Contacts of the helix formed by residues 279 - 299 (chain B) in PDB entry 1R88
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 279 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237B SER* 4.4 4.0 - - - -
238B ASP* 5.7 2.7 - - - -
241B ALA* 5.6 2.5 - - - -
277B ASP* 3.2 15.8 + - - +
278B ASN* 1.3 77.2 - - - +
280B TRP* 1.3 65.0 + - - -
281B GLY 3.3 2.7 - - - -
282B SER* 3.1 6.9 + - - -
283B TRP* 3.1 41.8 + - - -
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Residues in contact with TRP 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B ASP* 3.4 22.0 - - - -
67B ALA* 4.4 8.6 - - + +
69B ASN* 5.4 1.4 + - - -
76B ASN* 3.5 22.4 - - + +
77B TRP* 3.5 65.1 - + - -
80B ALA* 3.7 27.7 - - + +
81B GLY* 3.9 18.2 - - - -
144B ALA* 4.9 1.1 - - + -
237B SER* 5.0 2.0 + - - -
238B ASP* 5.9 5.4 - - + -
241B ALA* 5.3 5.9 - - + +
277B ASP* 4.3 0.4 + - - -
279B GLY* 1.3 71.6 - - - -
281B GLY* 1.3 62.4 + - - +
283B TRP* 3.6 34.0 - + + -
284B ALA* 3.1 28.9 + - - +
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Residues in contact with GLY 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237B SER* 5.6 0.6 + - - -
277B ASP* 4.6 7.7 + - - -
279B GLY 3.2 1.6 + - - -
280B TRP* 1.3 77.4 - - - +
282B SER* 1.3 57.2 + - - +
285B PRO* 3.2 19.5 - - - +
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Residues in contact with SER 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229B TRP* 3.5 19.2 - - - -
276B GLY* 3.7 7.3 - - - -
277B ASP* 3.0 46.2 + - - +
279B GLY 3.1 2.0 + - - -
281B GLY* 1.3 77.4 + - - +
283B TRP* 1.3 63.7 + - - +
284B ALA 3.4 1.6 - - - -
285B PRO* 3.4 7.4 - - - +
286B GLN* 3.1 25.1 + - - +
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Residues in contact with TRP 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B ALA* 3.9 22.9 - - + -
77B TRP* 3.8 6.9 - - + -
144B ALA* 3.5 26.7 - - + -
145B ALA* 4.5 1.8 - - + -
168B MET* 3.6 31.1 - - + +
169B SER* 3.1 25.2 + - - -
229B TRP* 3.7 20.0 - + - -
241B ALA* 4.2 8.7 - - + -
242B MET* 3.8 22.4 - - - -
278B ASN 3.4 9.0 - - - -
279B GLY* 3.1 45.4 + - - +
280B TRP* 3.4 37.7 + + + -
282B SER* 1.3 74.6 - - - +
284B ALA* 1.3 64.8 + - - +
286B GLN* 3.3 2.4 + - - +
287B LEU 3.1 18.2 + - - -
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Residues in contact with ALA 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B TRP* 4.6 1.8 - - - -
80B ALA 3.9 14.4 - - - +
81B GLY* 3.6 28.2 - - - +
82B ASN* 4.9 5.4 - - + -
86B THR* 4.7 6.2 + - - -
280B TRP* 3.1 15.5 + - - +
283B TRP* 1.3 76.2 - - - +
285B PRO* 1.3 70.6 - - + +
287B LEU* 3.2 18.4 + - - +
288B GLY 3.6 3.8 + - - -
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Residues in contact with PRO 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B GLY 3.2 26.5 - - - +
282B SER* 3.4 12.6 - - - +
284B ALA* 1.3 95.9 - - + +
286B GLN* 1.3 58.7 + - - +
288B GLY* 3.2 5.8 + - - +
289B ALA* 3.1 19.6 + - - +
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Residues in contact with GLN 286 (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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168B MET* 3.8 20.9 - - + -
227B TRP* 3.2 38.4 - - - +
229B TRP* 3.3 48.3 + - + -
271B ASP* 4.7 6.6 + - - +
282B SER 3.1 20.8 + - - +
283B TRP 3.5 6.1 - - - +
284B ALA 3.2 0.2 - - - -
285B PRO* 1.3 74.2 - - - +
287B LEU* 1.3 64.6 + - - +
289B ALA* 3.3 12.2 + - - +
290B MET* 3.1 23.1 + - + +
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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
----------------------------------------------------------
64B LEU* 4.1 19.7 - - + -
77B TRP* 3.7 28.3 - - + -
81B GLY 4.5 2.7 - - - +
83B ALA* 4.0 19.1 - - + -
86B THR* 4.0 9.4 - - + -
87B LEU* 3.9 29.2 - - + -
142B VAL* 4.4 11.9 - - + -
168B MET* 3.7 4.9 - - + +
283B TRP 3.1 11.3 + - - +
284B ALA 3.2 10.3 + - - +
286B GLN* 1.3 76.6 - - - +
288B GLY* 1.3 62.2 + - - +
290B MET* 3.4 3.4 + - + +
291B SER* 3.1 23.6 + - - -
294B ILE* 4.4 18.4 - - + -
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Residues in contact with GLY 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B THR* 3.5 20.9 - - - +
284B ALA 3.6 4.2 + - - -
285B PRO* 3.2 8.9 + - - -
287B LEU* 1.3 79.4 - - - +
289B ALA* 1.3 59.5 + - - +
291B SER* 2.8 22.0 + - - -
292B GLY 4.6 0.3 + - - -
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Residues in contact with ALA 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227B TRP* 3.9 12.6 - - + -
