Contacts of the helix formed by residues 362 - 369 (chain A) in PDB entry 2V40
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 LYS 362 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40A ASP 4.7 5.3 + - - -
41A GLU 5.1 1.1 - - - -
298A LYS* 3.7 15.2 - - + +
299A ALA* 3.9 7.0 - - - +
300A TYR* 3.4 27.5 - - + +
325A GLY* 3.0 24.9 + - - +
327A GLU* 3.1 17.2 + - - -
336A ARG* 5.0 2.2 - - - +
361A THR* 1.3 76.5 - - - +
363A LEU* 1.3 65.0 + - - +
364A ASP* 3.1 9.0 - - - -
365A ILE* 3.1 29.1 + - + +
366A LEU* 4.3 0.5 + - - +
444A GLY 3.6 0.6 + - - -
1457A GDP 2.8 80.5 + - + +
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Residues in contact with LEU 363 (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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299A ALA* 3.9 10.3 - - + -
360A LEU* 4.4 7.9 - - + +
361A THR 3.2 3.0 - - - +
362A LYS* 1.3 77.3 - - - +
364A ASP* 1.3 56.8 + - - +
366A LEU* 3.0 26.0 + - + +
408A TRP* 3.7 19.8 - - + -
412A ILE* 3.7 20.6 - - + -
421A LEU* 4.4 10.3 - - + -
425A ALA* 4.4 9.2 - - + +
428A TYR* 3.6 35.4 - - + -
429A VAL* 4.0 17.9 - - + -
443A ILE* 3.7 25.4 - - + -
444A GLY 3.1 13.8 + - - +
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Residues in contact with ASP 364 (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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324A ARG* 2.9 22.4 + - - +
362A LYS* 3.5 7.1 - - - -
363A LEU* 1.3 76.7 - - - +
365A ILE* 1.3 65.6 + - - +
367A ASP* 3.0 29.3 - - - +
412A ILE* 3.8 9.3 - - + +
413A SER* 4.9 6.1 - - - +
444A GLY 4.1 1.2 + - - -
445A VAL* 3.2 32.1 - - - +
446A GLY* 4.0 1.4 - - - -
1457A GDP 2.8 42.8 + - - -
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Residues in contact with ILE 365 (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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300A TYR* 3.5 26.0 - - + +
321A LEU* 3.8 25.6 - - + +
324A ARG* 2.7 52.5 + - + +
325A GLY* 3.5 26.9 - - - +
362A LYS* 3.1 23.0 + - + +
364A ASP* 1.3 81.8 - - - +
366A LEU* 1.3 58.8 + - + +
367A ASP 3.2 2.1 + - - -
369A PHE* 3.7 6.1 - - + -
1457A GDP 3.5 29.4 - - + +
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Residues in contact with LEU 366 (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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299A ALA* 3.8 18.6 - - + +
300A TYR* 4.6 7.4 - - + -
321A LEU* 3.9 27.4 - - + -
340A TRP* 5.2 2.7 - - + -
362A LYS 4.8 1.3 - - - +
363A LEU* 3.0 12.8 + - + +
365A ILE* 1.3 74.4 - - + +
367A ASP* 1.3 60.1 + - - +
368A MET 3.0 7.2 + - - -
369A PHE* 3.1 36.4 + - + +
372A ILE* 4.1 20.4 - - + +
408A TRP* 3.6 23.6 - - + -
428A TYR* 3.6 42.2 - - + +
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Residues in contact with ASP 367 (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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324A ARG* 3.6 9.4 + - - +
364A ASP* 3.0 29.1 + - - +
365A ILE 3.2 0.4 - - - -
366A LEU* 1.3 76.5 - - - +
368A MET* 1.3 59.5 + - + +
408A TRP* 2.7 31.8 + - - +
409A ASN* 3.2 30.0 - - - -
410A THR 3.1 20.6 + - - +
411A ASP* 3.5 9.3 - - - +
412A ILE* 3.0 37.7 + - - +
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Residues in contact with MET 368 (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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320A LEU* 5.0 11.2 - - + +
324A ARG* 3.2 46.9 - - - +
365A ILE 4.0 0.8 + - - -
366A LEU 3.1 1.4 - - - -
367A ASP* 1.3 80.2 - - + +
369A PHE* 1.3 66.0 + - + +
370A THR* 3.7 5.9 + - - +
409A ASN* 4.4 5.4 - - - +
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Residues in contact with PHE 369 (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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317A ILE* 4.0 14.1 - - + -
320A LEU* 3.6 38.8 - - + -
321A LEU* 3.5 31.2 - - + -
324A ARG* 4.8 1.3 - - - -
340A TRP* 4.0 29.4 - + - -
365A ILE* 3.7 18.4 - - + -
366A LEU* 3.1 29.6 + - + +
367A ASP 3.4 0.4 - - - -
368A MET* 1.3 82.0 - - - +
370A THR* 1.3 64.3 + - - +
371A GLU 3.7 19.3 - - - +
372A ILE* 3.8 9.4 - - + -
407A GLY* 3.3 15.4 - - - -
408A TRP 4.3 1.0 + - - -
409A ASN* 3.2 10.0 + - - +
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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