Contacts of the strand formed by residues 499 - 506 (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 THR 499 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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379B MET* 4.1 17.5 - - + +
488B LYS* 3.4 4.0 - - - +
489B ILE* 2.7 53.7 + - + +
497B PRO 4.0 4.9 + - - -
498B GLU* 1.3 75.4 - - - +
500B TRP* 1.3 66.4 + - - +
528B ILE* 3.4 33.0 - - + -
529B CYS 3.5 7.9 - - - +
530B GLN* 3.4 26.3 + - + +
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Residues in contact with TRP 500 (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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429B GLY* 3.7 10.5 - - - +
430B HIS* 3.4 67.5 - + + +
433B CYS* 3.6 17.9 - - + -
486B ILE* 3.9 30.1 - - + -
487B ARG* 3.5 20.0 - - - -
488B LYS* 3.4 45.5 - - + +
498B GLU* 4.5 7.0 + - + -
499B THR* 1.3 80.3 - - - +
501B ILE* 1.3 60.7 + - - +
528B ILE* 3.4 3.3 - - - +
529B CYS 2.7 38.2 + - - +
531B THR* 5.9 0.9 - - - -
598B PHE* 3.9 9.5 + - - -
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Residues in contact with ILE 501 (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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375B VAL* 4.5 21.5 - - + +
378B HIS* 4.1 18.8 - - + -
379B MET* 4.5 11.9 - - - -
433B CYS* 3.8 1.3 - - - -
485B VAL 3.7 0.9 - - - +
486B ILE* 3.6 3.3 - - - +
487B ARG* 2.9 46.0 + - + +
489B ILE* 4.6 9.4 - - + -
500B TRP* 1.3 77.7 - - - +
502B VAL* 1.3 68.3 + - - +
503B CYS* 3.7 26.2 - - - -
526B ALA* 4.2 1.3 - - + -
527B MET 3.3 4.9 - - - +
528B ILE* 3.7 30.7 - - + -
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Residues in contact with VAL 502 (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* 3.6 40.6 - - + +
436B PHE* 3.5 32.7 - - + -
437B TRP* 3.7 15.9 - - + -
484B SER* 3.9 7.2 - - - +
485B VAL 3.2 7.9 - - - +
486B ILE* 3.7 11.4 - - + -
501B ILE* 1.3 71.5 - - - +
503B CYS* 1.3 63.0 + - - +
504B ASN* 3.7 17.6 + - - +
526B ALA* 3.1 5.7 - - - +
527B MET 2.8 36.6 + - - +
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Residues in contact with CYS 503 (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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374B MET* 4.7 2.9 - - + -
375B VAL* 3.7 37.0 - - - -
378B HIS* 4.3 12.6 - - + -
483B LEU 3.2 5.0 - - - +
485B VAL* 2.9 46.1 + - + +
501B ILE* 3.7 23.6 - - - -
502B VAL* 1.3 69.8 - - - +
504B ASN* 1.3 64.8 + - - +
505B PHE* 4.1 15.6 - - + -
525B VAL 3.4 6.7 - - - +
526B ALA* 4.4 0.7 - - - -
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Residues in contact with ASN 504 (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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436B PHE* 3.6 19.3 - - - -
442B ARG* 5.6 0.9 + - - -
482B TYR* 3.7 18.7 - - + -
483B LEU 3.2 3.1 - - - -
484B SER* 2.6 37.2 + - - -
502B VAL* 3.7 9.3 - - - +
503B CYS* 1.3 73.8 + - - +
505B PHE* 1.3 59.7 + - - +
523B ILE* 3.8 7.6 - - + +
524B ASN* 3.5 0.9 - - - -
525B VAL* 2.6 43.5 + - + +
600B 16H 3.0 35.5 + - - +
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Residues in contact with PHE 505 (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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367B PHE* 4.9 0.4 - + - -
370B LYS* 3.5 37.0 - - + -
371B VAL* 3.7 22.4 - - + -
374B MET* 4.0 36.6 - - + -
482B TYR* 3.7 5.4 - - - +
483B LEU* 2.8 60.8 + - + +
485B VAL* 4.4 1.1 - - + -
503B CYS* 4.1 20.0 - - + -
504B ASN* 1.3 77.9 - - - +
506B SER* 1.3 72.4 + - - +
507B VAL* 3.8 17.3 - - + -
523B ILE* 3.4 11.7 - - - +
524B ASN* 4.3 1.8 - - + -
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Residues in contact with SER 506 (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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370B LYS* 5.6 1.9 - - - -
480B VAL* 4.3 3.1 - - - +
481B LEU 3.2 15.3 + - - -
482B TYR* 4.0 1.3 - - - +
505B PHE* 1.3 79.1 - - - +
507B VAL* 1.3 65.4 + - - +
521B ALA 3.8 5.2 + - - -
522B LYS* 3.3 28.0 - - - -
523B ILE* 2.9 39.5 + - - +
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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