Contacts of the strand formed by residues 469 - 476 (chain A) in PDB entry 2ZL6
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 ASN 469 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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460A HIS* 3.5 46.6 + - + +
461A TYR 3.9 2.7 - - - -
462A VAL* 4.7 4.9 - - + -
467A GLY 3.4 4.4 + - - +
468A ARG* 1.3 82.7 + - - +
470A LEU* 1.3 59.9 + - - +
471A GLY* 2.9 33.2 + - - +
472A GLU* 4.6 9.3 + - - +
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Residues in contact with LEU 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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461A TYR* 2.7 39.0 + - + +
462A VAL 4.5 0.2 - - - -
463A ASP* 4.1 23.8 - - + +
468A ARG* 3.8 50.5 - - + +
469A ASN* 1.3 72.4 - - - +
471A GLY* 1.3 56.4 + - - +
495A LEU* 3.8 18.4 - - + +
496A PRO* 3.8 31.0 - - + -
499A GLY* 5.5 1.3 - - - -
516A VAL* 3.4 20.0 - - - +
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Residues in contact with GLY 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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460A HIS* 3.4 1.4 - - - -
461A TYR* 2.9 27.4 + - - +
469A ASN* 2.9 13.7 + - - +
470A LEU* 1.3 81.9 - - - +
472A GLU* 1.3 62.7 + - - -
473A PHE* 3.5 14.7 - - - -
516A VAL* 4.2 15.7 - - - -
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Residues in contact with GLU 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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458A LEU* 4.2 12.2 - - + +
459A LEU 3.4 7.2 - - - +
460A HIS* 4.2 19.9 + - + +
469A ASN* 4.6 6.5 + - - +
471A GLY* 1.3 73.4 - - - -
473A PHE* 1.3 67.0 + - - +
483A CYS* 3.9 11.8 - - - +
484A VAL 4.9 0.2 + - - -
511A TYR* 4.3 14.0 + - - -
512A GLN 4.5 0.2 - - - +
513A LEU* 3.6 25.6 - - + +
514A LYS* 3.0 68.3 + - + +
516A VAL 4.7 1.9 + - - +
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Residues in contact with PHE 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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253A MET* 4.6 3.6 - - - -
419A VAL* 3.7 22.7 - - + -
458A LEU* 3.7 7.4 - - - +
459A LEU* 2.8 40.7 + - + +
461A TYR* 3.8 19.3 - - + -
471A GLY* 3.5 17.9 - - - -
472A GLU* 1.3 79.4 - - - +
474A LYS* 1.3 64.7 + - - +
481A LEU* 4.6 5.2 - - + -
482A THR 3.2 20.9 - - - +
483A CYS* 3.7 20.6 - - + -
492A PRO* 5.0 1.8 - - + -
495A LEU* 3.6 28.0 - - + -
501A PHE* 3.5 39.5 - + + -
513A LEU* 4.1 3.1 - - - -
516A VAL 4.6 2.5 - - - -
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Residues in contact with LYS 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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414A PHE* 5.0 0.4 - - - -
416A GLU* 2.9 21.5 + - - +
456A ALA* 3.8 21.3 - - + -
457A ALA 3.2 8.3 - - - +
458A LEU* 4.7 1.6 - - + -
459A LEU* 4.6 3.8 - - - -
473A PHE* 1.3 76.3 - - - +
475A ALA* 1.3 59.4 + - - +
476A TYR* 3.2 22.1 + - + -
480A PHE 3.9 0.3 - - - +
481A LEU* 3.2 3.8 - - - +
482A THR* 2.8 43.1 + - - +
507A VAL* 4.6 7.4 - - + -
508A SER 4.0 5.2 - - - -
509A ARG 2.6 28.9 + - - -
510A PHE* 4.0 0.8 - - - +
511A TYR* 2.7 33.7 + - + +
513A LEU* 3.7 20.9 - - + +
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Residues in contact with ALA 475 (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 PHE* 5.8 0.9 - - + -
233A LEU* 5.4 3.1 - - + -
272A LEU* 3.8 21.4 - - + +
456A ALA* 3.4 4.2 - - - -
457A ALA* 2.8 43.3 + - + -
459A LEU* 3.9 21.2 - - + +
474A LYS* 1.3 73.7 - - - +
476A TYR* 1.3 63.1 + - - +
480A PHE 3.3 4.9 - - - +
481A LEU* 4.0 14.6 - - + +
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Residues in contact with TYR 476 (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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272A LEU* 3.3 11.1 - - - +
412A PRO* 3.6 14.9 - - + +
414A PHE* 5.1 1.7 - - - -
416A GLU* 2.5 31.6 + - - -
455A GLU 4.4 4.3 - - - -
456A ALA* 4.5 3.4 - - + -
474A LYS* 3.2 33.1 + - + -
475A ALA* 1.3 77.2 - - - +
477A PRO* 1.3 67.4 - - + +
478A ASP 4.4 0.9 - - - +
479A GLY* 2.8 23.6 + - - -
480A PHE* 2.8 47.9 + + + +
482A THR* 3.4 18.6 - - + -
509A ARG* 3.6 52.1 + - + +
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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