Contacts of the helix formed by residues 488 - 496 (chain A) in PDB entry 1VOM
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 488 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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483A ASN 3.4 2.4 + - - +
484A HIS* 3.0 34.0 + - + +
487A PHE* 1.3 75.7 - - - +
489A VAL* 1.3 67.9 + - - +
491A GLN* 3.9 3.0 - - - +
492A GLU* 3.0 35.2 + - - +
503A PHE* 6.3 1.6 - - - -
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Residues in contact with VAL 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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484A HIS* 2.8 33.0 + - + +
485A HIS* 4.3 14.4 - - + +
488A LYS* 1.3 75.2 - - - +
490A GLU* 1.3 62.9 + - - +
492A GLU* 3.2 16.0 + - - +
493A GLU* 3.1 21.8 + - - +
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Residues in contact with GLU 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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485A HIS 4.0 8.4 + - - +
486A MET* 3.3 28.7 - - - +
487A PHE* 3.6 4.0 - - - +
489A VAL* 1.3 77.3 - - - +
491A GLN* 1.3 66.3 + - - +
493A GLU* 3.1 12.5 + - - +
494A TYR* 2.7 40.4 + - + +
687A ILE* 4.4 13.7 - - + -
693A PRO* 5.0 0.6 - - - +
695A ARG* 2.5 49.3 + - - +
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Residues in contact with GLN 491 (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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487A PHE* 3.0 19.1 + - - +
488A LYS* 4.1 2.4 - - - +
490A GLU* 1.3 80.2 - - - +
492A GLU* 1.3 58.2 + - - +
494A TYR* 3.0 11.6 - - + +
495A LEU* 2.8 33.2 + - + +
501A TRP* 2.4 34.7 + - + +
503A PHE* 3.3 26.1 - - + -
504A ILE 2.7 40.8 + - - -
506A PHE* 3.5 20.2 - - - -
687A ILE* 3.9 15.7 - - + -
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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
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484A HIS* 5.0 5.7 + - - -
488A LYS* 3.0 33.2 + - - +
489A VAL* 3.2 13.8 + - - +
491A GLN* 1.3 75.8 - - - +
493A GLU* 1.3 52.8 + - - +
495A LEU* 3.5 9.0 - - + +
496A LYS* 2.6 38.4 + - + +
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Residues in contact with GLU 493 (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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489A VAL 3.1 12.1 + - - +
490A GLU 3.1 8.0 + - - +
492A GLU* 1.3 74.9 - - - +
494A TYR* 1.3 57.9 + - + +
496A LYS* 2.9 7.0 + - - +
497A GLU* 2.6 41.2 + - + +
695A ARG* 4.4 21.3 - - - +
743A LYS* 5.9 4.3 - - - +
745A PHE* 4.8 6.5 - - + -
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Residues in contact with TYR 494 (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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490A GLU* 2.7 52.2 + - + +
491A GLN* 3.0 9.6 - - - +
493A GLU* 1.3 74.9 - - + +
495A LEU* 1.3 63.8 + - - +
497A GLU* 3.5 1.7 + - - -
498A LYS 3.1 16.1 + - - -
499A ILE* 3.2 21.9 + - + +
501A TRP* 3.3 66.5 - + + +
687A ILE* 4.6 6.3 + - + +
691A GLY* 4.0 3.8 - - - -
692A PHE* 3.2 43.7 + + + -
693A PRO* 4.2 0.7 - - - +
695A ARG* 3.7 5.6 - - - -
745A PHE* 4.1 16.6 - + - -
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Residues in contact with LEU 495 (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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491A GLN* 2.8 25.7 + - + +
492A GLU* 3.9 7.0 - - + +
494A TYR* 1.3 71.2 - - - +
496A LYS* 1.3 69.8 + - - +
498A LYS* 3.1 16.6 + - - +
501A TRP* 2.9 42.8 - - + +
503A PHE* 4.2 32.1 - - + +
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Residues in contact with LYS 496 (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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492A GLU* 2.6 22.1 + - + +
493A GLU* 3.2 8.5 - - - +
495A LEU* 1.3 74.9 - - - +
497A GLU* 1.3 61.7 - - + +
498A LYS* 2.7 18.5 + - - +
741A ILE* 4.7 4.2 - - - +
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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