Contacts of the helix formed by residues 396 - 407 (chain A) in PDB entry 2V3V
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 HIS 396 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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134A ASP* 3.7 4.0 - - - -
138A ARG* 3.4 27.4 - - - +
360A SER* 3.4 8.0 + - - +
394A GLY 3.2 6.3 + - - -
395A TYR* 1.3 72.2 - - - +
397A THR* 1.3 54.0 + - - +
398A VAL* 3.8 14.1 + - + +
399A ALA* 3.0 36.6 + - + +
400A LEU 2.7 31.0 + - - -
704A THR* 5.0 4.0 - - - -
709A ARG* 3.6 48.7 + - + +
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Residues in contact with THR 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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107A TYR* 3.4 26.3 - - + +
134A ASP* 2.7 27.1 + - - +
135A GLY 3.3 15.1 + - - -
138A ARG* 3.5 14.6 - - - +
139A LEU* 3.9 10.5 - - + -
396A HIS* 1.3 68.0 - - - +
398A VAL* 1.3 70.5 + - - +
400A LEU* 3.1 17.6 + - - +
401A PHE* 3.3 15.7 + - + -
423A LEU* 3.6 30.5 - - + -
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Residues in contact with VAL 398 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A ARG* 5.3 1.2 - - - +
139A LEU* 5.2 0.7 - - + -
396A HIS* 3.5 10.7 + - + +
397A THR* 1.3 83.7 - - + +
399A ALA* 1.3 62.0 + - - +
401A PHE* 3.4 5.0 + - - +
402A GLU* 3.2 40.0 + - + +
423A LEU* 5.6 2.0 - - + -
424A PRO* 4.5 8.1 - - + -
428A LYS* 5.4 0.2 - - - -
702A ASP* 3.2 36.8 - - - +
704A THR* 3.8 25.1 - - + -
709A ARG 5.0 2.2 + - - +
711A PRO* 4.0 17.7 - - + -
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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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395A TYR* 4.1 17.4 - - + -
396A HIS* 3.0 38.7 + - + +
398A VAL* 1.3 78.5 - - - +
400A LEU* 1.3 52.0 + - - +
402A GLU* 3.3 17.9 + - - +
403A ALA* 2.7 35.3 + - - +
406A ARG* 4.8 1.6 + - - -
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Residues in contact with LEU 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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105A ALA* 3.6 32.3 - - + -
106A TRP 4.5 5.2 - - - +
107A TYR* 4.1 32.5 - - + -
132A ASN* 5.1 2.2 - - + +
134A ASP* 4.9 5.2 - - + +
395A TYR* 3.5 24.6 - - + +
396A HIS 2.7 16.9 + - - +
397A THR* 3.1 11.6 + - - +
399A ALA* 1.3 73.5 - - - +
401A PHE* 1.3 69.6 + - + +
403A ALA* 3.2 2.8 + - - +
404A LEU* 2.9 24.8 + - - +
409A VAL* 3.9 18.8 - - + -
412A MET* 4.4 7.4 - - - -
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Residues in contact with PHE 401 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A TYR* 3.9 37.7 - + - -
397A THR* 3.3 15.0 + - + +
398A VAL* 4.2 5.4 - - - +
400A LEU* 1.3 85.3 - - + +
402A GLU* 1.3 60.9 + - - +
404A LEU* 3.7 11.9 - - + +
405A GLY 3.1 19.4 + - - -
412A MET* 3.9 29.4 - - + -
414A ILE* 4.6 0.7 - - + -
419A PRO* 3.9 8.7 - - + -
423A LEU* 3.6 33.2 - - + -
429A VAL* 4.3 12.3 - - + -
432A ALA* 3.2 17.8 - - + +
433A MET* 4.0 32.3 - - + -
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Residues in contact with GLU 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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398A VAL* 3.2 28.2 + - + +
399A ALA* 3.3 17.6 - - - +
401A PHE* 1.3 75.6 - - - +
403A ALA* 1.3 64.5 + - - +
405A GLY* 3.2 10.3 + - - -
406A ARG* 3.2 34.4 + - - +
428A LYS* 2.7 40.4 + - - -
432A ALA* 5.4 0.4 - - - -
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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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395A TYR* 3.6 39.5 - - + +
399A ALA 2.7 17.6 + - - +
400A LEU 3.3 8.7 - - - +
402A GLU* 1.3 71.8 - - - +
404A LEU* 1.3 61.6 + - - +
406A ARG* 3.2 16.8 + - - +
407A GLY 3.2 3.8 + - - -
408A ASP* 2.9 29.5 + - + +
409A VAL* 3.7 10.3 - - + -
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Residues in contact with LEU 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 LEU 2.9 13.5 + - - +
401A PHE* 3.7 14.4 - - + +
402A GLU 3.3 0.2 - - - -
403A ALA* 1.3 75.2 - - - +
405A GLY* 1.3 62.1 + - - +
407A GLY* 3.2 11.4 + - - -
409A VAL* 3.6 36.1 - - + +
410A LYS 5.0 3.1 - - - +
412A MET* 3.7 39.5 - - + +
432A ALA 3.6 19.5 - - - +
433A MET* 3.8 22.7 - - + -
435A HIS* 3.7 14.2 - - - +
438A SER* 4.2 19.9 - - - -
440A ILE* 4.4 6.1 - - + -
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Residues in contact with GLY 405 (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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401A PHE 3.1 10.3 + - - -
402A GLU* 3.2 5.5 + - - -
404A LEU* 1.3 77.8 - - - +
406A ARG* 1.3 57.4 + - - +
432A ALA* 3.6 29.3 - - - +
435A HIS* 3.2 18.3 - - - -
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Residues in contact with ARG 406 (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 TYR* 4.4 10.9 + - - -
399A ALA 4.8 1.4 + - - -
402A GLU* 3.2 34.8 + - - +
403A ALA* 3.2 23.2 + - - +
405A GLY* 1.3 77.9 - - - +
407A GLY* 1.3 59.9 + - - +
408A ASP* 3.0 30.5 + - - +
435A HIS* 4.2 4.4 + - - -
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Residues in contact with GLY 407 (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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403A ALA 3.2 2.4 + - - -
404A LEU 3.2 10.6 + - - -
405A GLY 3.3 1.2 + - - -
406A ARG* 1.3 79.7 - - - +
408A ASP* 1.3 63.4 + - - +
409A VAL 3.4 6.3 - - - -
410A LYS* 2.8 36.7 + - - +
435A HIS* 3.7 21.1 - - - -
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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