Contacts of the strand formed by residues 368 - 379 (chain A) in PDB entry 1KIX
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 368 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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342A HIS* 4.3 12.8 - - + -
345A LEU* 4.4 14.2 - - + +
366A GLN* 2.9 21.6 + - - +
367A ASP* 1.3 90.4 + - - +
369A PHE* 1.3 66.2 + - - +
478A VAL* 3.6 26.7 - - + -
479A VAL 3.3 4.9 - - - +
480A GLU* 3.9 2.4 - - - +
489A LYS* 2.7 28.5 + - - -
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Residues in contact with PHE 369 (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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345A LEU* 4.4 6.3 - - - -
348A THR* 3.7 15.0 - - - +
353A LEU* 3.5 27.8 - - + -
363A LEU* 3.4 34.5 - - + -
366A GLN* 3.4 32.3 - - + +
367A ASP* 3.5 26.2 - - - -
368A THR* 1.3 77.0 - - - +
370A ARG* 1.3 61.0 + - - +
478A VAL* 3.2 10.7 - - - +
479A VAL* 2.7 43.9 + - + +
481A ARG* 3.4 28.0 - - - -
486A TYR* 4.0 15.9 - + - -
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Residues in contact with ARG 370 (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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338A VAL* 3.5 24.0 - - - +
342A HIS 2.9 30.9 + - - -
343A ALA* 4.0 11.6 + - - +
345A LEU* 3.7 33.6 + - + +
346A PRO 3.9 3.9 + - - +
347A SER* 3.3 4.7 + - - +
348A THR* 2.7 33.6 + - - +
369A PHE* 1.3 77.9 - - - +
371A THR* 1.3 61.7 + - - +
372A GLN* 3.8 11.4 - - - +
476A ASP* 2.5 35.4 + - - +
477A ALA 3.3 12.3 - - - +
478A VAL* 4.1 12.6 - - + -
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Residues in contact with THR 371 (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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348A THR 2.7 26.7 + - - +
349A SER* 4.4 1.0 - - - -
350A LEU* 4.2 14.3 + - + +
353A LEU* 4.0 20.6 - - + -
370A ARG* 1.3 75.8 - - - +
372A GLN* 1.3 87.0 + - - +
373A PHE* 3.9 23.8 - - + -
419A ASP* 4.8 0.2 + - - -
431A VAL* 5.6 1.1 - - + -
475A VAL 3.8 0.5 - - - +
476A ASP* 3.6 0.3 - - - -
477A ALA* 3.0 35.4 + - - +
479A VAL* 4.9 10.1 - - + -
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Residues in contact with GLN 372 (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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347A SER* 2.9 36.7 + - - -
370A ARG* 3.8 3.8 - - - +
371A THR* 1.3 97.3 + - - +
373A PHE* 1.3 65.3 + - - +
419A ASP* 3.6 18.2 - - - +
474A TYR* 4.1 25.1 - - + -
475A VAL 3.1 7.4 - - - +
476A ASP* 2.8 30.9 + - + +
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Residues in contact with PHE 373 (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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350A LEU* 4.1 8.7 - - + -
371A THR* 3.9 24.7 - - + -
372A GLN* 1.3 79.4 - - - +
374A TYR* 1.3 62.6 + - - +
375A VAL* 4.1 5.8 - - + -
415A PHE* 4.9 3.4 - + - -
417A VAL* 3.3 40.6 - - + -
418A LYS 3.1 18.8 - - - +
419A ASP* 4.4 2.2 - - - +
431A VAL* 3.9 29.8 - - + -
474A TYR* 3.2 7.7 - - - +
475A VAL* 2.7 76.0 + - + -
477A ALA* 4.8 4.7 - - + -
479A VAL* 5.5 0.7 - - + -
488A ILE* 4.6 6.7 - - + -
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Residues in contact with TYR 374 (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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373A PHE* 1.3 76.4 - - - +
375A VAL* 1.3 65.3 + - - +
376A THR* 3.7 24.7 + - + +
417A VAL* 3.5 2.6 - - - -
418A LYS* 3.0 52.3 + - + +
419A ASP* 4.5 7.0 - - - -
423A GLN* 2.7 42.4 + - - +
468A LEU 5.8 0.2 - - - +
472A ASN* 5.8 2.0 - - - -
473A SER 3.7 20.4 - - - +
474A TYR* 4.4 4.7 - - + +
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Residues in contact with VAL 375 (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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373A PHE* 4.1 20.9 - - + -
374A TYR* 1.3 77.8 - - - +
376A THR* 1.3 60.7 + - - +
377A LYS 3.4 26.7 - - - +
378A ILE* 3.7 21.1 - - + -
415A PHE* 4.2 20.0 - - + -
416A LEU 3.6 5.8 - - - +
417A VAL* 4.3 0.9 - - + -
468A LEU* 3.3 33.9 + - + +
469A THR* 3.7 16.5 - - + +
473A SER 5.0 0.2 + - - -
475A VAL* 4.3 14.6 - - + +
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Residues in contact with THR 376 (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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374A TYR* 3.8 30.1 - - + +
375A VAL* 1.3 73.3 - - - +
377A LYS* 1.3 65.0 + - - +
416A LEU* 2.8 29.8 + - - +
417A VAL 5.1 0.2 - - - -
418A LYS* 4.1 20.0 - - + +
469A THR* 4.7 6.4 - - - +
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Residues in contact with LYS 377 (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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375A VAL* 3.4 8.3 - - - +
376A THR* 1.3 90.2 + - - +
378A ILE* 1.3 72.5 + - - +
379A GLU* 2.7 37.5 + - + +
381A SER* 5.1 10.0 + - - -
414A GLN 3.9 0.2 - - - +
415A PHE* 3.7 0.3 - - - -
416A LEU* 2.9 44.3 + - + +
469A THR* 4.7 3.8 - - - -
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Residues in contact with ILE 378 (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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375A VAL* 3.7 14.8 - - + -
377A LYS* 1.3 83.3 - - - +
379A GLU* 1.3 69.3 + - - +
380A PRO 3.4 9.6 - - - +
381A SER* 4.2 5.4 - - - -
386A TRP* 3.4 27.8 - - + +
413A VAL* 3.4 24.0 - - + -
414A GLN 3.3 4.3 - - - +
415A PHE* 3.7 15.0 - - + -
465A ALA* 3.6 42.8 - - + +
468A LEU* 4.1 11.2 - - + -
469A THR* 4.2 7.6 - - + +
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Residues in contact with GLU 379 (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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377A LYS* 2.7 37.1 + - - +
378A ILE* 1.3 81.2 - - - +
380A PRO* 1.3 70.1 - - + +
381A SER* 4.5 3.8 - - - +
413A VAL* 3.6 3.1 - - - +
414A GLN* 2.7 49.9 + - + +
416A LEU* 3.6 14.3 - - + +
430A ARG* 2.9 34.6 + - - -
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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