Contacts of the helix formed by residues 481 - 492 (chain A) in PDB entry 1JVN
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 ASP 481 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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407A ARG* 4.2 3.8 + - - +
436A TYR* 2.5 36.6 + - - -
470A CYS* 3.7 28.8 - - + +
473A LYS* 4.1 15.2 - - + +
480A TYR* 1.3 69.1 - - - +
482A LEU* 1.3 63.8 + - - +
483A GLU* 3.4 6.8 + - - +
484A LEU* 3.1 21.7 + - + +
485A ILE* 3.2 23.9 + - - +
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Residues in contact with LEU 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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425A TYR* 6.1 1.8 - - - +
480A TYR* 3.1 20.7 + - + +
481A ASP* 1.3 72.2 + - - +
483A GLU* 1.3 64.8 + - + +
485A ILE* 3.3 12.9 + - + +
486A GLU* 3.1 27.5 + - + +
507A HIS 5.9 0.2 - - - +
510A GLU* 3.7 43.3 - - + +
511A ALA* 4.7 5.6 - - + -
514A LYS* 4.1 17.9 - - + +
515A THR* 3.6 24.0 - - + +
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Residues in contact with GLU 483 (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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407A ARG* 2.7 29.3 + - - +
421A PHE* 3.7 15.2 - - + -
422A GLU 4.7 1.1 - - - +
423A THR* 2.6 30.2 + - - -
424A GLU* 2.9 32.9 + - - +
425A TYR* 3.7 20.8 - - + +
481A ASP* 3.4 3.4 + - - +
482A LEU* 1.3 76.0 - - + +
484A LEU* 1.3 60.4 + - - +
486A GLU* 3.4 7.1 + - - +
487A HIS* 2.9 30.6 + - - +
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Residues in contact with LEU 484 (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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405A PRO* 4.0 11.0 - - + +
436A TYR* 3.6 48.2 + - + -
451A VAL* 4.0 17.9 - - + -
468A LEU* 3.9 26.0 - - + -
469A ASN 4.1 3.4 - - - +
470A CYS* 3.9 27.4 - - + -
481A ASP* 3.1 28.5 + - + +
483A GLU* 1.3 75.1 - - - +
485A ILE* 1.3 64.5 + - - +
487A HIS* 3.3 5.3 + - + +
488A VAL* 3.0 30.9 + - + +
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Residues in contact with ILE 485 (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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468A LEU* 3.7 18.1 - - + +
470A CYS* 5.4 3.4 - - - -
480A TYR* 3.8 23.8 - - + -
481A ASP 3.2 10.9 + - - +
482A LEU* 3.4 9.4 - - + +
484A LEU* 1.3 77.7 - - + +
486A GLU* 1.3 58.8 + - - +
488A VAL* 3.3 3.6 + - - +
489A LYS* 2.9 32.9 + - + +
496A VAL* 5.0 5.7 - - + +
498A ALA* 3.7 29.4 - - + -
511A ALA* 4.7 1.3 - - + -
515A THR* 3.5 37.7 - - + +
517A ALA* 3.9 19.1 - - + +
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Residues in contact with GLU 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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482A LEU* 3.1 19.8 + - + +
483A GLU* 3.8 7.4 - - - +
484A LEU 3.3 0.2 - - - -
485A ILE* 1.3 74.5 - - - +
487A HIS* 1.3 60.2 + - - +
489A LYS* 3.4 0.8 + - - -
490A ASP* 3.0 37.8 + - - +
514A LYS 4.5 5.4 - - - +
515A THR* 3.2 16.7 - - + -
516A ARG* 2.7 66.1 + - - +
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Residues in contact with HIS 487 (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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419A LYS* 4.3 18.1 + - + -
420A VAL 4.9 0.4 - - - -
421A PHE* 3.3 48.0 - + + +
435A TRP* 5.3 0.2 - - - -
436A TYR* 4.6 9.1 + + - -
451A VAL* 3.6 28.5 - - + +
452A TRP* 3.4 44.7 - + + +
483A GLU 2.9 18.4 + - - +
484A LEU* 3.4 6.7 - - + +
485A ILE 3.3 0.2 - - - -
486A GLU* 1.3 76.4 - - - +
488A VAL* 1.3 56.2 + - - +
490A ASP* 3.2 11.7 + - - +
491A ALA* 3.1 24.3 + - - +
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Residues in contact with VAL 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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451A VAL* 3.8 35.2 - - + -
452A TRP* 6.1 0.2 - - - +
455A THR* 3.9 24.7 - - + +
466A ILE* 4.4 5.4 - - + -
468A LEU* 3.5 21.8 - - + -
484A LEU* 3.0 17.1 + - + +
485A ILE 3.9 1.3 - - - +
487A HIS* 1.3 73.4 - - - +
489A LYS* 1.3 65.1 + - - +
491A ALA* 3.1 6.4 + - - +
492A VAL* 3.0 26.7 + - + +
496A VAL* 3.9 25.6 - - + -
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Residues in contact with LYS 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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118A PRO* 3.8 15.6 - - - +
234A TYR* 5.3 5.2 + - - -
485A ILE* 2.9 26.2 + - + +
486A GLU* 3.7 3.6 - - - +
487A HIS 3.3 0.2 - - - -
488A VAL* 1.3 76.3 - - - +
490A ASP* 1.3 59.2 + - - +
492A VAL 3.1 24.8 + - - +
493A LYS* 5.2 1.6 + - - +
494A ILE 4.4 6.3 + - - -
496A VAL* 3.6 20.2 - - + -
516A ARG* 3.2 71.5 + - + +
518A ASP* 2.7 33.1 + - - +
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Residues in contact with ASP 490 (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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452A TRP* 3.8 21.1 - - + -
456A ARG* 4.6 1.9 + - - -
486A GLU* 3.0 23.1 + - - +
487A HIS* 3.3 12.9 + - - +
489A LYS* 1.3 77.9 - - - +
491A ALA* 1.3 63.2 + - - +
492A VAL 4.8 0.3 - - - +
516A ARG* 2.6 27.8 + - - +
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Residues in contact with ALA 491 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452A TRP* 3.6 35.7 - - + +
455A THR* 3.7 20.2 - - - +
456A ARG* 2.9 34.9 + - + +
459A GLU* 4.4 1.6 - - - +
487A HIS 3.1 8.0 + - - +
488A VAL* 3.1 12.3 + - - +
490A ASP* 1.3 78.3 - - - +
492A VAL* 1.3 62.5 + - - +
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Residues in contact with VAL 492 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455A THR* 3.4 44.0 - - - +
456A ARG* 3.6 3.8 - - - +
459A GLU* 3.5 21.8 - - + +
466A ILE* 4.4 4.5 - - + -
488A VAL* 3.0 18.3 + - + +
489A LYS* 3.1 23.7 + - - +
490A ASP 4.8 0.3 - - - +
491A ALA* 1.3 80.1 - - - +
493A LYS* 1.3 65.8 - - - +
494A ILE* 3.7 26.7 - - + +
496A VAL* 4.1 11.4 - - + -
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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