Contacts of the strand formed by residues 521 - 530 (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 521 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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362A GLY 5.2 6.6 + - - +
363A ILE* 5.3 14.5 - - + +
364A PRO* 5.8 4.9 - - - +
480A TYR* 3.1 27.2 + - - +
481A ILE* 4.1 16.8 - - + -
519A ASP* 3.1 14.0 + - - +
520A MET* 1.3 106.6 - - - +
522A GLY* 1.3 64.0 - - - +
523A HIS* 6.1 1.6 - - + +
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Residues in contact with GLY 522 (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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479A HIS* 3.5 8.5 + - - +
480A TYR* 3.2 44.5 + - - +
521A LYS* 1.3 80.7 - - - +
523A HIS* 1.3 78.0 + - - +
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Residues in contact with HIS 523 (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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477A GLN* 5.3 5.2 - - - +
478A ALA 3.7 6.5 - - - -
479A HIS* 3.9 19.7 + - + +
480A TYR* 3.6 7.3 + - - -
521A LYS* 6.1 1.7 - - + +
522A GLY* 1.3 84.4 - - - +
524A PHE* 1.3 65.7 + - - +
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Residues in contact with PHE 524 (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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477A GLN* 4.7 6.3 + - - +
478A ALA* 2.7 68.8 + - + +
480A TYR* 4.0 20.6 - + + +
495A PHE* 4.8 16.2 - + + -
511A HIS* 3.3 57.0 - + + +
513A LEU* 5.4 5.4 - - + -
523A HIS* 1.3 77.3 - - - +
525A SER* 1.3 74.9 + - - +
526A ILE* 4.5 11.4 - - + -
542A ILE* 4.8 8.3 - - + -
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Residues in contact with SER 525 (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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475A THR* 5.1 8.4 - - - -
476A VAL 3.2 17.7 - - - -
477A GLN* 3.6 27.8 + - - +
524A PHE* 1.3 90.9 - - - +
526A ILE* 1.4 63.8 + - - +
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Residues in contact with ILE 526 (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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461A LEU* 6.0 4.0 - - + -
475A THR* 4.4 2.7 - - - -
476A VAL* 2.8 48.5 + - + +
478A ALA* 5.6 3.6 - - + +
497A TYR* 3.8 51.8 - - + +
510A THR 4.5 8.7 - - - +
511A HIS* 4.7 13.5 - - + +
524A PHE* 4.6 12.1 - - + -
525A SER* 1.4 75.1 - - - +
527A SER* 1.3 74.0 + - - +
528A ILE* 5.9 0.9 - - + -
540A LEU* 5.5 8.3 - - + -
542A ILE* 5.6 7.9 - - + -
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Residues in contact with SER 527 (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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473A THR* 6.3 1.3 - - - -
474A GLN 3.8 4.5 - - - -
475A THR* 4.1 14.8 - - - +
497A TYR* 4.7 9.9 + - - -
526A ILE* 1.3 90.1 - - - +
528A ILE* 1.3 65.7 + - - +
529A PRO* 4.6 4.2 - - - +
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Residues in contact with ILE 528 (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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468A LEU* 6.4 1.8 - - + -
473A THR* 4.5 2.0 - - - -
474A GLN* 2.8 58.8 + - + +
475A THR* 4.3 0.2 - - - -
476A VAL* 3.7 25.1 - - + -
497A TYR* 6.4 0.7 - - + -
499A ILE* 3.8 43.5 - - + -
507A ARG* 5.5 0.2 - - - +
526A ILE* 4.4 1.3 - - + +
527A SER* 1.3 79.3 - - - +
529A PRO* 1.3 73.5 - - + +
530A VAL* 3.2 7.2 + - + +
534A ILE* 4.9 9.6 - - + -
538A ALA* 6.3 1.3 - - + -
540A LEU* 4.7 13.2 - - + -
558A TYR* 6.2 2.5 - - + -
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Residues in contact with PRO 529 (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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473A THR* 3.7 27.3 - - + -
499A ILE* 6.3 0.4 - - + -
507A ARG* 2.9 42.3 + - - +
527A SER* 4.6 4.9 - - - +
528A ILE* 1.3 86.0 - - + +
530A VAL* 1.3 65.9 + - - +
531A LYS* 3.3 9.3 + - + +
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Residues in contact with VAL 530 (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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468A LEU* 4.3 21.3 - - + -
469A PRO* 3.3 22.2 - - + +
470A CYS* 3.6 12.3 - - + +
471A GLY* 3.1 19.3 + - - -
472A HIS 3.2 28.1 + - - +
473A THR* 4.1 0.5 - - - +
474A GLN* 3.9 17.5 - - + -
507A ARG* 4.8 1.1 - - - +
528A ILE* 3.9 13.9 - - + +
529A PRO* 1.3 72.1 - - - +
531A LYS* 1.4 63.2 + - - +
534A ILE* 5.6 6.5 - - + -
560A VAL* 4.2 23.1 - - + -
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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