Contacts of the helix formed by residues 261 - 273 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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236A GLY 4.0 4.7 - - - -
237A CYS* 2.0 51.6 - - + -
238A GLN* 3.1 27.1 - - - +
259A ALA* 3.3 3.4 - - - +
260A ALA* 1.3 75.4 - - - +
262A ASN* 1.3 62.3 + - - +
264A LEU* 3.3 7.0 + - - +
265A ARG* 3.1 42.8 + - - +
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Residues in contact with ASN 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204A THR* 2.8 34.2 + - - +
205A ASP* 3.2 28.0 - - - +
232A LYS 3.4 15.1 - - - +
233A GLU* 3.9 6.3 - - - +
234A MET* 3.0 38.9 - - - +
237A CYS* 3.6 13.6 + - - +
238A GLN 4.4 10.1 + - - +
239A LYS* 5.4 4.9 - - - +
240A ASN* 5.6 3.9 + - - +
259A ALA 4.8 3.7 + - - +
260A ALA 3.4 0.6 - - - -
261A CYS* 1.3 78.9 - - - +
263A HIS* 1.3 62.0 + - - +
265A ARG* 3.4 5.0 + - - +
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Residues in contact with HIS 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A PHE* 4.3 18.6 - + + +
151A HIS* 2.9 29.8 + + - -
152A SER* 2.8 41.3 + - - -
176A ASP* 2.9 43.9 + - - +
178A ALA* 4.8 0.9 - - - -
204A THR* 3.8 1.1 + - - -
205A ASP* 3.7 14.0 + - - +
215A PHE* 3.8 34.9 - + + +
258A PHE* 4.9 7.9 - + + -
260A ALA* 3.3 9.7 + - - +
262A ASN* 1.3 80.3 - - - +
264A LEU* 1.3 60.4 + - + +
265A ARG 3.5 0.3 + - - -
266A SER* 3.1 12.6 + - - -
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Residues in contact with LEU 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A PHE* 3.9 28.3 - - + +
79A ASP* 3.8 32.5 - - + +
82A GLU* 3.9 8.3 - - + -
151A HIS* 3.8 22.9 - - + -
260A ALA* 3.1 20.9 + - + +
261A CYS* 3.3 5.4 + - - +
263A HIS* 1.3 77.2 - - + +
265A ARG* 1.3 65.2 + - - +
266A SER 3.2 1.7 + - - -
267A TYR* 3.2 39.0 + - + +
268A LYS* 3.3 28.6 + - - +
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Residues in contact with ARG 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204A THR* 4.3 0.4 - - + -
234A MET* 3.9 8.7 - - + -
235A PRO 3.3 18.8 + - - -
236A GLY* 3.8 13.9 + - - -
237A CYS* 3.8 14.3 - - - -
261A CYS* 3.1 32.4 + - - +
262A ASN 3.6 9.2 - - - +
263A HIS 3.3 0.8 - - - -
264A LEU* 1.3 76.6 - - - +
266A SER* 1.3 63.7 + - - +
268A LYS* 2.9 19.4 + - - +
269A TYR* 2.9 63.1 + - + +
331A ASP 3.0 26.9 + - - -
332A ALA* 4.7 1.2 - - - +
335A PHE* 3.8 24.9 - - - -
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Residues in contact with SER 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A HIS* 3.1 23.0 - - - -
175A LEU* 3.5 20.5 - - - +
176A ASP* 3.5 13.2 - - - +
202A ILE* 4.1 13.6 - - - +
204A THR* 3.6 28.1 + - - +
263A HIS 3.1 16.1 + - - -
265A ARG* 1.3 77.9 - - - +
267A TYR* 1.3 59.5 + - - +
269A TYR* 3.6 3.3 + - - +
270A TYR* 3.1 20.6 + - - +
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Residues in contact with TYR 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A PHE 5.1 1.4 + - - -
82A GLU* 2.6 37.7 + - - +
85A TRP* 3.5 60.5 - + + -
89A MET* 3.8 1.5 - - + +
151A HIS* 3.5 43.5 - + + -
175A LEU* 3.7 23.3 - - + -
