Contacts of the strand formed by residues 496 - 501 (chain A) in PDB entry 3VP1
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 MET 496 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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221A ILE* 4.4 8.1 - - - -
227A PHE* 3.5 39.7 - - + -
265A VAL* 3.8 9.0 - - + -
266A CYS 3.5 15.7 - - - +
267A THR* 3.7 8.7 - - + +
268A VAL* 4.1 3.2 - - - +
432A ALA* 4.4 0.4 - - - +
435A ALA* 3.3 11.9 - - - +
492A VAL* 2.9 51.8 + - + +
495A VAL* 1.3 86.0 - - + +
497A GLY* 1.3 60.7 + - - +
498A MET* 3.3 36.6 - - + -
521A LEU* 4.4 5.8 - - + -
527A PHE* 4.2 9.6 - - + -
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Residues in contact with GLY 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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264A SER 4.1 0.2 - - - +
266A CYS 2.9 32.4 + - - -
428A SER 3.7 7.6 - - - +
431A ALA* 3.6 7.2 - - - -
432A ALA* 3.4 26.1 - - - +
490A LEU 3.6 2.9 - - - -
491A VAL* 4.7 0.2 - - - -
496A MET* 1.3 76.8 - - - +
498A MET* 1.3 66.8 + - - +
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Residues in contact with MET 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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231A ILE* 5.1 0.7 - - - -
263A VAL* 3.7 10.1 - - + -
264A SER 3.4 5.4 - - - +
265A VAL* 3.4 26.0 - - + -
428A SER* 4.2 4.9 - - - -
431A ALA* 3.5 6.8 - - - +
488A ILE 4.4 0.4 - - - -
489A LEU* 3.7 3.3 - - - -
490A LEU* 2.8 51.5 + - + +
492A VAL* 6.3 0.4 - - + -
496A MET* 3.3 28.7 - - + -
497A GLY* 1.3 80.1 - - - +
499A MET* 1.3 60.8 + - - +
500A CYS* 3.3 23.6 - - - -
517A PHE* 3.1 36.6 - - + -
521A LEU* 4.1 9.0 - - - -
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Residues in contact with MET 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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262A GLY 3.9 0.9 - - - +
263A VAL* 3.5 3.5 - - - -
264A SER 3.1 29.0 + - - -
282A PHE* 4.0 26.2 - - + -
284A LEU* 4.6 10.1 - - + -
287A CYS* 4.4 12.8 - - - -
424A CYS* 3.5 36.0 - - - +
427A ALA* 3.5 28.7 - - + -
428A SER* 3.8 9.4 - - - +
488A ILE 3.5 21.3 - - - +
489A LEU* 4.1 22.0 - - + +
498A MET* 1.3 76.5 - - - +
500A CYS* 1.3 73.6 + - - +
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Residues in contact with CYS 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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261A TRP* 4.1 13.2 - - + -
262A GLY 3.5 5.4 - - - -
263A VAL* 4.5 4.3 - - - -
486A GLY 3.7 1.2 - - - +
487A GLY* 3.3 2.9 - - - -
488A ILE* 2.8 40.7 + - + +
490A LEU* 5.3 2.0 - - - -
498A MET* 3.3 31.6 - - - -
499A MET* 1.3 75.1 - - - +
501A TRP* 1.3 62.1 + - - +
514A GLY* 4.3 13.0 - - - -
517A PHE* 3.6 22.2 - - - -
518A CYS* 4.8 12.1 - - - -
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Residues in contact with TRP 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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256A PHE* 3.7 27.1 - + - -
260A LEU* 3.3 35.7 - - + -
261A TRP* 3.1 10.9 - - - -
262A GLY 3.0 29.8 + - - -
277A ASP* 3.7 28.7 - - + -
280A VAL* 3.9 29.6 - - + -
282A PHE* 3.5 42.1 - + + +
424A CYS* 3.5 16.6 - - - -
485A ALA 2.9 26.1 + - - -
486A GLY 3.4 12.1 - - - -
487A GLY 3.7 3.4 - - - -
500A CYS* 1.3 77.3 - - - +
502A SER* 1.3 67.2 + - - +
503A PRO* 3.8 13.2 - - + +
511A SER* 5.2 0.2 - - - -
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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