Contacts of the strand formed by residues 364 - 371 (chain A) in PDB entry 1KIT
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 GLY 364 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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361A GLY 2.8 16.3 - - - +
362A TRP 3.1 1.0 - - - -
363A GLY* 1.3 79.8 - - - +
365A SER* 1.3 53.3 + - - -
480A ASN* 3.1 0.5 + - - -
482A ASP 2.8 17.8 - - - +
483A ALA* 3.2 12.6 + - - +
532A THR 3.2 13.0 - - - -
533A GLY* 3.8 0.7 - - - -
534A ASN 2.8 16.8 + - - -
535A THR* 3.4 7.9 - - - -
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Residues in contact with SER 365 (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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364A GLY* 1.3 70.8 - - - -
366A GLU* 1.3 60.8 + - - +
367A LEU* 5.5 2.4 - - - +
480A ASN* 3.4 8.2 + - - +
481A ALA 2.8 29.6 + - - -
482A ASP 3.4 12.3 - - - -
483A ALA 3.4 0.7 - - - -
530A ILE* 4.5 3.1 + - - +
531A LYS* 3.0 10.4 - - - +
532A THR* 2.8 47.7 + - - +
535A THR* 3.4 1.3 - - - +
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Residues in contact with GLU 366 (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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359A ILE* 4.1 18.4 - - + +
365A SER* 1.3 71.4 - - - +
367A LEU* 1.3 60.2 + - - +
368A TYR* 3.2 33.1 + - - -
479A GLY* 3.3 3.6 - - - -
480A ASN* 2.7 43.0 + - - +
529A LYS* 3.4 20.5 + - + +
530A ILE 3.6 1.3 - - - -
531A LYS* 3.2 23.9 + - + -
535A THR* 2.5 32.8 + - + +
536A MET* 4.1 2.8 + - - -
537A SER* 3.7 22.4 + - - -
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Residues in contact with LEU 367 (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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365A SER* 5.5 1.6 - - - +
366A GLU* 1.3 78.1 - - - +
368A TYR* 1.3 65.3 + - - +
395A GLN* 5.1 7.4 - - + +
477A GLN* 4.4 29.2 - - + +
478A PHE* 3.2 29.6 - - - +
479A GLY* 3.6 11.0 - - - +
480A ASN 3.9 4.3 - - - +
481A ALA* 4.2 24.0 - - + +
528A THR 3.3 0.8 - - - +
529A LYS* 3.3 5.2 - - - +
530A ILE* 2.6 58.8 + - + +
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Residues in contact with TYR 368 (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 PHE* 3.5 22.0 - + - -
359A ILE* 4.0 5.8 - - + -
366A GLU* 3.2 27.1 + - - -
367A LEU* 1.3 75.4 - - - +
369A ARG* 1.3 59.8 + - - +
477A GLN* 3.4 5.9 - - - +
478A PHE* 3.0 59.7 + + + -
522A LEU* 3.5 40.5 - - + +
523A GLU* 5.1 3.4 - - + -
527A TRP* 3.6 18.0 - - + -
528A THR 3.4 1.3 - - - -
529A LYS* 3.5 47.3 + - + -
537A SER* 3.8 9.9 + - - -
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Residues in contact with ARG 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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368A TYR* 1.3 75.1 - - - +
370A ARG* 1.3 64.1 + - - +
371A ASN* 4.2 7.1 + - - +
397A GLN* 5.5 0.4 - - - +
473A GLU* 4.9 6.1 + - - -
475A ASN* 3.5 37.6 + - - +
476A ILE 3.8 5.4 - - - +
477A GLN* 2.9 41.9 + - + +
526A GLY 4.3 0.3 - - - +
527A TRP* 3.2 7.4 - - - -
528A THR* 2.6 52.3 + - - +
530A ILE* 3.8 26.6 - - + +
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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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369A ARG* 1.3 76.5 - - - +
371A ASN* 1.3 75.6 + - - +
372A THR* 3.5 1.5 + - - +
475A ASN* 3.6 3.5 - - - +
476A ILE* 3.0 51.6 + - + +
503A LEU 4.0 7.7 + - - -
504A VAL* 3.0 35.4 - - + +
525A LEU 5.6 0.6 + - - -
526A GLY* 4.2 25.9 + - - -
527A TRP* 3.6 28.9 - - + +
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Residues in contact with ASN 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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369A ARG* 4.2 8.1 + - - +
370A ARG* 1.3 90.2 + - - +
372A THR* 1.3 60.1 + - - +
373A SER* 5.2 0.5 + - - -
474A ASN 3.4 7.6 + - - +
475A ASN* 2.9 18.8 - - - +
528A THR* 5.9 0.6 + - - -
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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