264A LEU* 3.2 27.2 + - + +
266A SER* 1.3 78.6 + - - +
268A LYS* 1.3 77.5 + - + +
270A TYR* 3.8 2.2 - - - +
271A THR* 2.8 36.6 + - - -
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Residues in contact with LYS 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A GLU* 3.2 38.8 + - - -
264A LEU* 3.3 39.8 + - - +
265A ARG* 2.9 25.7 + - - +
267A TYR* 1.3 86.1 - - + +
269A TYR* 1.3 65.8 + - - +
271A THR* 3.5 7.2 + - - -
272A ASP* 3.2 22.9 + - - +
335A PHE* 3.8 28.4 - - + -
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Residues in contact with TYR 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202A ILE* 4.8 2.0 - - + -
204A THR* 3.8 24.0 - - + -
228A PRO* 3.9 14.6 - - + -
229A ASN* 3.2 10.3 + - - -
234A MET* 3.5 20.7 - - - +
235A PRO* 4.6 2.1 - - - +
265A ARG* 2.9 35.5 + - + +
266A SER* 3.9 4.0 - - - +
268A LYS* 1.3 71.7 - - - +
270A TYR* 1.3 67.3 + - - +
272A ASP* 3.2 3.3 + - - +
273A SER* 2.9 24.0 + - - -
280A PHE* 4.1 7.9 - - + -
307A MET* 3.7 33.4 - - + -
329A THR* 3.2 29.4 + - + -
330A GLY 4.6 1.2 + - - -
335A PHE* 3.6 39.0 - + + -
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Residues in contact with TYR 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A MET* 3.7 33.2 - - + -
93A MET* 4.6 1.1 - - + -
147A HIS* 3.4 21.8 - - - -
149A ILE* 3.8 12.2 - - + +
171A ARG* 4.0 0.8 + - - -
173A THR* 3.9 32.1 - - + -
175A LEU* 4.0 13.0 - - + -
202A ILE* 4.3 3.8 - - + +
266A SER 3.1 18.4 + - - +
267A TYR 3.8 4.5 - - - +
268A LYS 3.3 0.2 - - - -
269A TYR* 1.3 75.9 - - - +
271A THR* 1.3 61.8 + - - +
273A SER* 2.7 24.9 + - - -
274A ILE* 3.5 11.3 + - + +
308A GLY* 3.6 30.1 - - - -
309A HIS* 3.1 38.8 + - + -
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Residues in contact with THR 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A TRP* 5.2 1.7 + - - -
88A THR* 4.3 16.8 - - - +
89A MET* 3.6 23.9 + - - +
92A ASN* 3.1 40.7 + - - +
267A TYR* 2.8 22.7 + - - -
268A LYS* 3.7 7.5 - - - -
270A TYR* 1.3 75.7 - - - +
272A ASP* 1.3 65.3 + - - +
274A ILE* 3.5 20.3 - - - +
275A LEU 4.3 0.7 + - - -
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Residues in contact with ASP 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A ASN* 5.1 3.1 + - - +
268A LYS 3.2 8.8 + - - +
269A TYR 3.2 5.1 + - - +
271A THR* 1.3 83.0 - - - +
273A SER* 1.3 64.7 + - - +
274A ILE 3.3 0.5 + - - -
275A LEU* 3.3 7.1 + - - +
276A ASN* 2.9 27.4 + - - +
280A PHE* 3.8 15.9 - - + -
333A SER* 2.7 27.7 + - - -
334A ASN* 3.4 12.8 - - - +
335A PHE* 3.0 32.5 + - + -
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Residues in contact with SER 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269A TYR 2.9 13.1 + - - -
270A TYR 2.7 18.4 + - - -
272A ASP* 1.3 75.6 - - - +
274A ILE* 1.3 60.6 + - - +
276A ASN 3.0 16.2 + - - +
280A PHE* 3.5 20.8 - - - -
307A MET* 3.7 21.5 - - - -
308A GLY* 3.3 4.5 - - - -
309A HIS* 2.8 25.8 + - - +
310A TYR* 3.3 17.0 - - - -
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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