Contacts of the helix formed by residues 266 - 275 (chain A) in PDB entry 1HVD
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 266 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76A LYS* 3.1 41.4 + - + +
79A LYS* 6.5 0.7 - - + -
264A THR* 3.1 31.9 + - - +
265A ASP* 1.3 71.8 - - - +
267A HIS* 1.3 57.7 + - - +
269A LEU* 3.9 3.5 - - - +
270A ILE* 2.9 38.0 + - + +
303A ASP 5.6 0.2 - - - +
304A THR* 4.7 0.7 + - - -
308A TYR* 2.9 33.5 + - - +
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Residues in contact with HIS 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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91A TYR* 5.6 0.4 + - - -
95A GLU* 3.0 40.9 + - - -
98A HIS* 5.8 5.2 - - + +
106A ASN* 5.0 10.3 - - - -
109A VAL* 5.0 2.8 - - - +
265A ASP* 3.3 8.9 + - - +
266A ASP* 1.3 76.5 - - - +
268A THR* 1.3 56.6 + - - +
270A ILE* 3.6 7.5 + - - +
271A ARG* 2.9 35.3 + - - +
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Residues in contact with THR 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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108A LYS* 3.1 21.4 + - - +
112A GLU* 3.8 15.5 - - - +
254A THR* 4.0 17.3 - - - +
255A LEU* 4.9 0.9 - - + +
258A ALA* 4.0 12.8 - - + -
265A ASP* 2.8 30.6 + - - -
267A HIS* 1.3 73.7 - - - +
269A LEU* 1.3 67.5 + - - +
271A ARG* 3.0 22.6 + - - +
272A VAL* 2.9 28.5 + - + +
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Residues in contact with LEU 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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255A LEU* 4.2 17.6 - - + +
258A ALA* 4.5 6.0 - - + +
259A MET* 3.9 31.0 - - + -
264A THR* 3.7 24.9 - - + -
265A ASP 3.0 16.2 + - - +
266A ASP* 3.7 3.1 - - - +
268A THR* 1.3 77.0 - - - +
270A ILE* 1.3 61.8 + - - +
272A VAL* 4.3 0.2 - - - -
273A MET* 3.0 38.3 + - + +
300A ILE* 4.4 10.8 - - + -
304A THR* 3.9 15.5 - - - +
308A TYR* 3.6 18.2 - - - +
312A LEU* 3.9 14.6 - - + -
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Residues in contact with ILE 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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76A LYS* 4.0 2.7 - - - +
79A LYS* 4.0 18.8 - - + +
80A LEU* 3.9 35.0 - - + +
83A ALA* 3.8 28.3 - - + -
91A TYR* 4.3 3.4 - - - +
266A ASP* 2.9 26.6 + - + +
267A HIS* 3.9 7.0 - - - +
269A LEU* 1.3 75.4 - - - +
271A ARG* 1.3 63.5 + - - +
273A MET* 3.8 3.1 - - - +
274A VAL* 2.9 27.7 + - - +
308A TYR* 3.5 34.3 - - + +
312A LEU* 5.1 2.2 - - + -
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Residues in contact with ARG 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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91A TYR* 3.5 19.1 - - + +
92A ASP* 5.7 0.4 - - - +
95A GLU* 3.1 42.2 + - + +
108A LYS* 4.2 5.1 - - - +
109A VAL* 3.4 37.8 - - - +
112A GLU* 2.9 37.0 + - - +
113A ILE* 4.2 11.0 - - + +
117A ARG* 5.6 1.3 - - - +
267A HIS* 2.9 39.9 + - - +
268A THR* 3.0 27.0 + - - +
270A ILE* 1.3 75.8 - - - +
272A VAL* 1.3 52.0 + - - +
275A SER* 2.6 45.4 + - - +
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Residues in contact with VAL 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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112A GLU* 3.8 20.0 - - - +
251A LEU* 4.2 24.2 - - + +
254A THR* 3.7 20.9 - - - +
255A LEU* 3.6 32.5 - - + -
268A THR* 2.9 20.7 + - + +
271A ARG* 1.3 69.2 - - - +
273A MET* 1.3 66.8 + - - +
275A SER* 3.6 4.9 - - - -
276A ARG* 3.2 35.3 + - + +
281A LEU* 4.7 1.8 - - + +
284A ILE* 4.5 4.3 - - + -
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Residues in contact with MET 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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255A LEU* 4.7 9.0 - - + -
269A LEU* 3.0 31.1 + - + +
270A ILE 3.8 2.2 - - - +
272A VAL* 1.3 77.4 - - - +
274A VAL* 1.3 63.2 + - + +
277A SER* 3.2 23.2 + - - -
281A LEU* 3.8 22.0 - - + +
296A LEU* 4.1 18.2 - - + -
300A ILE* 3.6 30.1 - - + -
312A LEU* 3.6 41.3 - - + +
315A LEU* 4.3 12.4 - - + +
316A CYS* 3.7 18.8 - - + +
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Residues in contact with VAL 274 (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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50A ARG* 5.8 0.9 - - - +
80A LEU* 3.9 20.9 - - + -
83A ALA* 3.6 39.3 - - + +
84A LEU* 3.6 29.2 - - + +
91A TYR* 4.2 14.1 - - + -
270A ILE 2.9 21.6 + - - +
271A ARG 4.3 1.3 - - - +
273A MET* 1.3 74.3 - - + +
275A SER* 1.3 64.9 + - - +
277A SER* 2.8 24.4 + - - +
315A LEU* 4.4 2.7 - - + -
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Residues in contact with SER 275 (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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91A TYR* 3.9 15.9 - - - -
92A ASP* 3.9 11.7 - - - -
117A ARG* 3.4 27.6 + - - -
271A ARG* 2.6 29.7 + - - +
272A VAL* 3.6 3.8 - - - -
274A VAL* 1.3 72.4 - - - +
276A ARG* 1.3 68.8 + - - +
277A SER 3.9 0.2 + - - -
278A GLU 5.0 0.9 + - - -
279A ILE* 3.5 20.4 - - - +
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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