Contacts of the helix formed by residues 296 - 303 (chain A) in PDB entry 1HJV
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 TYR 296 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260A THR 3.1 21.0 + - - +
295A ALA* 1.3 72.2 - - - +
297A TYR* 1.3 56.8 + - - +
299A ILE* 3.1 14.5 + - + +
300A CYS* 3.0 37.5 + - - -
303A LEU* 5.9 3.1 - - + +
328A TYR* 4.3 19.5 - + + -
329A ASP 3.5 21.5 - - - -
330A ASP* 4.1 7.5 - - + +
331A GLN* 3.7 21.8 + - - -
356A LEU 2.8 14.8 + - - +
357A ASP* 4.0 4.3 - - - -
358A ASP 4.3 1.8 - - - -
364A CYS* 3.9 16.0 - - + +
371A PRO* 3.5 29.4 - - + -
372A LEU* 3.2 33.0 - - + -
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Residues in contact with TYR 297 (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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35A ARG* 4.2 14.2 + - - -
38A ASP 5.6 0.2 - - - -
39A GLY* 3.9 15.0 + - - -
287A PHE* 3.5 39.9 - + + +
288A THR* 4.3 4.2 - - - +
295A ALA* 3.3 21.9 - - + +
296A TYR* 1.3 78.8 - - - +
298A GLU* 1.3 70.7 + - + +
300A CYS* 3.5 9.6 + - - +
301A ASP* 3.4 3.8 - - - +
355A ASP 3.7 17.9 - - - -
356A LEU 3.9 0.2 + - - -
357A ASP 3.4 18.6 - - - -
358A ASP* 3.8 20.8 - - - +
359A PHE* 4.3 11.9 - + - -
363A PHE* 3.2 64.0 - + + +
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Residues in contact with GLU 298 (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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285A GLY* 3.0 22.1 - - - -
286A ARG* 4.7 2.7 - - + +
287A PHE* 3.1 15.6 + - + -
288A THR* 2.6 45.2 + - - -
294A LEU* 3.5 13.6 - - + -
295A ALA* 2.7 31.4 + - - +
297A TYR* 1.3 92.8 - - + +
299A ILE* 1.3 68.0 + - - +
300A CYS 3.0 1.8 - - - -
301A ASP* 2.9 13.3 + - - +
302A PHE* 2.9 22.1 + - - +
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Residues in contact with ILE 299 (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 PHE 4.4 0.9 - - - -
262A GLY* 3.7 22.0 - - - +
294A LEU* 3.7 22.7 - - + +
295A ALA 2.9 14.7 + - - +
296A TYR* 3.1 22.2 + - + +
298A GLU* 1.3 77.1 - - - +
300A CYS* 1.3 50.3 + - - +
302A PHE* 3.1 9.2 + - + +
303A LEU* 2.8 41.2 + - + +
326A VAL* 4.4 8.1 - - + -
328A TYR* 3.3 63.5 - - + -
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Residues in contact with CYS 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A TYR* 3.0 28.5 + - - -
297A TYR 3.5 8.5 - - - +
298A GLU 3.0 0.4 - - - -
299A ILE* 1.3 75.3 - - - +
301A ASP* 1.3 65.2 + - - +
303A LEU* 3.3 24.1 + - - +
304A ARG* 3.8 10.7 + - - +
363A PHE 3.5 16.5 - - - +
364A CYS* 2.0 50.0 - - + -
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Residues in contact with ASP 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A PHE* 4.6 6.2 - - - -
297A TYR 3.4 7.8 + - - +
298A GLU* 2.9 12.2 + - - +
300A CYS* 1.3 76.8 - - - +
302A PHE* 1.3 65.0 + - - +
304A ARG* 3.0 46.2 + - - +
321A LYS* 4.1 5.0 + - - -
363A PHE* 3.4 39.2 - - - +
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Residues in contact with PHE 302 (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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294A LEU* 4.8 13.2 - - + -
298A GLU 2.9 11.9 + - - +
299A ILE* 3.2 14.4 - - + +
301A ASP* 1.3 79.3 - - - +
303A LEU* 1.3 61.2 + - + +
304A ARG 3.1 0.4 - - - +
306A ALA* 3.3 11.3 - - + +
319A ALA* 3.7 21.5 - - + -
320A THR* 4.3 2.9 - - - -
321A LYS* 3.1 52.7 + - + +
324A GLN* 3.6 47.6 - - + -
326A VAL* 3.5 32.8 - - + -
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Residues in contact with LEU 303 (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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296A TYR* 5.9 3.4 - - + +
299A ILE* 2.8 27.8 + - + +
300A CYS* 3.6 18.6 - - - +
301A ASP 3.2 0.6 - - - -
302A PHE* 1.3 75.6 - - + +
304A ARG* 1.3 59.7 + - - +
305A GLY 3.1 1.2 + - - -
306A ALA* 3.0 27.8 + - + +
308A VAL* 3.2 32.8 - - + -
319A ALA* 3.6 18.4 - - + -
328A TYR* 3.8 14.8 - - + +
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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