Contacts of the helix formed by residues 265 - 274 (chain A) in PDB entry 1H5R
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 265 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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259A PHE* 4.0 7.0 - - - -
264A ILE* 1.3 75.5 - - - +
266A VAL* 1.3 66.5 + - - +
267A GLU* 3.5 14.4 + - - +
268A GLN* 3.1 22.9 + - - +
269A VAL* 3.1 23.0 + - - +
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Residues in contact with VAL 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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259A PHE* 3.6 29.9 - - + -
265A ASP* 1.3 76.9 - - - +
267A GLU* 1.3 66.9 - - - +
269A VAL* 3.3 4.7 + - - +
270A ARG* 3.1 50.7 + - - +
289A THR* 4.1 17.9 - - - +
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Residues in contact with GLU 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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265A ASP* 3.3 14.2 + - - +
266A VAL* 1.3 83.2 - - - +
268A GLN* 1.3 62.0 + - - +
270A ARG* 3.3 8.9 + - - +
271A LYS* 3.2 47.8 + - + +
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Residues in contact with GLN 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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72A SER 4.7 2.0 + - - +
73A GLN* 3.0 43.4 + - - +
264A ILE* 3.7 24.2 - - + -
265A ASP* 3.1 21.6 + - - +
267A GLU* 1.3 75.2 - - - +
269A VAL* 1.3 66.0 + - - +
271A LYS* 3.4 23.8 + - - +
272A LEU* 3.0 33.5 + - - +
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Residues in contact with VAL 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 GLU* 4.7 3.6 - - + +
259A PHE* 3.4 47.1 - - + -
264A ILE* 3.6 11.9 - - + -
265A ASP 3.1 11.3 + - - +
266A VAL 3.3 6.0 + - - +
268A GLN* 1.3 74.7 - - - +
270A ARG* 1.3 59.5 + - - +
272A LEU* 3.0 13.5 + - + +
273A ALA* 2.9 25.6 + - - +
285A LEU* 3.8 30.6 - - + +
288A MET* 5.3 3.6 - - - -
289A THR* 3.5 23.6 - - + -
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Residues in contact with ARG 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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266A VAL* 3.1 27.4 + - - +
267A GLU* 3.6 10.5 - - - +
268A GLN 3.2 0.2 - - - -
269A VAL* 1.3 78.3 - - - +
271A LYS* 1.3 60.4 + - + +
273A ALA* 3.2 15.3 + - - +
274A VAL* 3.2 19.4 + - - +
286A TYR* 3.7 39.2 + - + +
289A THR* 3.1 36.8 + - + +
290A LYS* 3.8 29.3 - - - +
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Residues in contact with LYS 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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267A GLU* 3.2 36.3 + - + +
268A GLN* 3.5 29.2 + - - +
270A ARG* 1.3 79.1 - - - +
272A LEU* 1.3 61.8 + - + +
273A ALA 3.2 0.7 + - - -
274A VAL* 3.2 19.4 + - + +
275A PRO* 3.4 9.2 - - - +
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Residues in contact with LEU 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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73A GLN* 3.5 35.9 - - + +
74A TRP* 3.5 29.2 - - + +
255A GLU* 3.6 23.3 - - + +
264A ILE* 3.6 22.7 - - + -
268A GLN* 3.0 26.3 + - - +
269A VAL* 3.3 8.5 - - - +
271A LYS* 1.3 76.3 - - - +
273A ALA* 1.3 62.2 + - - +
275A PRO* 3.2 15.3 - - - +
276A LEU* 3.5 18.0 - - + +
285A LEU* 4.7 3.6 - - + -
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Residues in contact with ALA 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 VAL 2.9 11.8 + - - +
270A ARG* 3.5 13.5 - - - +
271A LYS 3.1 0.8 - - - -
272A LEU* 1.3 78.5 - - - +
274A VAL* 1.3 53.2 + - - +
276A LEU* 2.8 7.3 + - - -
277A ILE* 2.6 46.1 + - + -
282A GLY* 3.9 19.5 - - - +
285A LEU* 4.1 17.9 - - + +
286A TYR* 4.3 7.9 - - + +
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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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270A ARG 3.2 18.4 - - - +
271A LYS* 3.5 12.1 - - + +
273A ALA* 1.3 77.0 - - - +
275A PRO* 1.3 72.0 - - + +
276A LEU 3.0 1.6 + - - -
277A ILE* 3.0 29.5 + - + +
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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