Contacts of the strand formed by residues 475 - 481 (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 VAL 475 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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335A LEU* 5.1 0.7 - - + -
336A THR* 4.0 19.5 - - + +
371A THR 3.8 0.9 - - - +
372A GLN* 3.1 7.1 - - - +
373A PHE* 2.7 71.4 + - + +
375A VAL* 4.3 7.2 - - + -
415A PHE* 5.7 2.0 - - + -
443A PHE* 4.8 8.7 - - + -
468A LEU* 3.5 32.1 - - + -
474A TYR* 1.3 77.4 - - - +
476A ASP* 1.3 62.8 + - - +
477A ALA* 3.7 18.4 - - + -
488A ILE* 5.3 1.3 - - + -
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Residues in contact with ASP 476 (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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334A VAL* 3.6 23.9 - - + +
336A THR* 2.5 26.5 + - - +
337A GLU* 5.9 0.2 - - - -
338A VAL* 3.5 11.1 + - + +
370A ARG* 2.5 39.0 + - - -
371A THR 3.6 2.4 - - - +
372A GLN* 2.8 34.8 + - + -
474A TYR* 4.2 2.7 + - + -
475A VAL* 1.3 71.9 - - - +
477A ALA* 1.3 60.5 + - - +
491A THR* 3.4 8.3 - - - +
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Residues in contact with ALA 477 (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* 4.3 2.0 - - - -
370A ARG* 3.3 4.0 - - - +
371A THR* 3.0 37.4 + - - +
373A PHE* 4.8 5.4 - - + -
475A VAL* 3.7 16.3 - - + -
476A ASP* 1.3 76.7 + - - +
478A VAL* 1.3 66.1 + - - +
479A VAL* 4.1 4.0 + - + -
488A ILE* 4.2 20.4 - - + -
491A THR* 3.5 20.4 - - + +
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Residues in contact with VAL 478 (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* 3.2 30.7 - - + -
342A HIS* 3.8 25.6 - - + +
345A LEU* 4.8 1.3 - - + -
368A THR* 3.6 21.5 - - + -
369A PHE 3.2 13.7 - - - +
370A ARG* 4.1 13.9 - - + -
477A ALA* 1.3 76.6 - - - +
479A VAL* 1.3 66.7 + - - +
488A ILE* 3.5 1.6 - - - +
489A LYS* 2.9 50.9 + - - +
491A THR* 3.1 7.0 + - - +
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Residues in contact with VAL 479 (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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353A LEU* 4.5 9.9 - - + -
367A ASP 3.7 0.5 - - - +
368A THR* 3.3 4.7 - - - +
369A PHE* 2.7 56.8 + - + +
371A THR* 4.9 10.3 - - + -
373A PHE* 5.5 0.4 - - + -
431A VAL* 4.3 12.3 - - + -
477A ALA* 4.6 7.9 - - + +
478A VAL* 1.3 84.2 - - - +
480A GLU* 1.3 59.6 + - - +
486A TYR* 3.6 34.8 - - + -
487A LEU 3.2 13.5 - - - +
488A ILE* 4.0 18.8 - - + -
489A LYS* 4.6 1.3 - - - +
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Residues in contact with GLU 480 (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 ASP* 3.1 24.4 - - - +
368A THR* 3.9 2.9 - - - +
439A LEU* 3.8 16.6 - - + +
479A VAL* 1.3 74.3 - - - +
481A ARG* 1.3 71.1 + - - +
482A ARG* 2.9 42.2 + - + +
485A PHE 3.4 1.0 - - - +
486A TYR* 4.4 2.5 - - - -
487A LEU* 3.0 27.9 + - - +
489A LYS* 2.7 44.0 + - + +
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Residues in contact with ARG 481 (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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357A ALA* 3.7 24.1 + - - +
363A LEU 3.5 9.7 + - - -
364A GLN* 4.8 6.2 + - - +
366A GLN 3.2 23.4 + - - -
367A ASP* 2.8 23.7 + - + +
369A PHE* 3.4 20.2 - - - -
480A GLU* 1.3 76.8 - - - +
482A ARG* 1.3 68.9 + - - +
483A ASN 5.0 0.9 - - - +
484A GLY* 4.5 12.8 - - - +
485A PHE 3.3 17.5 - - - +
486A TYR* 3.3 40.9 + - + -
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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