Contacts of the strand formed by residues 463 - 471 (chain B) 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 463 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1199A ASP 5.3 0.3 - - - +
423B TRP* 3.4 37.7 - - + -
424B GLY 3.9 0.2 - - - +
454B SER 4.1 0.2 - - - +
455B TYR 3.7 2.0 - - - -
456B ASP* 2.8 52.7 + - - +
462B GLY* 1.3 72.6 - - - -
464B THR* 1.3 71.9 + - - +
465B ILE* 3.9 11.3 - - + +
494B TYR* 3.4 28.3 - - + +
498B TYR* 4.0 27.1 - - + +
649B GLN* 4.8 15.7 - - + +
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Residues in contact with THR 464 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1199A ASP* 4.9 2.8 + - - +
422B PHE 3.7 0.3 - - - +
423B TRP* 3.6 0.5 - - - -
424B GLY* 2.9 40.2 + - - +
425B LEU 5.6 0.7 - - - -
426B GLY* 4.7 12.5 - - - -
430B THR* 6.1 2.2 - - - -
431B VAL* 3.4 32.4 - - + +
453B PHE* 4.7 2.5 - - + -
454B SER 3.3 13.9 - - - +
455B TYR* 3.7 25.2 - - + -
462B GLY 4.0 0.7 + - - -
463B ILE* 1.3 77.9 - - - +
465B ILE* 1.3 75.8 + - - +
466B SER* 4.0 2.5 - - - +
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Residues in contact with ILE 465 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421B GLN* 3.9 20.6 - - + -
422B PHE 3.3 8.5 - - - +
423B TRP* 3.9 31.0 - - + +
453B PHE* 3.7 0.2 - - - -
454B SER* 2.8 44.0 + - - +
463B ILE* 3.9 25.8 - - + +
464B THR* 1.3 79.2 - - - +
466B SER* 1.3 75.8 + - - +
467B HIS* 3.2 29.9 + - + +
649B GLN* 5.6 5.4 - - + +
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Residues in contact with SER 466 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421B GLN* 3.2 8.3 - - - -
422B PHE* 2.7 41.8 + - - -
430B THR* 4.3 3.6 - - - +
431B VAL* 4.0 9.4 - - - +
434B ASN* 2.6 35.2 + - - -
452B TYR 3.7 4.0 - - - -
453B PHE* 3.3 21.9 - - - -
464B THR* 4.4 1.4 - - - +
465B ILE* 1.3 77.3 - - - +
467B HIS* 1.3 63.2 - - - +
468B LEU* 4.1 2.2 - - - -
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Residues in contact with HIS 467 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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420B CYS 3.5 4.3 - - - -
421B GLN* 4.0 8.2 + - + -
450B GLN* 3.8 3.2 - - - +
451B GLY* 3.4 3.5 - - - -
452B TYR* 2.8 48.8 + - + +
454B SER* 4.5 6.3 - - - -
465B ILE* 3.2 39.9 + - + +
466B SER* 1.3 73.3 - - - +
468B LEU* 1.3 62.2 + - - +
469B ARG* 5.6 3.8 - - - +
480B LEU* 3.6 38.2 - - + +
481B VAL* 3.0 50.6 + - + +
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Residues in contact with LEU 468 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418B ILE 3.9 0.4 - - - +
419B GLN* 3.4 2.9 - - - -
420B CYS* 2.7 46.0 + - + +
422B PHE* 3.9 22.2 - - + -
434B ASN* 3.9 30.5 - - + +
437B ALA* 4.9 4.7 - - + -
438B ILE* 3.8 18.8 - - + -
450B GLN 3.3 4.5 - - - +
451B GLY* 3.9 15.0 - - - -
453B PHE* 4.2 9.9 - - + -
466B SER* 4.1 0.9 - - - -
467B HIS* 1.3 86.1 - - - +
469B ARG* 1.3 64.8 + - - +
470B PHE* 3.8 33.0 - - + -
481B VAL* 3.9 1.2 - - - +
567B PHE* 5.0 2.2 - - + -
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Residues in contact with ARG 469 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175B ARG* 5.5 0.2 - - - +
413B THR* 4.1 1.4 - - - +
417B THR* 4.2 9.6 - - + -
418B ILE 3.2 7.2 - - - +
419B GLN* 2.8 32.0 + - + -
449B ALA* 3.4 3.1 - - - -
450B GLN* 2.7 70.4 + - + +
467B HIS* 5.6 2.8 - - - +
468B LEU* 1.3 79.8 - - - +
470B PHE* 1.3 67.3 + - - +
475B ILE* 4.0 16.4 - - + -
477B SER* 3.2 28.5 + - - -
479B TYR* 3.1 37.6 + - - -
480B LEU* 3.1 28.5 + - - +
481B VAL* 3.5 16.9 - - + +
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Residues in contact with PHE 470 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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416B GLY 3.8 0.7 - - - +
417B THR* 3.3 5.3 - - - -
418B ILE* 2.8 39.0 + - + +
420B CYS* 4.8 2.5 - - - -
438B ILE* 4.2 15.3 - - + -
441B ILE* 3.8 33.4 - - + -
447B LEU* 4.5 7.9 - - + -
448B PHE 3.2 7.4 - - - +
449B ALA* 3.6 28.9 - - + -
468B LEU* 3.8 37.5 - - + -
469B ARG* 1.3 75.2 - - - +
471B GLY* 1.3 60.6 + - - +
475B ILE* 4.4 0.9 - - - -
567B PHE* 3.6 28.9 - + - -
573B VAL* 3.8 30.1 - - + -
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Residues in contact with GLY 471 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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416B GLY 3.8 10.8 - - - -
417B THR* 4.3 9.0 - - - -
447B LEU* 3.5 12.6 - - - +
448B PHE* 2.7 41.1 + - - +
470B PHE* 1.3 76.7 - - - +
472B GLU* 1.3 64.0 + - - -
473B LYS 3.2 8.7 - - - -
475B ILE* 4.2 2.7 - - - +
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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
------------------------------------------------------------
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