Contacts of the strand formed by residues 479 - 486 (chain A) in PDB entry 1VEP
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 ILE 479 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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424A ILE* 6.0 0.4 - - + -
442A ASN* 3.7 5.6 - - - +
443A ARG* 4.1 17.0 - - + -
446A LEU* 4.0 23.8 - - + -
473A LEU* 4.1 19.3 - - + -
474A PRO* 4.3 12.3 - - + -
477A ARG 4.1 1.6 - - - +
478A ASN* 1.3 80.4 - - - +
480A GLU* 1.3 65.7 + - - +
481A PHE* 3.9 22.4 - - + -
501A SER* 3.1 6.8 - - - -
502A TRP* 3.0 50.1 + - + +
503A ASN* 4.0 0.9 - - - +
505A VAL* 3.8 26.2 - - + -
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Residues in contact with GLU 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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441A GLY* 3.0 3.6 - - - -
442A ASN* 3.0 48.7 + - + +
446A LEU* 3.9 1.7 - - - +
449A TRP* 4.1 3.8 - - + -
478A ASN* 5.6 0.9 - - + -
479A ILE* 1.3 80.8 - - - +
481A PHE* 1.3 61.6 + - - +
499A GLN* 2.6 35.4 + - - +
500A GLN 3.2 7.9 - - - +
501A SER* 4.0 14.5 - - - +
503A ASN* 5.2 5.5 + - - +
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Residues in contact with PHE 481 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424A ILE* 4.2 28.5 - - + -
426A VAL* 5.8 1.6 - - + -
439A ILE* 4.5 22.0 - - + -
440A THR 3.3 17.3 - - - +
441A GLY* 4.0 3.4 - - - -
446A LEU* 4.2 8.3 - - + -
449A TRP* 3.8 4.6 - - - -
479A ILE* 3.9 27.4 - - + -
480A GLU* 1.3 78.3 - - - +
482A LYS* 1.3 70.0 + - - +
483A ALA 5.0 0.2 - - - -
496A GLN* 5.1 2.2 - - - -
499A GLN* 3.8 0.6 - - - +
500A GLN* 2.7 64.3 + - + +
501A SER* 4.1 9.6 - - - -
502A TRP* 4.9 0.9 - + + -
512A HIS* 3.6 31.6 - + - -
514A SER* 5.1 2.9 - - - -
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Residues in contact with LYS 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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439A ILE* 3.4 4.4 - - - -
440A THR* 3.1 31.1 + - - +
449A TRP* 4.3 4.0 - - + -
481A PHE* 1.3 83.9 - - - +
483A ALA* 1.3 63.1 + - - +
484A PHE* 4.2 0.9 - - - -
495A TRP* 3.9 15.4 - - + -
496A GLN* 2.7 41.7 + - - +
497A THR 3.3 13.1 + - - -
498A ILE 4.1 1.1 - - - +
499A GLN* 3.4 30.6 - - + +
1E GLC 2.6 36.6 + - - +
2E GLC 3.4 17.8 + - - +
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Residues in contact with ALA 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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426A VAL* 4.1 15.7 - - + -
437A VAL* 3.9 16.2 - - + -
438A TYR 3.1 13.5 - - - +
439A ILE* 3.9 12.9 - - + +
481A PHE* 5.0 0.2 - - - -
482A LYS* 1.3 75.5 - - - +
484A PHE* 1.3 63.7 + - - +
495A TRP* 3.7 3.3 - - - -
496A GLN* 2.9 43.3 + - - +
516A TRP* 4.0 11.7 - - + -
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Residues in contact with PHE 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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437A VAL* 3.4 6.1 - - - +
438A TYR* 2.9 66.1 + + + -
440A THR* 4.0 16.6 - - + -
451A THR* 3.9 22.9 - - + -
455A PRO* 3.6 23.1 - - + -
482A LYS 4.2 3.4 - - - -
483A ALA* 1.3 79.4 - - - +
485A ILE* 1.3 69.1 + - - +
486A LYS* 4.4 16.6 - - + -
492A VAL* 4.0 22.4 - - + -
494A SER 3.2 15.7 - - - +
495A TRP* 3.9 28.9 - + + -
516A TRP* 3.9 4.9 - - - -
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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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429A VAL* 3.6 28.3 - - + -
430A PRO* 4.0 19.5 - - + +
431A THR* 3.9 12.8 - - + -
435A ASP* 3.4 35.4 - - + +
436A THR 3.6 3.6 - - - +
437A VAL* 4.3 2.2 - - + -
484A PHE* 1.3 78.0 - - - +
486A LYS* 1.3 63.0 + - - +
492A VAL* 3.4 7.3 - - - +
493A LYS* 2.8 41.5 + - + -
494A SER* 2.9 28.5 + - - +
516A TRP* 3.8 13.9 - - + -
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Residues in contact with LYS 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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434A GLY 4.2 0.2 - - - +
435A ASP* 3.3 4.5 - - - -
436A THR* 2.9 30.1 + - - +
438A TYR* 3.7 41.5 + - + +
451A THR 2.8 28.2 + - - -
452A LYS* 3.7 13.8 + - - +
455A PRO* 4.0 9.9 - - - +
484A PHE* 4.1 11.9 + - + -
485A ILE* 1.3 76.1 - - - +
487A SER* 1.3 65.0 + - - +
490A GLY* 3.7 37.0 - - - -
491A THR 3.4 5.6 - - - +
492A VAL* 4.6 4.5 - - - +
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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