285B PRO 3.1 12.0 + - - +
286B GLN* 3.3 26.7 + - - +
288B GLY* 1.3 76.4 - - - +
290B MET* 1.3 58.3 + - - +
292B GLY* 4.8 2.6 + - - -
293B ASP 5.3 0.7 + - - -
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Residues in contact with MET 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B VAL* 4.0 24.0 - - + -
164B PHE* 4.3 4.9 - - - -
166B GLY* 4.6 5.6 - - - -
168B MET* 3.7 32.1 - - + -
227B TRP* 3.1 73.1 - - + +
286B GLN* 3.1 14.2 + - + +
287B LEU* 3.7 7.6 - - + +
288B GLY 3.3 0.2 - - - -
289B ALA* 1.3 74.8 - - - +
291B SER* 1.3 64.6 + - - +
292B GLY 3.3 2.7 - - - -
293B ASP* 3.1 6.0 + - - +
294B ILE* 3.0 44.5 + - + +
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Residues in contact with SER 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B THR* 4.9 1.1 - - - +
87B LEU* 3.9 19.9 - - - +
90B LYS* 4.0 25.7 + - - -
287B LEU 3.1 16.0 + - - -
288B GLY* 2.8 20.4 + - - -
290B MET* 1.3 77.0 - - - +
292B GLY* 1.3 63.1 + - - +
294B ILE* 3.3 10.9 + - - +
295B VAL* 3.1 30.0 + - - +
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Residues in contact with GLY 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B LYS* 6.3 0.2 - - - -
288B GLY 4.6 0.4 + - - -
289B ALA 4.8 2.8 + - - -
290B MET 3.3 0.6 - - - -
291B SER* 1.3 82.8 + - - +
293B ASP* 1.3 56.8 + - - +
295B VAL* 3.7 6.0 + - - +
296B GLY* 3.1 23.7 + - - -
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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
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164B PHE* 3.4 18.1 - - + -
225B ARG* 3.0 39.6 + - - -
227B TRP* 3.4 37.5 - - + -
289B ALA 5.3 1.2 + - - +
290B MET 3.1 6.7 + - - +
292B GLY* 1.3 75.0 - - - +
294B ILE* 1.3 64.7 + - - +
296B GLY* 3.5 1.5 + - - +
297B ALA* 3.2 22.7 + - - +
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Residues in contact with ILE 294 (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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62B VAL* 4.2 8.3 - - + -
87B LEU* 4.9 6.1 - - + -
92B ILE* 3.8 22.7 - - + -
140B ALA* 3.9 22.7 - - + -
142B VAL* 4.0 11.7 - - + -
164B PHE* 3.6 28.3 - - + -
287B LEU* 4.4 12.6 - - + -
290B MET* 3.0 40.9 + - + +
291B SER* 3.3 12.3 + - - +
293B ASP* 1.3 76.6 - - - +
295B VAL* 1.3 62.7 + - - +
297B ALA* 3.1 4.3 + - - +
298B ILE* 3.1 25.5 + - + +
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Residues in contact with VAL 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B LEU* 6.3 0.2 - - + -
90B LYS* 3.7 35.9 - - + +
92B ILE* 4.2 20.4 - - + -
291B SER 3.1 18.2 + - - +
292B GLY* 4.0 6.3 - - - +
294B ILE* 1.3 77.1 - - - +
296B GLY* 1.3 59.4 + - - +
299B ARG* 3.0 68.4 + - + +
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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
----------------------------------------------------------
292B GLY 3.1 17.2 + - - -
293B ASP* 3.9 2.7 - - - -
294B ILE 3.3 0.4 - - - -
295B VAL* 1.3 78.0 - - - +
297B ALA* 1.3 59.3 + - - +
299B ARG 5.0 4.3 + - - -
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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
----------------------------------------------------------
163B GLY 5.1 2.2 - - - +
164B PHE* 3.8 22.2 - - + -
225B ARG* 4.3 15.3 - - + -
293B ASP 3.2 16.2 + - - +
294B ILE 3.1 5.2 + - - +
296B GLY* 1.3 79.0 - - - +
298B ILE* 1.3 64.4 + - + +
299B ARG 5.3 0.4 - - - -
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Residues in contact with ILE 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B HIS* 3.0 30.9 + - + -
61B ALA 3.5 35.4 - - - +
92B ILE* 3.7 26.5 - - + -
138B GLY 3.3 23.1 - - - +
139B HIS 3.9 13.9 - - - +
140B ALA* 4.0 10.1 - - + +
163B GLY 5.3 1.8 - - - -
164B PHE* 4.1 11.4 - - + +
294B ILE* 3.1 32.2 + - + +
297B ALA* 1.3 81.1 - - + +
299B ARG* 1.3 66.8 + - - +
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Residues in contact with ARG 299 (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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60B HIS* 4.8 7.1 - - - -
90B LYS* 3.3 27.8 + - - +
91B GLY* 3.6 25.9 - - - +
92B ILE* 4.0 14.8 - - + -
295B VAL* 3.0 33.4 + - + +
296B GLY 5.1 4.7 - - - -
297B ALA 5.3 0.4 - - - -
298B ILE* 1.3 81.7 - - - +
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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