Contacts of the strand formed by residues 462 - 469 (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 ALA 462 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365B HIS* 4.1 15.7 - - - +
437B TRP* 3.6 1.6 - - - -
458B LEU* 2.9 37.3 + - + +
459B ALA* 3.2 10.9 + - + +
461B ASN* 1.3 87.8 - - - +
463B ILE* 1.3 62.9 + - - +
483B LEU* 4.5 7.4 - - + -
484B SER 3.3 6.3 - - - +
485B VAL* 4.0 15.7 - - + -
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Residues in contact with ILE 463 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437B TRP* 4.2 30.7 - - + +
439B VAL* 3.7 32.1 - - + -
454B VAL* 4.3 13.9 - - + -
456B GLU 3.4 13.7 - - - +
457B THR* 4.2 19.7 - - + +
458B LEU* 4.4 2.2 - - - +
459B ALA 4.8 1.1 - - - +
462B ALA* 1.3 80.0 - - - +
464B ILE* 1.3 60.9 + - - +
465B ILE* 3.9 18.4 - - + -
483B LEU* 3.4 4.9 - - - +
484B SER* 2.7 41.5 + - - +
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Residues in contact with ILE 464 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366B ARG* 4.2 0.2 - - - +
367B PHE* 3.9 28.3 - - + -
454B VAL* 3.7 2.9 - - - +
455B VAL* 2.8 38.3 + - + +
456B GLU* 3.0 21.6 + - + +
458B LEU* 3.7 19.7 - - + -
463B ILE* 1.3 77.2 - - - +
465B ILE* 1.3 63.1 + - - +
481B LEU* 3.6 26.7 - - + -
482B TYR 3.3 8.3 - - - +
483B LEU* 4.6 3.1 - - + -
507B VAL* 4.0 18.6 - - + -
508B ASP 4.9 0.4 - - - +
509B HIS* 3.9 22.7 - - + -
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Residues in contact with ILE 465 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439B VAL* 3.7 18.8 - - + -
442B ARG* 3.2 29.4 - - - +
452B PHE* 4.0 11.7 - - + -
453B HIS 3.6 11.0 - - - +
454B VAL* 4.5 4.9 - - + -
463B ILE* 3.9 21.3 - - + -
464B ILE* 1.3 78.6 - - - +
466B TYR* 1.3 71.5 + - - +
467B GLN* 3.8 9.9 - - - +
480B VAL 3.9 0.7 - - - +
481B LEU* 3.3 9.5 - - - +
482B TYR* 2.8 65.4 + - + +
484B SER* 4.3 4.0 - - - -
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Residues in contact with TYR 466 (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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451B ASN* 5.0 4.5 - - - -
452B PHE* 3.1 2.6 - - - +
453B HIS* 2.9 59.2 + + + +
455B VAL* 3.7 21.2 - - + +
465B ILE* 1.3 74.4 - - - +
467B GLN* 1.3 63.9 + - - +
468B THR* 3.4 23.5 - - + +
479B ASP* 2.6 45.2 + - + +
480B VAL 3.5 10.1 - - - -
481B LEU* 4.2 7.0 - - + -
512B ALA* 4.1 19.7 - - + -
515B ASN* 3.6 9.9 + - - -
517B ARG* 4.8 3.6 + - - -
518B CYS* 4.4 2.1 - - - -
520B ARG* 3.7 12.3 - - - -
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Residues in contact with GLN 467 (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* 4.6 4.2 + - - +
449B ILE* 3.0 31.6 - - + +
451B ASN 3.3 4.9 - - - +
452B PHE* 3.3 20.8 - - + +
465B ILE* 3.8 6.4 - - - +
466B TYR* 1.3 77.7 - - - +
468B THR* 1.3 63.5 + - - +
469B HIS* 3.0 16.4 + - - +
479B ASP* 3.2 6.1 - - - +
480B VAL* 2.9 52.7 + - + +
482B TYR* 2.7 30.4 + - + -
600B 16H 3.2 22.9 + - - +
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Residues in contact with THR 468 (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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449B ILE* 3.7 4.5 - - - +
450B GLU* 2.7 45.2 + - - +
451B ASN* 2.8 37.2 + - - +
466B TYR* 3.4 32.3 - - + +
467B GLN* 1.3 74.8 - - - +
469B HIS* 1.3 57.2 + - - +
477B GLN* 4.3 9.0 - - - +
478B ARG 3.8 5.4 - - - -
479B ASP* 3.9 5.4 - - + -
517B ARG* 5.6 2.2 - - - +
518B CYS* 4.1 12.3 - - - -
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Residues in contact with HIS 469 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446B GLU* 4.6 2.9 - - - -
448B THR* 3.2 33.5 + - - +
449B ILE* 3.6 4.2 - - + +
450B GLU* 4.2 3.1 - - - -
467B GLN* 3.0 30.7 + - + -
468B THR* 1.3 78.6 - - - +
470B LYS* 1.3 74.3 + - - +
477B GLN* 3.1 27.4 - - - +
478B ARG* 3.0 24.0 + - + +
480B VAL* 3.9 15.6 - - + +
600B 16H 3.4 56.9 - + + +
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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