Contacts of the helix formed by residues 261 - 273 (chain B) in PDB entry 1HPL
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 CYS 261 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79B ASP* 5.4 0.6 + - - -
236B GLY 4.2 0.4 - - - -
237B CYS* 2.0 50.9 - - + -
238B GLN* 3.1 32.7 + - - +
259B ALA 3.4 1.8 - - - -
260B ALA* 1.3 73.9 - - - +
262B ASN* 1.3 62.4 + - - +
264B LEU* 3.2 8.7 + - - +
265B ARG* 3.0 42.5 + - - +
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Residues in contact with ASN 262 (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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204B THR* 2.8 36.6 + - - +
205B ASP* 3.3 27.6 + - - +
232B LYS 3.4 13.5 + - - -
233B GLU* 3.9 7.5 - - - +
234B MET* 2.9 29.4 + - - +
237B CYS* 3.4 17.5 - - - +
238B GLN 4.7 10.4 + - - -
239B LYS* 5.6 4.9 - - - +
240B ASN* 5.4 5.8 - - - +
259B ALA 4.9 3.9 + - - +
260B ALA 3.3 0.6 - - - -
261B CYS* 1.3 78.6 - - - +
263B HIS* 1.3 60.5 + - - +
265B ARG* 3.3 7.4 + - - +
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Residues in contact with HIS 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B PHE* 4.0 19.6 - + + +
151B HIS* 2.9 34.5 + + - -
152B SER* 2.9 32.8 + - - -
176B ASP* 3.0 47.7 + - - +
178B ALA 5.0 0.9 - - - -
204B THR* 3.9 1.4 + - - -
205B ASP* 3.8 12.0 + - - +
215B PHE* 3.6 37.7 - + + +
258B PHE* 5.1 2.9 - + + -
260B ALA* 3.1 14.0 + - - +
262B ASN* 1.3 79.0 - - - +
264B LEU* 1.3 60.6 + - + +
266B SER* 3.1 13.0 + - - -
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Residues in contact with LEU 264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B PHE* 4.2 27.4 - - + +
79B ASP* 3.9 17.5 - - + +
82B GLU* 3.8 23.6 - - + +
151B HIS* 4.1 10.3 - - + -
260B ALA* 3.0 23.7 + - + +
261B CYS* 3.9 5.8 - - - +
263B HIS* 1.3 76.6 - - + +
265B ARG* 1.3 65.5 + - - +
266B SER 3.0 4.3 + - - -
267B TYR* 3.1 53.9 + - + +
268B LYS* 3.3 20.2 + - + +
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Residues in contact with ARG 265 (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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204B THR* 4.4 0.4 - - - -
234B MET* 3.8 8.7 - - + -
235B PRO 3.3 15.0 + - - -
236B GLY 3.9 15.2 + - - -
237B CYS* 3.7 11.8 - - - -
261B CYS* 3.0 33.6 + - - +
262B ASN 3.3 10.3 + - - +
264B LEU* 1.3 76.5 - - - +
266B SER* 1.3 54.8 + - - +
268B LYS* 3.0 21.1 + - - +
269B TYR* 2.9 69.8 + - + +
331B ASP 3.2 24.4 + - - -
332B ALA* 4.9 0.6 - - - +
335B PHE* 3.6 27.9 - - - -
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Residues in contact with SER 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B HIS* 3.3 15.8 - - - -
175B LEU* 3.6 22.9 - - - +
176B ASP* 3.7 11.5 - - - +
202B ILE* 4.0 11.8 - - - +
204B THR* 3.7 28.6 + - - +
263B HIS 3.1 16.3 + - - -
265B ARG* 1.3 74.3 - - - +
267B TYR* 1.3 63.0 + - - -
269B TYR* 3.6 3.6 + - - +
270B TYR* 3.2 20.4 + - - +
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Residues in contact with TYR 267 (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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77B PHE 5.2 1.2 + - - -
79B ASP 5.3 0.5 + - - -
82B GLU* 2.8 29.2 + - - +
85B TRP* 3.5 69.5 - + + -
89B MET* 4.6 1.4 - - - +
151B HIS* 3.5 40.8 - + - -
175B LEU* 3.7 17.9 - - + +
264B LEU* 3.1 38.6 + - + +
266B SER* 1.3 82.2 + - - +
268B LYS* 1.3 77.3 + - + +
