Contacts of the helix formed by residues 478 - 492 (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 PRO 478 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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392A GLU* 5.1 7.0 - - + -
433A TYR* 4.5 11.9 - - + +
476A ARG 3.6 4.7 - - - +
477A LEU* 1.3 90.0 - - + +
479A ALA* 1.3 65.2 + - - +
480A ARG* 4.3 13.7 - - + +
481A VAL* 2.9 37.4 + - + +
482A TYR* 3.2 9.2 + - - +
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Residues in contact with ALA 479 (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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470A ARG* 4.4 23.4 - - - +
477A LEU 3.4 3.5 + - - -
478A PRO* 1.3 71.6 - - - +
480A ARG* 1.3 58.3 + - - +
482A TYR* 3.3 10.4 + - + +
483A GLN* 3.0 30.3 + - - +
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Residues in contact with ARG 480 (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* 5.3 1.0 + - - -
428A VAL* 3.6 30.2 + - + +
429A GLU* 3.0 42.1 + - + +
431A ASP* 2.8 30.3 + - - -
433A TYR* 3.1 32.3 + - - -
478A PRO* 4.3 13.8 - - + +
479A ALA* 1.3 79.3 - - - +
481A VAL* 1.3 59.9 + - + +
483A GLN* 3.6 11.7 + - - +
484A ALA* 3.1 26.2 + - - +
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Residues in contact with VAL 481 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392A GLU 5.0 7.2 - - - +
426A LEU* 4.5 15.9 - - + -
428A VAL* 4.1 15.7 - - + -
433A TYR* 3.8 40.2 - - + +
435A ILE* 5.1 5.2 - - + -
477A LEU* 4.0 17.0 - - + -
478A PRO* 2.9 30.2 + - + +
480A ARG* 1.3 75.8 - - + +
482A TYR* 1.3 65.6 + - - +
484A ALA* 3.1 4.1 + - - +
485A LEU* 2.9 25.5 + - + +
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Residues in contact with TYR 482 (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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466A ARG* 2.7 34.7 + - + -
467A GLU* 5.7 0.2 - - - -
469A LEU* 3.4 22.3 - - + +
470A ARG* 3.5 32.3 - - + -
474A PHE* 3.5 46.4 - + + -
477A LEU* 4.1 16.6 - - + +
478A PRO 3.2 9.3 + - - +
479A ALA* 3.6 9.4 - - - +
481A VAL* 1.3 78.1 - - - +
483A GLN* 1.3 65.1 + - + +
485A LEU* 3.2 8.8 + - + +
486A LEU* 3.0 56.5 + - + +
489A TRP* 6.3 0.2 - + - -
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Residues in contact with GLN 483 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466A ARG* 4.1 18.6 - - - +
479A ALA 3.0 17.7 + - - +
480A ARG* 3.8 10.0 - - - +
482A TYR* 1.3 81.2 - - + +
484A ALA* 1.3 57.8 + - - +
486A LEU* 3.3 6.7 + - - +
487A GLU* 3.0 59.2 + - - +
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Residues in contact with ALA 484 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426A LEU* 4.1 9.3 - - + +
427A ARG 4.0 11.0 - - - +
428A VAL* 4.0 25.1 - - + -
480A ARG 3.1 16.2 + - - +
481A VAL 3.1 7.6 + - - +
483A GLN* 1.3 75.7 - - - +
485A LEU* 1.3 57.8 + - - +
487A GLU* 3.4 11.8 + - - +
488A GLU* 2.9 28.9 + - - +
491A ARG* 5.1 1.0 + - - -
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Residues in contact with LEU 485 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426A LEU* 3.9 19.3 - - + -
435A ILE* 4.8 0.9 - - + -
440A TYR* 3.7 35.9 - - + -
443A TRP* 3.6 29.6 - - + -
474A PHE* 4.2 10.8 - - + -
477A LEU* 3.7 23.6 - - + -
