Contacts of the strand formed by residues 478 - 489 (chain B) in PDB entry 3H3T
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 ARG 478 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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468B THR* 3.8 0.5 - - - -
469B HIS* 3.0 35.0 + - + +
470B LYS 5.3 1.2 + - - -
473B TRP* 3.4 37.0 - - + +
475B ALA* 4.1 4.2 - - - +
476B SER* 2.7 39.4 + - - +
477B GLN* 1.3 75.9 - - - +
479B ASP* 1.3 64.2 + - - +
518B CYS* 4.3 1.6 - - - -
519B VAL* 3.0 28.3 - - - +
521B ALA* 4.2 5.6 - - + -
559B PRO* 3.0 24.0 + - - +
560B GLY 3.1 22.2 + - - -
561B GLY* 4.3 1.8 - - - -
562B TRP 3.9 18.6 + - - +
563B ALA* 4.6 0.4 - - - +
600B 16H 4.1 33.0 - - + -
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Residues in contact with ASP 479 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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466B TYR* 2.6 26.0 + - + +
467B GLN 3.2 13.9 - - - +
468B THR* 3.9 5.2 - - + -
469B HIS* 5.2 0.4 - - - -
478B ARG* 1.3 76.2 - - - +
480B VAL* 1.3 63.6 + - - +
515B ASN* 3.0 10.2 + - - -
518B CYS* 3.4 16.8 - - + +
519B VAL 2.8 8.9 + - - +
520B ARG* 2.5 58.3 + - - +
521B ALA* 2.9 26.7 + - - +
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Residues in contact with VAL 480 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465B ILE 3.9 0.2 - - - +
466B TYR* 3.5 7.9 - - - -
467B GLN* 2.9 70.2 + - + +
469B HIS* 3.9 12.1 - - + +
479B ASP* 1.3 77.8 - - - +
481B LEU* 1.3 63.8 + - - +
482B TYR* 3.8 19.3 - - + -
506B SER* 4.3 3.6 - - - +
520B ARG* 4.4 4.7 - - - +
521B ALA* 4.2 11.2 - - + +
523B ILE* 3.6 35.0 - - + -
600B 16H 4.9 3.8 - - + -
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Residues in contact with LEU 481 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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455B VAL* 4.1 12.8 - - + -
464B ILE* 3.6 23.8 - - + -
465B ILE 3.3 19.7 - - - +
466B TYR* 4.2 5.2 - - + -
480B VAL* 1.3 77.1 - - - +
482B TYR* 1.3 58.8 + - - +
506B SER* 3.2 10.8 + - - -
507B VAL* 3.0 39.9 + - + +
508B ASP* 4.3 1.6 - - - +
509B HIS* 3.9 20.4 - - + +
512B ALA* 3.4 37.5 - - + +
520B ARG* 4.0 21.7 - - - +
521B ALA 4.9 0.2 + - - -
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Residues in contact with TYR 482 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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442B ARG* 3.4 19.4 + - - -
464B ILE* 3.3 1.4 - - - -
465B ILE* 2.8 61.2 + - + +
467B GLN* 2.7 39.9 + - + -
480B VAL* 3.8 22.9 - - + -
481B LEU* 1.3 76.9 - - - +
483B LEU* 1.3 65.3 + - - +
484B SER* 3.6 10.7 + - - -
504B ASN* 3.7 37.5 - - + -
505B PHE 3.3 20.2 - - - +
506B SER* 4.0 2.2 - - - +
507B VAL* 4.1 5.8 - - - +
523B ILE* 4.0 11.2 - - + -
600B 16H 3.7 14.4 - - + -
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Residues in contact with LEU 483 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365B HIS* 4.7 0.7 - - + -
367B PHE* 3.4 45.1 - - + -
371B VAL* 3.9 7.6 - - + -
458B LEU* 3.8 13.2 - - + -
462B ALA* 4.5 6.3 - - + -
463B ILE 3.4 9.6 - - - +
464B ILE* 4.3 3.8 - - + +
482B TYR* 1.3 71.0 - - - +
484B SER* 1.3 67.5 + - - +
485B VAL* 3.6 31.4 - - + -
503B CYS 3.2 5.5 - - - +
504B ASN* 3.2 1.6 - - - -
505B PHE* 2.8 58.5 + - + +
507B VAL* 3.8 12.1 - - + +
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Residues in contact with SER 484 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437B TRP* 3.0 31.1 + - - -
442B ARG* 4.9 3.3 + - - -
462B ALA* 3.3 0.7 - - - -
463B ILE* 2.7 45.4 + - - -
465B ILE* 4.3 7.0 - - - +
482B TYR* 3.6 15.2 + - - -
483B LEU* 1.3 73.7 - - - +
485B VAL* 1.3 60.5 + - - +
502B VAL* 3.9 1.7 - - - +
504B ASN* 2.6 26.9 + - - +
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Residues in contact with VAL 485 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365B HIS* 5.9 0.4 - - - +
371B VAL* 3.9 34.1 - - + -
375B VAL* 5.1 2.0 - - + -
437B TRP* 3.9 2.7 - - - -
461B ASN* 3.2 26.5 - - - +
462B ALA* 4.0 9.0 - - + -
483B LEU* 3.6 17.7 - - + -
484B SER* 1.3 77.3 + - - +
486B ILE* 1.3 64.1 + - - +
487B ARG* 4.2 7.6 - - + +
501B ILE 3.7 1.4 - - - +
502B VAL* 3.2 6.1 - - - +
503B CYS* 2.9 55.9 + - + +
505B PHE* 4.4 2.0 - - + -
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Residues in contact with ILE 486 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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433B CYS* 3.5 39.5 - - + +
434B ASN* 3.7 20.6 - - - +
437B TRP* 3.7 29.7 - - + +
460B ASP 5.4 0.2 - - - +
461B ASN* 2.9 53.0 + - + +
485B VAL* 1.3 72.2 - - - +
487B ARG* 1.3 64.2 + - - +
500B TRP* 3.9 24.2 - - + -
501B ILE 3.6 2.9 - - - +
502B VAL* 3.7 10.8 - - + -
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Residues in contact with ARG 487 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368B VAL 5.6 0.2 + - - -
371B VAL* 3.8 21.3 - - - +
372B GLU* 3.2 41.2 + - - +
375B VAL* 4.8 17.7 - - + +
461B ASN* 3.9 18.1 - - - +
485B VAL* 4.1 11.1 + - + +
486B ILE* 1.3 79.6 - - - +
488B LYS* 1.3 67.7 + - - +
489B ILE* 4.2 7.8 - - + +
500B TRP* 3.5 11.2 - - - -
501B ILE* 2.9 47.6 + - + +
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Residues in contact with LYS 488 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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487B ARG* 1.3 82.3 + - - +
489B ILE* 1.3 71.7 + - - +
490B PRO* 3.2 17.4 - - - +
498B GLU* 3.2 32.8 - - - +
499B THR 3.4 7.2 - - - +
500B TRP* 3.4 49.3 - - + +
598B PHE* 5.7 0.2 - - - +
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Residues in contact with ILE 489 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375B VAL* 3.7 29.8 - - + -
379B MET* 4.0 35.7 - - + -
487B ARG* 5.1 9.2 - - + +
488B LYS* 1.3 77.7 - - - +
490B PRO* 1.3 77.2 - - + +
491B ALA 3.3 0.7 + - - -
498B GLU* 4.1 2.4 - - - +
499B THR* 2.7 45.8 + - + +
501B ILE* 4.6 10.3 - - + -
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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