Contacts of the strand formed by residues 433 - 438 (chain A) in PDB entry 2XWB
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 TYR 433 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343A LYS* 3.9 17.0 - - + -
344A PRO* 3.6 36.5 - - + +
346A MET* 3.6 20.9 - - - -
395A GLN* 4.0 9.0 + - - -
424A TYR* 3.3 42.2 + + + -
426A THR* 3.4 16.5 + - - -
431A ASN* 3.1 49.4 + - + -
432A ASN* 1.3 73.5 - - - +
434A LEU* 1.3 63.8 + - - +
455A LEU* 3.5 12.8 - - - +
456A ARG* 3.3 32.2 + - + -
513A TYR* 2.8 16.1 + - - -
525A VAL* 3.7 4.5 - - - -
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Residues in contact with LEU 434 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A LYS* 3.5 12.5 - - - +
346A MET* 4.6 1.8 - - - -
424A TYR* 5.8 0.4 - - - -
433A TYR* 1.3 79.4 - - - +
435A HIS* 1.3 66.3 + - - +
436A LEU* 4.6 7.0 - - + -
453A PHE* 4.7 1.8 - - + -
454A LEU 3.2 26.2 - - - +
455A LEU* 4.5 0.4 - - - -
468A TYR* 3.6 31.6 - - + +
511A ALA* 3.3 38.8 - - + +
512A TYR* 4.3 1.3 - - - -
513A TYR* 3.6 26.9 - - + -
525A VAL* 3.9 10.3 - - + +
526A ALA* 4.5 3.2 + - - +
527A ASP* 3.3 25.8 - - + +
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Residues in contact with HIS 435 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A LYS* 3.6 26.9 + - + +
346A MET* 3.5 25.3 - - + +
347A PRO* 3.4 29.8 + - + +
348A PHE* 4.8 4.7 - + - -
349A ASP* 3.8 30.1 + - + +
434A LEU* 1.3 75.6 - - - +
436A LEU* 1.3 82.1 + - - +
437A SER* 3.7 19.0 + - - -
452A ASN 3.4 1.4 - - - +
454A LEU* 2.9 45.8 + - + +
527A ASP* 3.5 2.5 - - - -
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Residues in contact with LEU 436 (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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434A LEU* 4.6 5.8 - - + -
435A HIS* 1.3 91.1 + - - +
437A SER* 1.3 62.4 + - - +
438A VAL* 3.8 3.0 + - + +
451A VAL* 4.8 5.4 - - + -
452A ASN 3.2 9.2 - - - +
453A PHE* 3.4 35.9 - - + -
509A LEU* 3.5 33.2 - - + +
511A ALA* 3.9 10.5 - - + -
527A ASP* 3.2 41.0 + - + +
529A VAL* 3.8 30.0 - - + +
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Residues in contact with SER 437 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349A ASP* 3.8 21.1 - - - -
386A LYS* 5.7 1.8 - - - -
435A HIS* 3.7 14.0 + - - -
436A LEU* 1.3 73.3 - - - +
438A VAL* 1.3 61.6 + - - +
450A ASN 4.2 0.2 - - - +
452A ASN* 3.1 54.9 + - - +
454A LEU* 5.7 4.1 - - - +
492A LEU* 5.3 1.6 - - - +
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Residues in contact with VAL 438 (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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349A ASP* 4.9 2.2 + - - -
386A LYS* 3.3 15.3 + - - +
436A LEU 3.8 9.2 + - - +
437A SER* 1.3 80.2 - - - +
439A LEU* 1.3 66.0 + - - +
440A ARG* 2.8 15.0 + - - +
449A LEU* 3.5 37.5 - - + -
450A ASN 4.3 3.8 - - - +
451A VAL* 4.3 27.8 - - + -
529A VAL* 4.7 17.5 - - + +
531A VAL* 4.8 14.8 - - + -
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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