22.2 + - + +
288B VAL 3.7 4.3 - - - +
290B THR* 1.3 78.5 - - - +
292B ALA* 1.3 65.2 + - - +
293B ASP 3.0 0.5 + - - -
294B LEU* 3.1 7.5 + - - +
295B LEU* 2.9 24.4 + - - +
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Residues in contact with ALA 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B LEU* 5.5 0.2 - - - +
237B LEU* 5.3 10.1 - - + +
240B MET* 5.1 9.9 - - - +
241B GLU* 4.1 20.2 - - + +
244B ILE* 3.7 18.9 - - + +
288B VAL 3.0 16.1 + - - +
289B ILE* 3.8 6.1 - - + +
291B ALA* 1.3 78.4 - - - +
293B ASP* 1.3 64.2 + - - +
295B LEU* 3.6 8.1 - - - +
296B GLY* 3.2 18.0 + - - -
502B 0XV 4.9 1.7 - - - +
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Residues in contact with ASP 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B ASN* 3.2 33.6 + - - +
111B GLY* 3.8 1.6 - - - -
112B ILE* 3.3 12.1 + - + +
113B VAL* 3.2 38.5 + - + +
289B ILE* 2.9 21.0 + - - +
290B THR* 3.3 7.4 - - - +
291B ALA 3.0 0.2 - - - -
292B ALA* 1.3 75.4 - - - +
294B LEU* 1.3 68.3 + - + +
295B LEU 3.1 1.5 + - - -
296B GLY 3.2 3.5 + - - -
297B ALA* 3.0 26.3 + - - +
501B HEM 5.8 0.7 - - + -
502B 0XV 3.4 16.4 - - - +
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Residues in contact with LEU 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B ILE* 5.2 5.2 - - + -
127B SER* 5.2 3.1 - - - +
131B LEU* 5.0 8.1 - - + -
178B ILE* 4.4 9.0 - - + +
181B ILE* 6.6 0.2 - - + -
182B ILE* 4.7 11.9 - - + -
263B PHE* 4.0 26.9 - - + -
290B THR* 2.9 39.4 + - + +
291B ALA* 3.7 5.8 - - - +
293B ASP* 1.3 74.1 - - + +
295B LEU* 1.3 61.4 + - - +
297B ALA* 3.8 4.2 - - - +
298B GLY* 3.0 23.0 + - - -
436B VAL* 4.9 8.1 - - + -
501B HEM 3.8 54.8 - - + +
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Residues in contact with LEU 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B CYS* 5.0 2.7 - - - +
178B ILE* 3.9 25.0 - - + +
179B CYS* 4.4 21.3 - - - -
182B ILE* 4.0 10.3 - - + -
183B PHE* 5.3 5.2 - - + -
197B LEU* 3.5 33.7 - - + -
201B LEU* 3.9 13.5 - - + +
240B MET* 3.9 20.6 - - + -
244B ILE* 4.9 10.5 - - + -
291B ALA 2.9 16.3 + - - +
292B ALA* 3.6 5.2 - - - +
294B LEU* 1.3 79.6 - - - +
296B GLY* 1.3 58.2 + - - +
297B ALA 3.2 3.6 + - - -
299B THR* 3.1 29.8 + - - +
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Residues in contact with GLY 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201B LEU* 4.0 16.1 - - - +
205B ILE* 4.4 15.0 - - - +
292B ALA 3.2 8.3 + - - -
293B ASP 3.2 7.1 + - - -
295B LEU* 1.3 78.3 - - - +
297B ALA* 1.3 57.6 + - - +
298B GLY 3.8 0.2 - - - -
299B THR* 4.8 3.6 - - - -
300B GLU* 5.1 2.8 - - - +
502B 0XV 3.6 33.6 - - - +
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Residues in contact with ALA 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B VAL* 4.8 1.3 - - + -
293B ASP 3.0 17.6 + - - +
294B LEU* 3.8 2.2 - - - +
295B LEU 3.1 0.2 - - - -
296B GLY* 1.3 79.8 - - - +
298B GLY* 1.3 60.2 + - - +
299B THR 3.6 1.1 - - - -
301B THR* 2.7 25.4 + - - +
501B HEM 3.1 40.3 + - + -
502B 0XV 3.0 27.6 - - + +
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Residues in contact with GLY 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B PRO* 3.5 10.7 - - - +
178B ILE* 4.3 11.7 - - - +
294B LEU 3.0 12.0 + - - -
295B LEU 4.3 0.4 - - - -
297B ALA* 1.3 78.9 - - - +
299B THR* 1.3 59.9 + - - +
301B THR* 3.5 5.8 - - - -
302B THR* 3.2 16.3 + - - -
444B GLU* 4.6 1.0 - - - +
501B HEM 3.4 30.7 - - - +
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Residues in contact with THR 299 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B GLY 4.3 7.9 - - - +
174B PRO* 3.9 7.1 - - - +
175B CYS* 3.4 39.6 - - + +
178B ILE* 4.5 4.0 - - - +
198B MET* 4.8 7.0 - - + -
201B LEU* 4.1 17.5 - - + +
202B ASN* 5.0 8.3 - - - +
295B LEU* 3.1 20.8 + - - +
296B GLY* 5.3 1.3 - - - -
297B ALA 3.6 1.0 - - - -
298B GLY* 1.3 79.0 - - - +
300B GLU* 1.3 72.8 + - + +
301B THR 3.1 1.3 + - - -
302B THR 3.3 1.6 + - - -
303B SER* 2.9 27.1 + - - -
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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
------------------------------------------------------------
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