Contacts of the strand formed by residues 379 - 384 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344C TYR* 4.6 13.9 - - - +
345C ALA 3.3 11.8 + - - -
346C GLU* 4.7 14.2 + - - +
374C ILE* 4.6 2.9 - - - -
378C CYS* 1.3 81.4 - - - +
380C LEU* 1.3 66.9 + - - +
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Residues in contact with LEU 380 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344C TYR* 4.3 2.9 - - - -
345C ALA 2.9 33.7 + - - -
355C VAL* 5.4 1.6 - - + -
360C CYS* 4.5 6.5 - - - -
364C HIS* 4.4 19.1 - - + +
372C CYS* 3.8 33.9 - - + -
373C LYS 5.3 2.0 - - - +
374C ILE* 4.0 24.9 - - + -
379C SER* 1.3 78.2 + - - +
381C LYS* 1.3 80.8 + - + +
382C ILE* 3.2 15.2 + - + +
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Residues in contact with LYS 381 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342C GLU* 2.7 34.2 + - + +
343C VAL 3.6 7.2 - - - +
344C TYR* 3.3 44.9 + - + -
360C CYS* 3.7 11.1 - - - +
363C HIS* 5.3 15.9 + - + -
364C HIS* 4.8 4.9 - - + -
380C LEU* 1.3 84.5 - - + +
382C ILE* 1.3 59.7 + - - +
383C PHE 4.0 11.9 - - - +
384C ASN* 4.8 7.0 - - + -
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Residues in contact with ILE 382 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336C LEU* 3.9 18.6 - - + -
343C VAL* 2.8 31.9 + - + +
344C TYR 4.5 0.2 - - - -
345C ALA* 3.7 28.5 - - + +
355C VAL* 4.1 16.6 - - + -
357C SER* 2.8 33.8 + - - +
359C ASN* 4.1 0.8 + - - -
360C CYS* 3.8 13.2 - - - +
380C LEU* 3.2 28.0 + - + +
381C LYS* 1.3 74.6 - - - +
383C PHE* 1.3 62.3 + - - +
412C ILE* 3.9 14.8 - - + +
414C MET* 4.1 10.5 - - + -
438C ILE* 5.2 1.6 - - + -
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Residues in contact with PHE 383 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342C GLU* 3.0 9.6 - - - +
343C VAL* 2.8 54.2 + - + +
357C SER* 4.7 0.4 - - - -
359C ASN* 3.4 35.7 - - + +
381C LYS* 3.6 5.8 - - - +
382C ILE* 1.3 80.5 - - - +
384C ASN* 1.3 67.1 + - - +
385C ASN* 3.5 28.7 - - + -
388C PHE* 3.8 24.2 - + + -
409C MET 3.7 20.9 - - - -
412C ILE* 4.3 11.4 - - + -
440C LEU* 4.5 14.4 - - + -
443C PRO* 3.4 34.8 - - + -
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Residues in contact with ASN 384 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341C GLY 3.7 4.2 - - - +
342C GLU* 2.9 33.4 - - + +
359C ASN* 3.0 16.5 - - - +
381C LYS* 4.8 5.2 - - + -
383C PHE* 1.3 77.0 - - - +
385C ASN* 1.3 62.6 + - - +
386C GLN* 3.2 16.1 + - - +
387C GLU* 2.6 67.8 + - - +
388C PHE 3.3 11.4 + - - -
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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