Contacts of the strand formed by residues 449 - 457 (chain A) in PDB entry 1VDV
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 VAL 449 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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440A VAL* 4.4 2.0 - - + -
441A LEU 4.0 3.1 - - - -
442A PHE* 4.0 7.9 - - + -
443A GLN* 5.0 1.6 + - - -
447A MET 4.8 0.7 - - - +
448A GLN* 1.3 73.4 - - - +
450A LYS* 1.3 60.4 + - - +
451A GLU 3.7 25.8 - - - +
452A LEU* 3.9 13.9 - - + -
473A GLN* 3.5 15.7 - - + +
474A LEU* 4.1 7.6 - - + -
475A SER* 2.7 31.0 + - - -
476A LYS 2.8 21.3 + - - +
478A TRP* 3.8 32.3 - - + +
482A LEU* 4.0 13.5 - - + -
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Residues in contact with LYS 450 (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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413A ARG* 6.1 0.2 - - - +
441A LEU* 2.6 43.5 + - + +
442A PHE 4.1 10.1 - - - +
443A GLN* 3.5 34.8 + - - +
444A PRO* 5.7 2.9 - - + +
448A GLN 3.4 0.6 + - - -
449A VAL* 1.3 75.6 - - - +
451A GLU* 1.3 69.4 + - + +
474A LEU* 3.5 19.1 - - - +
475A SER 5.0 0.2 - - - +
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Residues in contact with GLU 451 (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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413A ARG* 4.0 10.3 + - - -
439A ARG* 2.9 29.1 + - - +
440A VAL* 3.3 7.3 - - - +
441A LEU* 2.8 62.0 + - + +
449A VAL* 3.7 2.5 - - - +
450A LYS* 1.3 91.5 - - + +
452A LEU* 1.3 62.5 + - - +
474A LEU* 4.0 3.8 - - - -
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Residues in contact with LEU 452 (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 ARG* 3.4 18.2 - - - +
440A VAL* 4.1 15.0 - - + -
449A VAL* 3.9 11.2 - - + -
451A GLU* 1.3 75.3 - - - +
453A ALA* 1.3 62.2 + - - +
454A LEU* 4.0 18.8 - - + -
467A LEU* 5.8 1.2 - - - +
470A THR* 3.4 45.8 + - + +
471A GLN* 5.4 3.6 + - - -
473A GLN* 4.0 28.7 - - + -
474A LEU* 4.1 7.3 - - + +
478A TRP* 4.2 22.9 - - + -
482A LEU* 5.5 0.4 - - + -
486A VAL* 4.9 9.0 - - + -
516A PHE* 5.1 0.9 - - + -
519A PHE* 4.3 1.1 - - + -
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Residues in contact with ALA 453 (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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366A MET 5.4 0.9 - - - +
367A ALA* 3.8 16.0 - - - +
437A GLY 3.9 0.9 - - - +
438A MET* 3.3 4.7 - - - -
439A ARG* 2.8 63.7 + - - +
452A LEU* 1.3 76.0 - - - +
454A LEU* 1.3 64.4 + - - +
455A CYS* 4.0 6.5 - - - -
465A SER* 5.1 4.9 - - - +
467A LEU* 6.5 0.2 - - - -
470A THR* 4.5 1.1 - - - -
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Residues in contact with LEU 454 (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 GLY 3.9 3.1 - - - -
438A MET* 3.8 23.8 - - + -
452A LEU* 4.0 17.9 - - + -
453A ALA* 1.3 78.4 - - - +
455A CYS* 1.3 62.2 + - - +
456A TYR* 3.9 21.9 - - + +
465A SER* 3.5 2.6 + - - -
466A ALA* 3.0 27.7 + - + -
469A THR* 5.2 0.4 - - + -
470A THR* 3.5 28.6 - - + +
486A VAL* 3.9 16.8 - - + -
490A LEU* 4.3 13.9 - - + -
516A PHE* 3.7 33.2 - - + -
519A PHE* 4.1 3.1 - - + -
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Residues in contact with CYS 455 (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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363A PRO* 3.5 24.4 - - + +
366A MET* 3.6 28.7 - - - -
367A ALA* 3.7 25.8 - - - -
436A CYS* 3.2 6.6 - - - +
437A GLY 2.9 34.2 + - - +
453A ALA* 4.6 3.8 - - - -
454A LEU* 1.3 79.3 - - - +
456A TYR* 1.3 63.1 + - - +
463A THR* 4.8 0.2 - - + -
464A ILE 3.2 8.5 - - - +
465A SER* 3.9 14.1 - - - -
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Residues in contact with TYR 456 (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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363A PRO* 4.1 5.2 - - - -
434A VAL* 4.0 16.2 - - + -
435A THR 3.3 3.4 - - - +
436A CYS* 3.7 13.7 - - + -
438A MET* 3.1 27.7 - - + +
454A LEU* 3.9 26.1 - - + +
455A CYS* 1.3 77.6 - - - +
457A GLY* 1.3 64.1 + - - +
459A MET* 4.3 14.3 + - + -
462A ARG 4.3 0.5 - - - +
463A THR* 3.5 5.0 - - - +
464A ILE* 2.9 40.6 + - + +
466A ALA* 4.7 3.1 - - + -
490A LEU* 3.4 20.0 - - + +
494A LEU* 3.7 22.2 - - + -
512A THR* 2.8 46.3 + - + -
515A PHE* 4.6 3.6 - - + -
516A PHE* 4.2 0.2 - - - +
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Residues in contact with GLY 457 (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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357A PRO 3.3 13.7 - - - -
358A ILE* 4.8 0.4 - - - -
359A SER 4.7 0.4 - - - -
363A PRO* 3.9 7.1 - - - +
434A VAL* 3.5 8.7 - - - +
435A THR* 2.7 46.4 + - - +
456A TYR* 1.3 74.9 - - - +
458A GLY* 1.3 62.8 + - - -
459A MET 3.3 4.1 + - - -
462A ARG 5.2 0.2 - - - -
463A THR* 4.9 2.0 - - - -
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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