Contacts of the strand formed by residues 491 - 498 (chain A) in PDB entry 1ZJA
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 VAL 491 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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299A LEU* 3.7 3.6 - - - -
303A ARG* 2.9 17.0 + - - -
488A ASN* 3.0 19.4 + - - +
490A ASP* 1.3 85.7 - - + +
492A TYR* 1.3 64.4 + - - +
493A ALA* 3.7 3.6 + - - +
506A VAL* 3.5 31.9 - - + -
507A VAL 3.5 8.1 - - - +
508A ASN* 4.1 4.7 - - - +
514A ARG* 3.8 22.0 - - + -
515A SER 4.3 8.1 - - - +
516A PHE* 4.4 13.5 - - + -
546A LEU* 3.6 23.6 - - + -
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Residues in contact with TYR 492 (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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299A LEU* 3.6 11.2 - - + +
302A PHE* 3.9 18.6 - + - -
303A ARG* 3.6 35.9 - - + +
306A ILE* 3.6 15.1 - - + +
353A VAL* 4.0 19.7 - - + -
357A GLN* 3.2 22.4 + - - -
481A TYR* 2.7 29.4 + - - -
483A ASP* 4.0 5.6 - - - -
491A VAL* 1.3 69.8 - - - +
493A ALA* 1.3 62.5 + - - +
494A TYR* 3.4 29.7 - + - -
505A VAL 3.6 1.0 - - - +
506A VAL* 3.4 2.8 - - - -
507A VAL* 2.8 38.9 + - + +
509A PHE* 3.8 23.3 - + + -
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Residues in contact with ALA 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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303A ARG* 3.2 17.9 + - - +
483A ASP* 3.4 2.9 - - - +
484A ILE* 3.1 28.3 + - + -
491A VAL 3.7 2.7 + - - +
492A TYR* 1.3 76.7 - - - +
494A TYR* 1.3 63.3 + - - +
505A VAL 3.2 9.0 - - - +
506A VAL* 4.4 3.6 - - + -
516A PHE* 3.4 43.3 - - + -
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Residues in contact with TYR 494 (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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353A VAL* 3.5 12.9 + - + -
356A THR* 2.6 44.5 + - - -
357A GLN* 3.0 21.3 + - - -
481A TYR* 3.4 27.1 - + + -
482A ARG 3.1 16.2 - - - +
483A ASP* 4.0 2.7 - - - -
484A ILE* 4.2 4.1 - - - +
492A TYR* 3.4 41.5 - + - -
493A ALA* 1.3 77.9 - - - +
495A THR* 1.3 66.0 + - - +
496A ARG* 4.2 7.6 - - + -
504A LEU* 3.5 4.6 - - - +
505A VAL* 2.8 57.1 + - + +
507A VAL* 5.3 0.4 - - + -
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Residues in contact with THR 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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480A SER 3.7 0.3 - - - +
481A TYR* 3.5 5.4 - - - -
482A ARG* 2.9 50.7 + - - +
484A ILE* 4.3 7.6 - - + -
494A TYR* 1.3 80.0 - - - +
496A ARG* 1.3 66.2 + - - +
497A SER* 4.3 5.5 + - - -
502A THR* 3.9 19.9 - - + +
503A TYR 3.1 12.8 - - - +
504A LEU* 4.0 16.6 - - + -
522A MET* 4.1 21.5 - - + -
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Residues in contact with ARG 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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356A THR 2.8 36.9 + - - +
357A GLN 3.2 6.3 + - - -
358A ARG* 3.4 16.1 - - - +
475A ALA* 3.2 28.0 + - + +
476A LEU* 2.7 43.2 + - + +
477A SER 3.0 26.9 + - - -
479A GLY 3.0 18.4 + - - -
480A SER 3.0 22.5 + - - -
481A TYR* 4.1 16.8 - - - -
494A TYR* 4.2 8.3 - - + -
495A THR* 1.3 79.4 - - - +
497A SER* 1.3 62.6 + - - +
501A GLU 4.0 0.5 - - - +
502A THR* 3.5 0.2 - - - -
503A TYR* 2.9 35.5 + - + +
505A VAL* 5.0 3.4 - - + -
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Residues in contact with SER 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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475A ALA* 4.1 2.0 - - - -
479A GLY* 3.0 6.2 - - - -
480A SER* 2.9 42.4 + - - +
495A THR* 4.3 6.1 + - - -
496A ARG* 1.3 77.5 + - - +
498A GLN* 1.3 61.8 + - - +
500A GLY 6.1 0.7 - - - -
501A GLU 3.2 5.2 - - - -
502A THR* 3.3 28.8 + - - +
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Residues in contact with GLN 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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474A PRO* 3.5 29.9 - - + +
475A ALA* 3.9 16.0 - - + +
478A THR* 2.9 41.9 + - - +
479A GLY* 3.3 0.6 + - - -
497A SER* 1.3 77.5 - - - +
499A ASP* 1.3 93.6 + - + +
500A GLY 3.2 1.5 - - - +
501A GLU* 2.9 28.6 + - - +
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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