Contacts of the strand formed by residues 492 - 501 (chain A) in PDB entry 1ISR
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 TYR 492 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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324A ASP* 5.6 1.9 - - - +
327A ILE* 5.5 3.0 - - + +
331A GLU* 3.4 46.0 - - + +
332A VAL* 4.7 15.9 - - + +
335A ASN* 3.9 31.4 - - + -
484A LEU* 4.3 12.5 - - + +
485A GLN 3.7 3.4 - - - +
486A TYR* 3.5 46.6 - + + -
490A ASN* 5.5 2.9 - - - -
491A ARG* 1.3 89.2 + - - +
493A ASP* 1.3 64.0 + - - +
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Residues in contact with ASP 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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324A ASP* 5.3 4.9 - - - +
483A ASN 3.8 0.2 - - - +
484A LEU* 3.6 9.5 - - - +
485A GLN 3.3 30.1 + - - +
487A THR* 4.5 15.3 - - + -
491A ARG* 3.7 29.5 + - + +
492A TYR* 1.3 74.1 - - - +
494A TYR* 1.3 94.3 + - - +
495A VAL* 3.5 8.0 + - + +
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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
----------------------------------------------------------
320A TRP* 3.2 24.5 + + - -
321A ALA 3.1 25.1 - - - -
322A ASP* 3.7 19.7 - - + -
323A ARG 2.8 27.6 + - - -
324A ASP* 3.8 14.6 - - - -
327A ILE* 3.2 35.2 - - + +
339A THR* 4.4 5.8 - - + -
482A MET* 3.9 34.3 - - + +
483A ASN 4.0 4.0 - - - -
484A LEU* 4.1 17.5 - - + +
493A ASP* 1.3 91.7 + - - +
495A VAL* 1.3 62.6 + - - +
496A HIS 4.0 0.7 + - - -
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Residues in contact with VAL 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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482A MET* 3.6 6.4 - - - -
483A ASN 3.1 26.8 + - - +
485A GLN* 3.6 44.0 - - + +
487A THR* 4.9 12.6 - - + -
493A ASP* 3.9 7.0 - - + +
494A TYR* 1.3 74.9 - - - +
496A HIS* 1.3 70.7 + - - +
497A VAL* 3.1 14.0 + - + +
511A LYS* 5.5 6.7 - - + +
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Residues in contact with HIS 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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480A ASP* 3.8 20.5 + - + +
481A ILE 4.3 3.1 - - - -
482A MET* 4.1 14.3 - - + +
494A TYR 4.0 1.8 + - - -
495A VAL* 1.3 77.8 - - + +
497A VAL* 1.3 63.2 + - - +
498A GLY 3.5 24.6 + - - -
499A THR* 3.8 15.2 - - + +
511A LYS* 4.0 17.8 + - - +
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Residues in contact with VAL 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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338A ILE* 5.8 0.7 - - + -
481A ILE* 3.1 32.0 + - + +
482A MET 4.1 2.2 - - - -
483A ASN* 3.6 28.5 - - + -
495A VAL* 3.1 19.0 + - + +
496A HIS* 1.3 77.2 - - - +
498A GLY* 1.3 58.4 + - - +
507A ILE* 4.9 2.5 - - + -
508A ASP* 3.0 33.7 + - - +
511A LYS* 4.1 27.6 - - + +
512A ILE* 4.2 23.3 - - + -
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Residues in contact with GLY 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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480A ASP* 3.4 2.9 - - - -
481A ILE* 2.8 35.6 + - - -
496A HIS* 3.5 9.1 + - - -
497A VAL* 1.3 85.4 - - - +
499A THR* 1.3 67.7 + - - +
506A ASN 3.2 13.5 - - - -
507A ILE* 4.4 2.7 - - - -
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Residues in contact with THR 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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343A GLN* 5.1 6.7 - - - +
479A TYR 3.3 8.3 - - - +
480A ASP* 3.5 20.0 - - - +
481A ILE* 4.3 3.5 - - - +
496A HIS* 3.8 12.1 - - + +
498A GLY* 1.3 80.4 - - - +
500A TRP* 1.3 64.6 + - - +
501A HIS* 6.0 1.5 - - - +
504A VAL 3.8 0.6 - - - +
505A LEU* 3.8 6.8 - - - +
506A ASN* 3.1 47.6 + - - +
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Residues in contact with TRP 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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210A LEU* 3.5 53.6 - - + -
213A ARG* 3.7 21.8 - - + -
214A ALA* 3.7 23.9 - - + +
217A ASP* 3.4 17.5 + - + -
477A GLY 6.0 0.4 - - - -
478A ARG* 3.5 5.3 - - - +
479A TYR* 2.9 53.2 + + + +
481A ILE* 4.9 4.5 - - + -
499A THR* 1.3 76.6 - - - +
501A HIS* 1.3 63.9 + - - +
502A GLU* 4.2 8.7 - - - -
503A GLY* 3.4 34.5 - - - -
504A VAL 3.2 18.8 + - - -
505A LEU* 3.6 28.3 - - + -
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Residues in contact with HIS 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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477A GLY 4.0 9.2 + - - -
478A ARG* 3.3 52.1 + - + +
499A THR* 6.0 2.0 - - - +
500A TRP* 1.3 78.2 - - - +
502A GLU* 1.3 105.8 + - + +
503A GLY 3.6 0.2 - - - -
504A VAL* 3.0 25.7 + - + +
506A ASN* 6.1 0.2 - - - +
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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