Contacts of the strand formed by residues 466 - 474 (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 ASP 466 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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425A VAL* 3.7 10.5 - - - +
426A VAL 3.2 15.5 - - - +
427A LYS* 2.6 46.0 + - + +
428A ASN 5.1 0.4 - - - +
429A VAL* 5.9 0.2 - - - -
460A TYR* 3.8 1.0 - - - -
461A ASP* 2.8 26.4 + - - +
464A SER* 2.9 17.7 + - - +
465A ASN* 1.3 79.7 - - - +
467A TRP* 1.3 66.6 + - - +
468A ARG* 2.8 29.4 + - - +
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Residues in contact with TRP 467 (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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424A ILE 4.0 0.3 - - - +
425A VAL* 3.5 1.4 - - - +
426A VAL* 2.7 43.2 + - + +
429A VAL* 3.9 19.6 + - + +
431A THR* 3.4 37.4 + - + +
435A ASP 3.8 8.7 - - - -
436A THR* 3.7 22.9 - - + -
437A VAL* 3.4 44.6 - - + -
458A LEU* 3.8 26.1 - - + +
459A TYR* 3.6 7.2 - - - -
460A TYR* 3.3 51.5 - + + -
465A ASN 5.0 1.1 - - - -
466A ASP* 1.3 78.4 - - - +
468A ARG* 1.3 59.5 + - - +
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Residues in contact with ARG 468 (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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423A THR* 4.6 9.9 - - + +
424A ILE 3.1 15.0 - - - +
425A VAL* 3.7 25.0 - - + +
458A LEU* 3.5 8.7 - - - +
459A TYR* 2.6 47.5 + - + +
461A ASP* 3.3 27.3 + - + -
464A SER* 3.8 2.6 + - - -
466A ASP* 2.8 36.4 + - - +
467A TRP* 1.3 74.5 - - - +
469A GLY* 1.3 60.2 + - - +
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Residues in contact with GLY 469 (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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423A THR* 3.6 1.6 - - - +
424A ILE* 3.0 27.4 + - - +
457A GLN 5.5 1.1 - - - -
458A LEU* 4.7 6.0 - - - +
459A TYR* 4.6 12.8 - - - -
468A ARG* 1.3 83.1 - - - +
470A ASN* 1.3 70.4 + - - -
471A VAL* 3.5 10.3 + - - +
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Residues in contact with ASN 470 (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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421A MET* 3.7 31.7 - - + +
422A GLN 3.3 3.1 - - - -
423A THR* 2.9 33.1 + - - +
459A TYR* 6.1 0.4 - - - -
469A GLY* 1.3 72.0 - - - -
471A VAL* 1.3 60.9 + - - +
472A VAL* 5.7 0.3 - - - +
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Residues in contact with VAL 471 (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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6A GLY* 5.1 4.0 - - - -
421A MET* 3.6 4.0 - - - -
422A GLN* 2.7 38.0 + - - +
424A ILE* 4.1 19.1 - - + -
439A ILE* 4.4 8.3 - - + -
456A ILE* 4.0 44.9 - - + -
457A GLN 5.4 2.0 - - - +
458A LEU* 5.2 5.2 - - + -
469A GLY* 3.8 13.5 - - - +
470A ASN* 1.3 78.8 - - - +
472A VAL* 1.3 73.7 + - - +
473A LEU* 3.5 13.9 + - + +
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Residues in contact with VAL 472 (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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6A GLY* 5.3 4.4 - - - -
7A MET* 3.4 56.4 + - + +
9A PRO* 4.1 18.4 - - + -
419A PRO* 3.4 27.8 - - + -
420A VAL 3.7 7.6 - - - +
421A MET* 3.3 28.7 - - + -
445A GLU* 4.8 5.0 - - - +
471A VAL* 1.3 79.4 - - - +
473A LEU* 1.3 68.1 + - - +
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Residues in contact with LEU 473 (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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7A MET* 4.4 3.4 - - - -
419A PRO* 3.3 5.3 - - - +
420A VAL* 2.8 38.8 + - - +
422A GLN* 3.9 22.9 - - + -
424A ILE* 4.4 11.2 - - + -
439A ILE* 5.9 1.1 - - + -
445A GLU 5.4 0.2 - - - +
446A LEU* 3.6 32.5 - - + -
471A VAL* 4.0 14.1 - - + +
472A VAL* 1.3 82.2 - - - +
474A PRO* 1.3 75.7 - - + +
475A ALA 3.4 0.2 + - - -
479A ILE* 4.1 16.2 - - + -
502A TRP* 3.9 22.7 - - + -
505A VAL* 4.1 11.7 - - + -
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Residues in contact with PRO 474 (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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7A MET* 4.5 1.5 - - - -
417A VAL* 4.0 23.6 - - + -
418A THR 3.9 4.7 - - - +
419A PRO* 4.8 0.7 - - + -
443A ARG* 4.1 9.2 - - - +
445A GLU* 3.4 46.2 - - + +
473A LEU* 1.3 94.5 - - + +
475A ALA* 1.3 66.3 + - - +
477A ARG* 3.7 14.5 + - + -
479A ILE* 4.3 12.8 - - + -
505A VAL* 3.4 16.0 - - - +
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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