Contacts of the helix formed by residues 396 - 404 (chain A) in PDB entry 2V9V
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 TRP 396 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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394A LEU 3.3 4.0 + - - -
395A ASP* 1.3 76.0 + - - +
397A GLN* 1.3 75.2 + - + +
399A ALA* 3.4 9.0 + - - +
400A ALA* 2.9 27.0 + - - +
407A LEU* 3.4 58.1 - - + -
410A THR* 4.0 21.6 - - + +
411A ARG* 4.0 20.6 - - + -
414A LEU* 3.9 23.3 - - + -
425A LEU* 6.1 0.2 - - + -
432A LEU* 2.9 63.4 + - + +
433A TYR 5.4 0.2 - - - -
434A ALA* 4.9 6.3 - - + -
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Residues in contact with GLN 397 (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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395A ASP* 2.9 16.4 + - - +
396A TRP* 1.3 89.5 - - - +
398A GLU* 1.3 61.6 + - - +
400A ALA* 3.3 2.8 + - - +
401A THR* 3.0 33.5 + - - +
407A LEU* 3.8 42.9 - - + +
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Residues in contact with GLU 398 (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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394A LEU* 4.1 6.5 - - + -
395A ASP* 2.9 14.4 + - + +
397A GLN* 1.3 77.3 - - - +
399A ALA* 1.3 58.9 + - - +
401A THR* 3.2 11.5 + - - +
402A ARG* 2.9 77.1 + - - +
1513A CL 4.1 19.7 - - + -
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Residues in contact with ALA 399 (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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383A LEU* 3.9 21.9 - - + +
386A ILE* 4.3 8.0 - - + +
387A ILE* 4.7 5.4 - - + -
394A LEU* 3.7 28.3 - - + +
395A ASP 3.0 9.7 + - - +
396A TRP* 3.6 11.9 - - - +
398A GLU* 1.3 76.5 - - - +
400A ALA* 1.3 61.6 + - - +
402A ARG* 3.2 2.6 + - - +
403A ALA* 2.9 26.2 + - - +
410A THR* 5.0 2.5 - - + -
414A LEU* 6.2 0.7 - - + -
434A ALA* 5.7 1.6 - - + -
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Residues in contact with ALA 400 (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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396A TRP 2.9 14.2 + - - +
397A GLN 3.5 8.5 - - - +
398A GLU 3.3 0.2 - - - -
399A ALA* 1.3 74.5 - - - +
401A THR* 1.3 62.9 + - - +
403A ALA* 3.3 2.7 + - - -
404A SER* 3.0 4.7 + - - -
405A LEU* 2.9 40.0 + - - +
406A SER 4.3 0.2 - - - +
407A LEU* 3.9 20.6 - - + -
410A THR* 3.3 27.5 + - - +
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Residues in contact with THR 401 (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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397A GLN* 3.0 19.5 + - - +
398A GLU* 3.6 14.8 + - - +
400A ALA* 1.3 77.1 - - - +
402A ARG* 1.3 64.2 + - + +
404A SER* 3.1 16.8 + - - +
405A LEU 5.2 0.2 - - - -
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Residues in contact with ARG 402 (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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382A ILE* 4.8 3.1 - - - +
386A ILE* 3.7 26.1 - - + +
390A HIS* 3.9 28.1 + - - -
394A LEU* 4.1 14.4 - - - +
398A GLU* 2.9 54.5 + - - +
399A ALA 3.7 4.3 - - - +
401A THR* 1.3 78.4 - - + +
403A ALA* 1.3 57.5 + - - +
404A SER* 3.6 2.9 + - - -
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Residues in contact with ALA 403 (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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379A PRO* 5.1 2.5 - - - +
382A ILE* 4.0 21.1 - - + +
383A LEU* 4.2 10.3 - - + +
386A ILE* 3.9 15.3 - - + -
399A ALA 2.9 16.9 + - - +
400A ALA 3.9 1.3 - - - +
402A ARG* 1.3 74.1 - - - +
404A SER* 1.3 69.0 + - - +
405A LEU* 3.4 31.9 + - + +
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Residues in contact with SER 404 (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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400A ALA 3.0 5.6 + - - -
401A THR* 3.1 12.8 + - - +
402A ARG 3.3 2.8 + - - -
403A ALA* 1.3 80.1 - - - +
405A LEU* 1.3 63.3 + - - +
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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