481A VAL* 2.9 16.9 + - + +
482A TYR* 3.5 9.4 - - + +
484A ALA* 1.3 73.1 - - - +
486A LEU* 1.3 66.6 + - - +
488A GLU* 3.2 5.6 + - + +
489A TRP* 2.9 46.3 + - + -
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Residues in contact with LEU 486 (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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447A VAL* 5.6 0.2 - - + -
466A ARG* 3.8 34.5 - - + +
469A LEU* 4.3 13.0 - - + -
482A TYR* 3.0 60.5 + - + +
483A GLN* 3.3 6.9 + - - +
485A LEU* 1.3 76.7 - - - +
487A GLU* 1.3 58.5 + - - +
489A TRP* 3.4 15.9 + - + +
490A SER* 2.9 29.8 + - - -
495A LEU* 4.0 20.5 - - + +
497A LEU* 3.8 18.5 - - + +
502A VAL* 4.5 4.7 - - + -
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Residues in contact with GLU 487 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466A ARG* 5.1 2.7 + - - +
483A GLN* 3.0 51.4 + - + +
484A ALA* 3.8 9.7 - - - +
486A LEU* 1.3 76.5 - - + +
488A GLU* 1.3 57.1 + - - +
490A SER* 3.4 2.6 + - - -
491A ARG* 3.0 42.4 + - - +
497A LEU* 4.2 17.7 - - + -
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Residues in contact with GLU 488 (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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424A THR* 4.9 4.7 - - - +
425A LEU 5.4 2.8 - - - +
426A LEU* 3.7 22.7 - - + +
440A TYR* 2.6 37.5 + - - +
484A ALA 2.9 18.3 + - - +
485A LEU* 3.2 7.6 + - + +
487A GLU* 1.3 76.3 - - - +
489A TRP* 1.3 64.6 + - + +
491A ARG* 3.2 21.7 + - - +
492A GLU* 3.0 43.4 + - + +
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Residues in contact with TRP 489 (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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440A TYR* 3.0 40.6 + + - -
443A TRP* 4.0 20.9 - - + -
444A TRP* 3.6 42.2 - + + -
447A VAL* 4.0 18.8 - - + -
474A PHE* 4.3 9.2 - + - -
482A TYR* 6.2 0.2 - + - -
485A LEU* 2.9 51.7 + - + +
486A LEU* 4.4 8.5 - - + -
488A GLU* 1.3 75.9 - - + +
490A SER* 1.3 61.0 + - - +
492A GLU* 3.5 3.7 + - - -
493A GLY 3.5 1.9 + - - -
494A ARG* 2.9 60.3 + - - +
495A LEU* 3.3 28.4 + - + -
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Residues in contact with SER 490 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486A LEU 2.9 18.0 + - - -
487A GLU* 3.7 4.7 - - - -
488A GLU 3.2 0.2 - - - -
489A TRP* 1.3 74.7 - - - +
491A ARG* 1.3 65.2 + - - +
493A GLY* 3.0 14.9 + - - -
495A LEU* 3.2 27.2 + - - +
496A GLN* 4.1 5.4 - - - -
497A LEU* 3.9 23.8 + - - +
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Residues in contact with ARG 491 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426A LEU* 6.2 0.6 - - - +
484A ALA 5.1 0.6 + - - -
487A GLU* 3.0 20.9 + - - +
488A GLU* 3.2 36.1 + - - +
490A SER* 1.3 75.7 - - - +
492A GLU* 1.3 61.7 + - + +
493A GLY* 3.1 5.4 + - - -
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Residues in contact with GLU 492 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440A TYR* 4.3 1.5 + - - -
488A GLU* 3.0 43.6 + - + +
489A TRP* 3.9 6.1 - - - +
490A SER 3.2 0.4 - - - -
491A ARG* 1.3 79.1 - - + +
493A GLY* 1.3 59.6 + - - +
494A ARG* 2.8 43.5 + - + +
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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