Contacts of the strand formed by residues 462 - 469 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365A HIS* 4.1 20.9 - - + +
437A TRP* 3.9 1.4 - - - -
458A LEU* 2.9 39.6 + - + -
459A ALA 3.2 11.0 + - - +
460A ASP 3.6 0.6 - - - -
461A ASN* 1.3 88.9 - - - +
463A ILE* 1.3 63.7 + - - +
483A LEU* 4.4 4.3 - - + -
484A SER 3.6 4.5 - - - -
485A VAL* 3.9 16.4 - - + -
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Residues in contact with ILE 463 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437A TRP* 4.2 31.0 - - + +
439A VAL* 3.7 31.9 - - + +
454A VAL* 4.3 15.3 - - + -
456A GLU 3.4 13.7 - - - +
457A THR* 4.1 18.4 - - + +
458A LEU* 4.6 2.2 - - - +
459A ALA 4.9 0.7 - - - +
462A ALA* 1.3 79.7 - - - +
464A ILE* 1.3 64.6 + - - +
465A ILE* 3.9 17.3 - - + -
482A TYR 3.9 0.2 - - - +
483A LEU* 3.3 4.0 - - - +
484A SER* 2.8 40.1 + - - +
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Residues in contact with ILE 464 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367A PHE* 4.0 21.1 - - + -
454A VAL* 3.8 3.6 - - - +
455A VAL* 2.9 31.9 + - + -
456A GLU* 3.0 38.2 + - + +
458A LEU* 3.9 23.6 - - + -
463A ILE* 1.3 76.4 - - - +
465A ILE* 1.3 63.4 + - - +
481A LEU* 4.2 21.1 - - + -
482A TYR 3.4 7.9 - - - +
483A LEU* 4.3 5.6 - - + -
507A VAL* 4.1 24.0 - - + -
508A ASP 5.4 0.2 - - - +
509A HIS* 4.0 14.8 - - + -
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Residues in contact with ILE 465 (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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437A TRP 5.6 0.2 - - - +
439A VAL* 3.7 18.8 - - + -
442A ARG* 3.7 16.6 - - - +
452A PHE* 4.0 12.6 - - + -
453A HIS 3.7 9.2 - - - +
454A VAL* 4.7 4.3 - - + -
455A VAL* 4.2 2.5 - - - -
463A ILE* 3.9 22.0 - - + -
464A ILE* 1.3 78.6 - - - +
466A TYR* 1.3 75.3 + - - +
467A GLN* 3.8 15.3 - - - +
481A LEU* 3.5 4.0 - - - +
482A TYR* 2.7 69.7 + - + +
484A SER* 4.4 4.7 - - - +
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Residues in contact with TYR 466 (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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452A PHE* 3.1 5.6 - - - +
453A HIS* 2.9 58.1 + + + +
455A VAL* 3.6 19.8 - - + +
465A ILE* 1.3 74.6 - - - +
467A GLN* 1.3 62.2 + - - +
468A THR* 3.6 19.7 - - + +
479A ASP* 2.4 48.7 + - + +
480A VAL 3.4 13.5 - - - -
481A LEU* 3.8 14.4 - - + -
512A ALA* 4.5 9.0 - - + -
513A PRO 5.3 1.8 - - - -
515A ASN* 3.4 22.4 + - + +
520A ARG* 3.5 17.0 - - - -
380B THR* 6.2 1.6 - - + -
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Residues in contact with GLN 467 (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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442A ARG* 4.7 1.0 + - - -
449A ILE* 3.4 19.0 - - + +
451A ASN 3.3 6.1 - - - +
452A PHE* 3.2 15.4 - - + +
465A ILE* 3.8 5.7 - - - +
466A TYR* 1.3 81.3 - - - +
468A THR* 1.3 62.0 + - - +
469A HIS* 3.0 31.5 + - + +
479A ASP* 3.2 5.4 - - - +
480A VAL* 2.9 51.9 + - + +
482A TYR* 2.8 29.7 + - + -
600A 16H 3.3 26.3 + - - +
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Residues in contact with THR 468 (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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449A ILE* 3.7 3.1 - - - +
450A GLU* 2.7 45.4 + - - +
451A ASN* 2.9 30.3 + - - +
466A TYR* 3.6 31.1 - - + +
467A GLN* 1.3 73.2 - - - +
469A HIS* 1.3 55.1 + - - +
477A GLN* 4.5 4.7 - - - +
478A ARG 3.8 4.5 - - - -
479A ASP* 3.9 6.1 - - + -
515A ASN* 5.1 0.2 - - - +
518A CYS* 4.1 14.6 - - - -
384B GLN* 4.7 12.2 - - + +
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Residues in contact with HIS 469 (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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446A GLU* 5.0 2.5 - - - -
448A THR* 3.1 37.4 + - - +
449A ILE* 4.1 5.1 + - + -
450A GLU* 4.2 2.7 - - - -
467A GLN* 3.0 31.6 + - + -
468A THR* 1.3 76.5 - - - +
470A LYS* 1.3 71.2 + - - +
477A GLN* 3.4 28.1 - - - +
478A ARG 2.8 21.6 + - - +
480A VAL* 3.9 16.7 - - + +
600A 16H 3.8 57.7 - + + +
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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