Contacts of the strand formed by residues 451 - 456 (chain A) in PDB entry 2H3W
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 451 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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434A GLN* 4.3 5.4 - - - +
437A LEU* 5.1 1.1 - - + -
438A GLN* 2.9 26.1 + - - +
449A CYS 2.9 15.1 + - - -
450A ALA* 1.3 72.9 + - - +
452A TYR* 1.3 67.0 + - - +
469A ARG* 3.5 31.6 - - - +
470A SER* 3.4 28.9 - - - +
471A ALA* 4.0 7.4 - - - +
549A PHE* 3.7 4.0 - - - -
551A LEU* 3.4 27.4 - - + +
553A THR* 4.7 4.5 - - + -
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Residues in contact with TYR 452 (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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102A TRP* 4.5 4.4 - + - -
451A THR* 1.3 75.3 - - - +
453A GLU* 1.3 55.9 + - - +
454A SER* 3.6 18.2 - - - -
465A THR* 4.0 0.2 + - - -
466A ASP 4.1 4.3 + - - -
467A THR* 2.9 35.2 - - + -
468A ILE 3.9 1.8 - - - -
518A ARG* 2.8 24.4 + - - -
549A PHE* 3.4 41.1 - + + -
551A LEU 2.8 11.9 + - - +
552A SER* 4.2 6.7 - - - +
553A THR* 2.7 45.0 + - - +
1602A HC5 2.7 49.8 + - - -
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Residues in contact with GLU 453 (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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430A ASP* 2.5 31.5 - - - +
434A GLN* 3.1 13.6 - - - +
452A TYR* 1.3 79.5 - - - +
454A SER* 1.3 74.2 + - - +
455A ALA 3.5 0.3 + - - -
466A ASP 3.9 1.6 - - - +
467A THR* 3.9 0.5 - - - -
468A ILE* 3.0 51.5 + - + +
470A SER* 4.0 5.6 - - - +
503A HIS* 2.9 37.7 + - - -
553A THR* 3.4 13.5 - - - +
554A ALA* 4.9 3.6 - - - -
555A GLN* 4.6 5.1 + - - +
578A TYR* 3.3 4.5 + - - -
1601A COA 4.3 5.2 - - - +
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Residues in contact with SER 454 (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 TYR* 3.6 9.8 - - - -
453A GLU* 1.3 84.5 - - - +
455A ALA* 1.3 59.1 + - - +
465A THR* 5.1 1.3 - - - -
466A ASP 4.1 1.6 - - - -
468A ILE* 4.3 1.9 - - - +
553A THR 3.2 8.0 + - - -
554A ALA* 3.2 12.0 - - - +
555A GLN 5.3 0.3 + - - -
1601A COA 3.7 40.9 - - - +
1602A HC5 2.8 43.7 + - - -
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Residues in contact with ALA 455 (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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454A SER* 1.3 74.1 - - - +
456A SER* 1.3 59.4 + - - +
457A LEU* 3.3 4.2 - - + +
465A THR* 3.0 9.0 - - - -
466A ASP 2.8 40.6 + - - +
468A ILE* 3.5 31.9 - - + -
510A ALA* 3.8 15.7 - - + -
511A ILE* 4.6 4.3 - - + -
1601A COA 3.5 8.5 - - - +
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Residues in contact with SER 456 (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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163A LEU* 3.9 17.4 - - - +
349A PRO* 5.3 3.6 - - - -
455A ALA* 1.3 71.2 - - - +
457A LEU* 1.3 63.0 + - - +
458A ARG* 3.2 34.4 + - - +
459A MET 5.2 0.3 + - - -
464A ARG 3.6 5.9 + - - -
511A ILE* 3.5 24.8 - - - +
1601A COA 2.8 40.4 + - - -
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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