Contacts of the helix formed by residues 490 - 501 (chain A) in PDB entry 1V9P
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 SER 490 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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485A ARG 5.0 1.8 - - - -
486A MET* 2.8 44.7 - - - +
487A GLY 3.9 2.0 - - - +
488A GLU 3.8 0.2 - - - +
489A LYS* 1.3 84.8 - - - +
491A ALA* 1.3 66.0 + - - +
493A ASN* 3.7 6.2 - - - +
494A LEU* 3.6 16.5 + - - +
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Residues in contact with ALA 491 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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478A GLU* 4.3 18.8 - - + +
481A LEU* 4.1 29.2 - - + +
486A MET* 4.3 4.0 - - - +
487A GLY 3.1 23.0 + - - +
488A GLU* 4.0 5.8 - - + -
489A LYS 4.0 0.2 - - - +
490A SER* 1.3 74.8 + - - +
492A GLN* 1.3 66.2 + - - +
493A ASN 2.7 6.6 + - - -
494A LEU* 2.8 15.6 + - - +
495A LEU* 2.9 13.6 + - - +
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Residues in contact with GLN 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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478A GLU* 2.9 26.4 + - - +
488A GLU* 2.7 43.1 + - + +
489A LYS 5.7 0.4 - - - +
490A SER 3.8 0.2 - - - -
491A ALA* 1.3 77.7 - - - +
493A ASN* 1.3 62.6 + - - +
495A LEU* 3.5 10.2 - - - +
496A ARG* 3.3 20.8 + - - +
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Residues in contact with ASN 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 LYS 4.1 16.4 + - - +
490A SER* 3.7 11.6 - - - +
491A ALA 2.7 4.4 + - - -
492A GLN* 1.3 75.7 - - - +
494A LEU* 1.3 58.5 + - - +
496A ARG* 2.7 64.9 + - - +
497A GLN* 3.7 8.7 + - - +
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Residues in contact with LEU 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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449A ILE* 4.8 1.3 - - + -
451A GLY* 3.7 29.2 - - - -
452A LEU* 3.8 10.3 - - + -
456A LEU* 3.5 32.5 - - + -
460A LEU* 6.0 0.2 - - + -
481A LEU* 4.4 14.4 - - + -
486A MET* 4.7 7.9 - - - -
490A SER 3.6 7.7 + - - +
491A ALA 2.8 9.9 + - - +
493A ASN* 1.3 73.6 - - - +
495A LEU* 1.3 60.0 + - - +
497A GLN* 2.7 35.8 + - - +
498A ILE* 3.1 39.0 + - + +
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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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475A LEU* 4.0 7.9 - - + +
476A ARG* 3.2 47.6 - - + +
478A GLU* 3.7 17.5 - - + +
481A LEU* 4.2 14.3 - - + +
491A ALA 2.9 12.0 + - - +
492A GLN* 3.5 16.8 - - - +
494A LEU* 1.3 81.0 - - - +
496A ARG* 1.3 59.7 + - - +
498A ILE* 3.7 9.8 + - + +
499A GLU* 3.6 18.2 + - + +
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Residues in contact with ARG 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 GLN 3.3 7.7 + - - +
493A ASN* 2.7 53.5 + - - +
494A LEU 3.0 1.0 + - - -
495A LEU* 1.3 78.9 - - - +
497A GLN* 1.3 81.3 + - - +
499A GLU* 3.1 9.8 - - + +
500A GLU* 2.8 59.4 + - + +
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Residues in contact with GLN 497 (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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448A ASP 5.2 3.0 + - - +
449A ILE* 4.4 15.8 - - + +
450A GLU* 3.3 41.6 + - - +
451A GLY* 2.8 32.6 + - - -
493A ASN* 3.8 11.8 + - - +
494A LEU* 2.7 20.2 + - - +
496A ARG* 1.3 91.3 - - - +
498A ILE* 1.3 58.1 + - - +
499A GLU 2.7 10.3 + - - -
500A GLU* 4.3 9.4 - - - +
501A SER* 2.9 28.0 + - - -
504A ARG* 4.7 2.4 + - - +
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Residues in contact with ILE 498 (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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449A ILE* 4.1 17.0 - - + -
452A LEU* 4.3 7.6 - - + -
472A LEU* 3.4 49.4 - - + +
473A TYR* 3.0 41.7 - - + +
475A LEU* 4.4 16.2 - - + -
481A LEU* 5.5 1.6 - - + -
494A LEU* 3.1 34.0 + - + -
495A LEU* 4.1 14.1 - - + +
497A GLN* 1.3 75.2 - - - +
499A GLU* 1.3 56.5 + - - +
501A SER* 3.3 7.0 + - - -
502A LYS* 4.4 0.3 - - - -
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Residues in contact with GLU 499 (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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476A ARG* 6.1 0.9 - - - +
495A LEU* 3.6 11.0 + - + +
496A ARG* 3.1 17.7 - - + +
497A GLN 2.7 1.0 - - - -
498A ILE* 1.3 78.4 - - - +
500A GLU* 1.3 64.2 + - + +
501A SER 3.1 1.1 - - - -
502A LYS* 2.9 70.8 + - - +
503A HIS* 3.9 11.7 + - - +
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Residues in contact with GLU 500 (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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496A ARG* 2.8 56.8 + - + +
497A GLN* 3.3 6.7 + - - +
499A GLU* 1.3 74.5 - - + +
501A SER* 1.3 63.2 + - - +
503A HIS* 3.0 31.5 + - + +
504A ARG* 3.8 19.8 + - - +
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Residues in contact with SER 501 (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 MET* 3.2 35.8 - - - +
448A ASP 4.2 1.3 - - - -
449A ILE* 4.1 10.4 - - - +
473A TYR* 3.2 18.8 + - - -
497A GLN 2.9 19.0 + - - -
498A ILE* 3.3 11.8 + - - -
500A GLU* 1.3 71.8 - - - +
502A LYS* 1.3 68.5 + - - +
503A HIS 2.9 3.4 + - - -
504A ARG* 3.0 32.1 + - - +
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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