Contacts of the strand formed by residues 437 - 442 (chain A) in PDB entry 5KZW
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 ARG 437 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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367A TRP* 3.3 64.7 - - + +
399A ASP* 2.8 10.2 + - - +
400A VAL* 3.3 6.5 - - + -
401A GLN* 3.1 22.7 + - - +
431A LEU* 4.4 5.6 - - - +
432A HIS* 4.3 3.1 - - + -
435A GLY 4.2 4.2 + - - -
436A ARG* 1.3 82.6 - - - +
438A TYR* 1.3 62.0 + - - +
513A ASP* 3.3 31.9 + - + +
591A ARG* 5.3 2.2 - - - +
833A THR* 4.6 3.2 + - - -
834A THR* 3.5 23.2 + - - +
863A GLU* 3.0 34.2 + - - -
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Residues in contact with TYR 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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400A VAL* 4.1 0.2 - - - -
401A GLN* 3.1 25.1 - - + -
402A TRP 4.2 1.1 - - - -
403A ASN* 2.7 43.6 + - - +
424A PHE* 3.2 33.9 - + - -
427A MET* 3.7 11.2 - - + -
428A VAL* 3.7 31.0 - - + -
431A LEU* 3.7 20.6 - - + -
432A HIS* 4.9 0.7 - - - +
437A ARG* 1.3 75.7 - - - +
439A MET* 1.3 75.4 + - - +
440A MET* 3.6 17.8 - - + +
510A VAL* 5.0 0.2 - - + -
512A PHE* 3.9 14.4 - - + -
513A ASP* 2.9 39.5 + - - +
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Residues in contact with MET 439 (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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367A TRP* 4.8 2.7 - - + -
400A VAL* 3.5 20.6 - - + +
401A GLN 3.1 4.9 + - - -
402A TRP* 3.0 71.2 - - + +
403A ASN 3.1 3.8 + - - -
438A TYR* 1.3 79.6 - - - +
440A MET* 1.3 63.1 + - - +
513A ASP 4.4 1.3 - - - -
514A GLY* 3.4 36.1 - - - -
515A MET 3.7 29.4 - - - +
516A TRP* 3.9 0.9 - - - +
596A PHE* 3.6 30.1 - - + -
598A ILE* 4.4 3.8 - - + -
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Residues in contact with MET 440 (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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403A ASN 3.2 7.6 - - - +
407A TYR* 3.4 34.1 - - + +
414A PHE* 6.3 0.9 - - + -
424A PHE* 5.1 2.0 - - + -
438A TYR* 3.6 20.0 - - + +
439A MET* 1.3 78.0 - - - +
441A ILE* 1.3 62.5 + - - +
442A VAL* 3.6 24.9 + - + +
506A PHE* 4.3 13.7 - - + -
510A VAL* 6.3 0.2 - - - -
512A PHE* 3.4 60.1 - - + -
514A GLY 4.1 5.9 + - - +
515A MET* 4.1 1.6 - - + -
516A TRP* 3.2 26.5 + - - -
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Residues in contact with ILE 441 (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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403A ASN 3.1 6.5 + - - -
404A ASP* 3.4 32.8 - - - +
405A LEU* 3.5 11.0 - - + +
407A TYR* 2.6 29.4 + - + -
408A MET* 3.5 12.5 - - + +
440A MET* 1.3 74.7 - - - +
442A VAL* 1.3 59.9 + - - +
443A ASP* 4.1 9.6 - - - +
516A TRP* 3.4 41.4 - - + +
518A ASP* 3.7 28.7 - - + +
1014A GLC 3.3 25.4 - - - +
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Residues in contact with VAL 442 (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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407A TYR* 4.4 2.7 - - - +
413A ASP* 3.7 13.7 - - - +
414A PHE* 4.6 11.0 - - + -
440A MET* 3.9 28.3 - - + +
441A ILE* 1.3 80.8 - - - +
443A ASP* 1.3 75.2 + - - +
499A TRP* 3.8 27.1 - - + -
515A MET* 4.1 23.3 - - + -
516A TRP 2.7 12.4 + - - +
517A ILE* 3.4 7.6 - - + +
518A ASP* 3.1 24.1 + - - +
579A GLU* 4.8 0.2 - - - +
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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