Contacts of the strand formed by residues 492 - 501 (chain A) in PDB entry 6TAV
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 LYS 492 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82A ASP* 3.6 27.6 + - - +
490A LEU* 3.5 28.3 - - + +
491A LYS* 1.3 76.7 - - - +
493A LEU* 1.3 62.7 + - - +
494A SER* 3.0 31.1 + - - +
512A GLY* 5.0 14.6 - - - +
513A LEU 4.0 5.2 - - - +
514A LEU* 4.2 8.5 - - + +
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Residues in contact with LEU 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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53A TYR* 4.9 2.2 - - - +
482A LEU* 3.8 33.9 - - + -
486A THR* 4.9 15.3 - - + +
490A LEU 5.8 0.7 - - - +
491A LYS 3.4 4.0 + - - +
492A LYS* 1.3 75.7 - - - +
494A SER* 1.3 70.5 + - - +
495A PHE* 3.6 23.7 + - + -
513A LEU* 2.9 36.8 + - + +
515A VAL* 5.3 9.0 - - + -
544A ALA* 4.7 4.0 - - + -
545A VAL 3.2 33.7 - - - +
546A LEU* 4.8 9.4 - - + -
547A PRO* 5.7 1.8 - - + -
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Residues in contact with SER 494 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A ASP* 4.4 5.6 + - - +
492A LYS* 3.0 31.2 + - - -
493A LEU* 1.3 83.1 - - - +
495A PHE* 1.4 64.0 + - - +
496A TYR* 3.2 41.4 + - - -
510A THR* 4.7 4.3 - - - -
511A HIS 3.8 5.4 - - - -
512A GLY* 4.6 3.4 - - - -
544A ALA* 4.1 0.2 - - - -
545A VAL* 4.0 12.9 + - - +
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Residues in contact with PHE 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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459A VAL* 3.3 41.7 - - + -
478A ALA* 6.4 0.2 - - + -
480A TYR* 4.3 17.9 - + + -
482A LEU* 4.8 4.7 - - + -
493A LEU* 3.7 36.6 - - + -
494A SER* 1.4 76.1 - - - +
496A TYR* 1.3 62.0 + - - +
497A TYR* 4.9 0.9 - - - -
510A THR* 3.4 3.6 + - - -
511A HIS* 2.8 51.6 + - + +
513A LEU* 4.4 19.1 - - + -
524A PHE* 4.8 12.1 - + + -
542A ILE* 4.0 27.4 - - + -
543A TYR 3.9 4.5 - - - -
544A ALA* 4.0 11.4 - - + -
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Residues in contact with TYR 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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50A LEU* 3.3 28.3 - - + +
82A ASP* 2.8 33.3 + - - +
83A VAL* 4.6 0.2 - - - -
84A LEU* 3.5 45.5 - - + -
494A SER* 3.2 40.1 + - - -
495A PHE* 1.3 72.6 - - - +
497A TYR* 1.3 61.6 + - - +
509A GLY 3.9 2.7 - - - -
510A THR* 3.6 24.9 - - + -
542A ILE* 3.2 6.0 - - - +
543A TYR* 2.9 56.0 + + + -
545A VAL* 4.3 9.9 - - + -
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Residues in contact with TYR 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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495A PHE 4.9 0.9 - - - -
496A TYR* 1.3 77.2 - - - +
498A LEU* 1.3 70.8 + - - +
499A ILE* 4.9 13.0 - - + -
508A THR* 3.4 15.6 + - - -
509A GLY* 3.2 37.9 + - - +
510A THR* 3.2 32.7 + - - -
511A HIS* 5.5 2.2 - - + -
526A ILE* 3.8 40.9 - - + +
527A SER* 4.7 8.5 + - - -
528A ILE* 6.4 0.7 - - + -
540A LEU* 4.2 15.5 - - + -
541A LEU* 3.2 18.6 - - - +
542A ILE* 4.4 11.9 - - + -
543A TYR* 5.4 0.4 - - - -
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Residues in contact with LEU 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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34A LEU* 3.7 30.1 - - + -
48A CYS* 4.6 8.3 - - + -
84A LEU* 4.0 15.0 - - + -
497A TYR* 1.3 78.5 - - - +
499A ILE* 1.3 62.8 + - - +
500A MET* 5.8 1.1 - - + -
505A ILE* 3.5 31.9 - - + -
507A ARG 3.6 3.1 - - - +
508A THR* 3.1 36.8 - - - +
539A ARG 3.8 1.4 - - - +
540A LEU* 3.5 4.8 - - - +
541A LEU* 3.0 49.6 + - + +
543A TYR* 5.2 5.2 - - + -
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Residues in contact with ILE 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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497A TYR* 4.9 13.5 - - + -
498A LEU* 1.3 70.4 - - - +
500A MET* 1.3 60.4 + - - +
505A ILE* 3.9 2.9 - - - +
506A VAL* 2.9 34.0 + - + +
507A ARG* 3.2 49.6 + - + +
508A THR 4.5 0.7 - - - +
528A ILE* 3.8 35.0 - - + -
529A PRO* 6.3 0.2 - - + -
534A ILE* 4.6 13.5 - - + -
538A ALA* 4.9 7.6 - - + -
539A ARG 3.4 6.7 - - - +
540A LEU* 3.7 31.0 - - + -
558A TYR* 6.3 0.2 - - + -
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Residues in contact with MET 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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36A PRO* 5.1 8.5 - - + -
498A LEU* 5.7 0.9 - - + +
499A ILE* 1.3 74.0 - - - +
501A ALA* 1.3 63.3 + - - +
503A GLY* 4.3 3.6 - - - +
504A GLY* 3.3 36.6 - - - +
505A ILE* 3.7 10.1 - - + +
506A VAL* 4.1 2.5 - - - -
534A ILE* 4.8 0.9 - - - +
537A VAL* 3.8 1.3 - - - +
538A ALA* 3.6 5.0 - - - -
539A ARG* 2.9 47.5 + - + +
541A LEU* 6.5 1.3 - - - -
627A LEU* 4.0 38.6 - - + +
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Residues in contact with ALA 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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500A MET* 1.3 77.8 - - - +
502A LYS* 1.3 72.0 + - + +
503A GLY 3.1 6.3 - - - +
504A GLY* 2.9 19.9 + - - +
506A VAL* 4.2 7.7 - - + +
533A ASP 4.6 2.5 - - - +
534A ILE* 4.1 11.0 - - + -
535A ALA 3.7 19.7 - - - +
537A VAL* 3.3 26.2 - - + +
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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