Contacts of the strand formed by residues 379 - 384 (chain A) in PDB entry 1KHU
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 SER 379 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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344A TYR* 4.6 12.8 - - - +
345A ALA 3.4 13.9 + - - -
346A GLU* 4.5 11.5 - - - +
374A ILE* 4.1 3.5 - - - +
378A CYS* 1.3 82.5 - - - +
380A LEU* 1.3 67.9 + - - +
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Residues in contact with LEU 380 (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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344A TYR* 3.4 6.0 - - - -
345A ALA 2.9 33.9 + - - +
355A VAL* 5.4 2.0 - - + -
360A CYS* 4.4 13.9 - - - -
364A HIS* 4.4 13.0 - - + +
372A CYS* 4.1 23.3 - - + -
373A LYS 5.3 1.3 - - - +
374A ILE* 4.0 33.2 - - + -
379A SER* 1.3 78.8 + - - +
381A LYS* 1.3 82.3 + - + +
382A ILE* 3.4 12.8 + - + +
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Residues in contact with LYS 381 (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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342A GLU* 3.0 42.5 + - + +
343A VAL 3.7 10.8 - - - +
344A TYR* 3.4 30.6 + - + -
360A CYS* 3.4 21.0 - - - +
363A HIS* 5.3 18.2 + - + +
364A HIS* 4.7 4.7 - - + -
380A LEU* 1.3 79.7 - - + +
382A ILE* 1.3 60.1 + - - +
383A PHE 4.0 13.7 - - - +
384A ASN* 5.0 4.0 - - + -
387A GLU* 5.9 0.2 - - - +
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Residues in contact with ILE 382 (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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336A LEU* 4.3 14.8 - - + -
343A VAL* 3.0 28.8 + - + +
344A TYR 4.4 2.5 - - - -
345A ALA* 3.7 27.4 - - + -
355A VAL* 4.1 17.7 - - + -
357A SER* 2.6 36.6 + - - -
359A ASN* 3.9 0.2 + - - -
360A CYS* 3.7 13.8 + - - +
374A ILE* 4.7 0.4 - - + -
380A LEU* 3.4 24.2 + - + +
381A LYS* 1.3 76.1 - - - +
383A PHE* 1.3 61.5 + - - +
412A ILE* 4.0 15.7 - - + +
414A MET* 4.3 9.2 - - + -
438A ILE* 5.2 2.0 - - + -
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Residues in contact with PHE 383 (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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342A GLU* 3.3 9.0 - - - +
343A VAL* 3.1 48.2 + - + +
357A SER* 4.6 1.8 - - - -
359A ASN* 2.8 40.6 - - + +
381A LYS* 3.6 7.9 - - - +
382A ILE* 1.3 79.7 - - - +
384A ASN* 1.3 86.8 + - - +
385A ASN* 3.8 15.9 - - - -
388A PHE* 3.4 31.2 - + + -
409A MET 3.6 20.0 - - - -
410A CYS* 5.0 2.0 - - - -
412A ILE* 4.6 9.9 - - + -
440A LEU* 5.0 8.3 - - + -
443A PRO* 3.7 28.7 - - + -
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Residues in contact with ASN 384 (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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340A GLY 5.3 0.2 - - - +
341A GLY 3.7 4.8 - - - +
342A GLU* 2.7 34.0 - - + +
359A ASN* 2.6 14.1 - - - +
381A LYS* 5.0 4.5 - - + -
383A PHE* 1.3 78.0 - - - +
385A ASN* 1.3 63.3 + - - +
386A GLN* 3.5 16.9 + - - +
387A GLU* 2.7 67.0 + - - +
388A PHE* 3.1 18.7 + - - +
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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
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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