Contacts of the helix formed by residues 256 - 267 (chain A) in PDB entry 1H25
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 256 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101A LEU* 4.7 11.4 - - - +
105A LYS* 5.1 3.6 + - - -
254A PRO 3.7 2.4 + - - -
255A LEU* 1.3 76.3 - - - +
257A GLU* 1.3 59.5 + - - +
258A ASP* 2.7 36.2 + - - +
259A GLY* 2.7 15.0 + - - -
260A ARG* 3.0 31.0 + - - +
285A PHE* 3.9 14.4 - - - -
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Residues in contact with GLU 257 (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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256A ASP* 1.3 80.0 - - - +
258A ASP* 1.3 64.0 + - - +
260A ARG* 3.4 25.0 + - + +
261A SER* 3.0 26.6 + - - -
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Residues in contact with ASP 258 (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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256A ASP* 2.7 14.8 + - - +
257A GLU* 1.3 77.2 - - - +
259A GLY* 1.3 59.3 + - - +
260A ARG 3.0 1.3 - - - -
261A SER* 2.8 2.3 + - - -
262A LEU* 2.7 34.0 + - - +
283A HIS* 3.3 13.9 - - + -
284A PRO* 4.0 14.8 - - - +
285A PHE* 3.5 30.6 - - - +
287A GLN* 3.9 18.2 + - - -
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Residues in contact with GLY 259 (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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193A PHE* 3.8 7.1 - - - -
255A LEU* 3.9 18.2 - - - -
256A ASP* 2.7 13.3 + - - -
258A ASP* 1.3 76.8 - - - +
260A ARG* 1.3 61.9 + - - -
262A LEU* 3.3 1.5 + - - +
263A LEU* 2.9 25.3 + - - +
285A PHE* 3.4 26.6 - - - -
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Residues in contact with ARG 260 (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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248A PHE* 3.9 19.5 - - + +
249A SER* 3.4 46.0 - - - +
252A VAL* 5.3 2.2 + - + +
253A PRO 5.4 1.2 + - - -
255A LEU* 2.6 44.4 + - + -
256A ASP* 3.0 20.7 + - - +
257A GLU* 3.8 29.6 + - - +
258A ASP 3.0 0.2 - - - -
259A GLY* 1.3 77.0 - - - +
261A SER* 1.3 58.0 + - - +
263A LEU* 3.9 4.5 - - - +
264A SER* 2.7 32.9 + - - -
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Residues in contact with SER 261 (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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257A GLU* 3.0 18.2 + - - -
258A ASP* 2.8 5.3 + - - -
260A ARG* 1.3 78.3 - - - +
262A LEU* 1.3 61.5 + - - +
264A SER* 3.1 8.7 - - - -
265A GLN* 3.0 34.5 + - - +
283A HIS* 2.6 29.1 + - - -
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Residues in contact with LEU 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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108A LEU* 3.9 13.0 - - + -
112A LEU* 4.9 1.1 - - + -
193A PHE* 4.5 2.7 - - + -
258A ASP 2.7 19.6 + - - +
259A GLY* 3.8 3.4 - - - +
261A SER* 1.3 69.3 + - - +
263A LEU* 1.3 70.8 + - - +
264A SER 2.7 1.3 - - - -
265A GLN* 2.6 15.3 + - - +
266A MET* 2.8 29.6 + - + +
275A ILE* 4.2 8.3 - - + -
280A ALA* 4.1 23.6 - - + -
283A HIS* 3.8 28.0 - - + +
285A PHE* 3.6 30.3 - - + -
286A PHE* 3.7 22.4 - - + -
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Residues in contact with LEU 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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190A GLY* 3.6 31.9 - - - +
193A PHE* 3.3 30.2 - - + -
194A ALA* 4.2 8.3 - - + +
248A PHE* 3.7 20.0 - - + -
251A VAL* 4.8 2.5 - - + -
252A VAL* 4.0 26.7 - - + -
255A LEU* 4.5 9.0 - - + -
259A GLY 2.9 14.3 + - - +
260A ARG 3.9 2.5 - - - +
262A LEU* 1.3 80.2 - - - +
264A SER* 1.3 67.0 + - - +
266A MET* 2.8 12.5 + - + +
267A LEU* 3.0 30.4 + - + +
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Residues in contact with SER 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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245A ARG* 4.1 15.1 + - - -
248A PHE* 3.8 22.3 - - - -
260A ARG 2.7 21.1 + - - -
261A SER* 3.1 13.2 - - - -
262A LEU 2.7 1.4 - - - -
263A LEU* 1.3 80.8 - - - +
265A GLN* 1.3 60.4 + - - +
266A MET 3.5 0.2 + - - -
267A LEU* 3.6 2.4 + - - +
268A HIS* 3.6 18.5 + - - +
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Residues in contact with GLN 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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261A SER* 3.0 30.9 + - - +
262A LEU 2.6 13.8 + - - +
264A SER* 1.3 76.7 - - - +
266A MET* 1.3 60.1 + - - +
267A LEU 3.2 0.4 + - - -
268A HIS* 3.5 14.9 - - - +
273A LYS 5.9 0.7 - - - +
274A ARG* 3.5 6.2 - - - +
275A ILE* 3.1 58.1 + - + +
283A HIS* 3.3 14.8 + - - -
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Residues in contact with MET 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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108A LEU* 4.6 10.1 - - + -
112A LEU* 4.4 18.4 - - + -
186A ILE* 3.5 21.6 - - + +
187A TRP* 3.8 9.2 - - - -
189A LEU* 3.4 21.5 - - + +
190A GLY* 3.4 36.6 - - - +
193A PHE* 4.4 13.7 - - - -
262A LEU* 2.8 34.8 + - + +
263A LEU 2.8 6.5 + - - +
265A GLN* 1.3 79.0 - - - +
267A LEU* 1.3 57.4 + - - +
268A HIS 3.4 1.3 - - - -
274A ARG* 3.3 21.4 - - - -
275A ILE* 3.8 15.7 - - + -
280A ALA* 5.5 0.7 - - + -
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Residues in contact with LEU 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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187A TRP* 3.4 52.2 - - + +
190A GLY* 4.3 1.1 - - - -
191A CYS* 4.2 15.5 - - - +
202A LEU* 3.9 22.0 - - + -
203A PHE* 4.7 3.6 - - + -
219A LEU* 3.7 31.8 - - + +
245A ARG* 5.7 1.0 + - - -
248A PHE* 3.9 11.9 - - + -
251A VAL* 5.4 1.8 - - + -
263A LEU* 3.0 39.3 + - + +
264A SER 4.0 4.9 - - - +
265A GLN 3.2 0.2 - - - -
266A MET* 1.3 80.5 - - - +
268A HIS* 1.3 63.4 + - - +
269A TYR* 3.5 3.1 + - - -
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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
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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