Contacts of the strand formed by residues 418 - 425 (chain A) in PDB entry 1KEK
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 ILE 418 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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416A GLY 3.0 19.7 - - - +
417A THR* 1.3 71.1 - - - +
419A GLN* 1.3 62.6 + - - +
420A CYS* 3.8 19.7 - - - -
447A LEU* 6.1 2.9 - - + -
468A LEU 3.8 0.5 - - - +
469A ARG* 3.3 4.0 - - - +
470A PHE* 2.7 49.8 + - + +
471A GLY* 5.6 0.4 - - - -
485A ASP* 3.4 18.6 - - + +
486A TYR* 5.4 0.7 - - + -
571A ALA 3.6 20.2 - - - +
572A GLY 4.4 18.6 - - - +
573A VAL* 4.5 13.7 - - + -
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Residues in contact with GLN 419 (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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411A ASP* 3.0 28.3 + - - +
413A THR* 3.3 23.6 + - - +
417A THR* 4.2 8.8 + - + +
418A ILE* 1.3 77.0 - - - +
420A CYS* 1.3 62.4 + - - +
468A LEU 3.4 5.2 - - - -
469A ARG* 2.7 39.9 + - + -
479A TYR* 5.2 0.5 + - - -
481A VAL* 3.8 15.3 - - + +
482A ASN 5.1 1.2 + - - -
483A ARG 3.3 22.7 + - - +
484A ALA* 3.5 1.8 - - - -
485A ASP* 2.7 42.2 + - - +
486A TYR 3.3 4.0 + - - -
505A LYS* 4.1 7.3 - - - +
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Residues in contact with CYS 420 (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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418A ILE* 3.8 22.7 - - - -
419A GLN* 1.3 78.6 - - - +
421A GLN* 1.3 69.0 + - - +
422A PHE* 3.7 22.4 - - + -
466A SER 3.6 0.2 - - - +
467A HIS* 3.6 2.1 - - - -
468A LEU* 2.8 41.3 + - + +
470A PHE* 4.9 3.8 - - - -
481A VAL* 4.1 2.4 - - - +
486A TYR* 3.1 21.3 - - + +
567A PHE* 4.0 24.0 - - - -
571A ALA* 4.5 0.9 - - - -
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Residues in contact with GLN 421 (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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420A CYS* 1.3 78.8 - - - +
422A PHE* 1.3 65.5 + - - +
423A TRP* 4.6 8.6 - - - +
465A ILE* 3.8 14.2 - - + +
466A SER 3.1 7.2 - - - +
467A HIS* 4.1 12.0 + - + -
481A VAL* 2.8 44.5 - - + +
482A ASN* 4.6 2.4 - - - -
484A ALA* 3.8 7.0 - - + +
486A TYR* 2.8 9.8 + - - +
487A VAL* 3.4 29.2 - - + +
488A ALA 3.0 23.7 + - - -
500A ILE 4.6 4.2 + - - -
502A GLU 4.4 15.2 + - - +
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Residues in contact with PHE 422 (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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420A CYS* 3.7 14.4 - - + -
421A GLN* 1.3 76.7 - - - +
423A TRP* 1.3 63.9 + - - +
424A GLY 3.8 0.3 + - - -
430A THR* 4.0 17.1 - - + +
434A ASN* 3.6 25.1 - - - -
464A THR 3.5 1.7 - - - +
465A ILE* 3.1 5.9 - - - -
466A SER* 2.8 50.4 + - - -
468A LEU* 3.7 22.7 - - + -
486A TYR* 3.7 20.6 - + - -
488A ALA* 3.5 11.2 - - + +
490A HIS* 3.9 24.2 - + + -
563A MET 5.5 1.1 - - - -
567A PHE* 3.6 38.8 - + + -
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Residues in contact with TRP 423 (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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421A GLN* 4.6 5.9 - - - +
422A PHE* 1.3 76.7 - - - +
424A GLY* 1.3 59.3 + - - +
463A ILE* 3.5 25.6 - - + -
464A THR 3.4 4.5 - - - -
465A ILE* 4.0 27.4 - - + +
487A VAL* 4.1 9.0 - - + +
488A ALA 2.9 21.7 + - - +
489A CYS* 4.2 7.4 - - - -
490A HIS* 2.9 34.4 + - - +
491A ASN 4.1 2.1 + - - -
494A TYR* 4.1 16.8 - + + -
498A TYR* 3.5 37.2 - + + -
499A ASP* 4.2 7.2 - - + -
500A ILE* 3.6 51.7 + - + -
649A GLN* 4.9 13.0 - - + -
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Residues in contact with GLY 424 (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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422A PHE 3.8 1.4 + - - -
423A TRP* 1.3 74.4 - - - +
425A LEU* 1.3 57.2 + - - -
428A ASP* 3.7 10.3 - - - -
430A THR* 4.0 16.8 - - - +
464A THR* 2.6 37.3 + - - -
490A HIS* 4.4 0.4 - - - -
491A ASN* 5.4 0.2 - - - -
494A TYR* 2.6 26.3 + - - -
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Residues in contact with LEU 425 (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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424A GLY* 1.3 73.2 - - - -
426A GLY* 1.3 66.9 + - - +
428A ASP* 2.9 36.0 + - + +
461A GLY* 3.4 39.5 - - - +
462A GLY 3.5 2.2 - - - +
464A THR* 5.3 0.9 - - - -
491A ASN* 3.6 30.2 - - + +
494A TYR* 3.2 15.0 - - + +
677A VAL* 5.4 5.6 - - + -
1216B ARG* 4.0 26.0 - - - +
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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