270B TYR* 3.5 3.3 + - - +
271B THR* 2.7 34.6 + - - -
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Residues in contact with LYS 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B GLU* 3.2 34.4 + - - -
85B TRP* 5.6 0.6 - - - +
264B LEU* 3.3 21.0 + - + +
265B ARG* 3.0 34.3 + - - +
267B TYR* 1.3 87.4 - - + +
269B TYR* 1.3 65.4 + - - +
271B THR* 3.4 7.9 + - - -
272B ASP* 3.2 26.7 + - - +
335B PHE* 4.1 19.3 - - + -
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Residues in contact with TYR 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B ILE* 4.7 1.6 - - + -
204B THR* 3.9 26.0 - - + -
228B PRO* 3.9 12.1 - - + -
229B ASN* 3.0 19.8 + - - -
234B MET* 3.4 19.4 - - - +
235B PRO* 4.5 1.4 - - - +
265B ARG* 2.9 32.6 + - + +
266B SER* 3.8 4.5 - - - +
268B LYS* 1.3 71.6 - - - +
270B TYR* 1.4 68.8 + - - +
272B ASP* 3.1 5.5 + - - +
273B SER* 2.9 22.2 + - - -
280B PHE* 4.0 8.7 - - + -
307B MET* 3.8 31.6 - - + -
329B THR* 3.2 17.9 + - + -
330B GLY 4.7 0.9 + - - -
335B PHE* 3.5 46.9 - + + -
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Residues in contact with TYR 270 (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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89B MET* 3.6 19.5 - - + -
93B MET* 4.7 1.3 - - + -
147B HIS* 3.2 23.0 - - - -
149B ILE* 3.8 18.4 - - + +
171B ARG* 4.1 0.4 + - - -
173B THR* 3.7 22.7 - - + -
175B LEU* 3.8 26.0 - - + -
202B ILE* 4.4 3.2 - - + +
266B SER 3.2 12.5 + - - +
267B TYR* 3.6 9.9 - - - +
268B LYS 3.3 0.2 - - - -
269B TYR* 1.4 77.6 - - - +
271B THR* 1.3 62.8 + - - +
273B SER* 2.8 24.9 + - - -
274B ILE* 3.5 10.1 + - + +
308B GLY* 3.7 19.7 - - - -
309B HIS* 3.0 50.1 + + + -
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Residues in contact with THR 271 (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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85B TRP* 5.1 2.3 + - - -
88B THR* 4.3 18.6 + - - +
89B MET* 4.1 21.9 - - - +
92B ASN* 3.1 38.7 + - + +
267B TYR* 2.7 25.4 + - - -
268B LYS* 3.7 8.0 - - - -
269B TYR 3.3 0.2 - - - -
270B TYR* 1.3 72.5 - - - +
272B ASP* 1.3 65.7 + - - +
273B SER 3.5 0.2 + - - -
274B ILE* 3.5 20.1 + - - +
275B LEU 4.3 0.2 + - - -
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Residues in contact with ASP 272 (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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92B ASN* 4.9 3.9 + - - +
268B LYS 3.2 8.8 + - - +
269B TYR 3.1 8.2 + - - +
271B THR* 1.3 80.5 - - - +
273B SER* 1.3 64.1 + - - +
274B ILE 3.2 0.7 + - - -
275B LEU* 3.3 6.9 + - - +
276B ASN* 2.9 25.5 + - - +
280B PHE* 3.9 14.4 - - + -
333B SER* 2.8 28.4 + - - -
334B ASN* 3.4 10.9 - - - +
335B PHE* 3.0 33.4 + - + -
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Residues in contact with SER 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269B TYR 2.9 10.9 + - - -
270B TYR 2.8 18.1 + - - -
272B ASP* 1.3 76.3 - - - +
274B ILE* 1.3 61.6 + - - +
276B ASN 3.1 14.2 + - - +
280B PHE* 3.6 21.7 - - - -
306B GLN* 6.5 0.2 - - - -
307B MET 3.6 21.1 - - - -
308B GLY* 3.5 3.9 - - - -
309B HIS* 2.9 25.8 + - - +
310B TYR* 3.2 19.7 - - - -
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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
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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