Contacts of the strand formed by residues 353 - 356 (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 ILE 353 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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333C GLY* 4.3 3.8 - - - -
334C VAL* 3.3 40.2 - - + +
347C CYS* 4.2 13.5 - - + -
349C SER* 5.2 1.8 - - - -
351C SER 5.0 0.2 - - - +
352C SER* 1.3 79.3 - - - +
354C PHE* 1.3 69.6 + - - +
355C VAL* 3.9 22.2 - - + -
373C LYS* 3.4 4.3 - - - +
374C ILE* 2.7 45.9 + - + +
414C MET* 4.3 9.0 - - - -
415C SER 3.6 15.5 - - - +
416C PHE* 3.6 26.9 - - + -
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Residues in contact with PHE 354 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463A SER* 4.2 5.6 - - - -
352C SER* 4.0 12.6 - - - -
353C ILE* 1.3 82.3 - - - +
355C VAL* 1.3 63.6 + - - +
371C VAL* 3.7 20.2 - - + -
372C CYS 3.4 2.7 - - - -
373C LYS* 3.6 35.7 - - + -
414C MET* 2.9 27.4 - - - +
415C SER* 3.1 20.0 + - - +
417C VAL 3.4 19.5 - - - -
418C LYS 3.7 5.8 - - - -
419C GLY* 3.3 32.8 - - - -
420C TRP* 3.5 5.9 - - + -
424C TYR* 2.8 40.6 - + - -
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Residues in contact with VAL 355 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353C ILE* 3.9 6.7 - - + -
354C PHE* 1.3 79.5 - - - +
356C GLN* 1.3 64.6 + - - +
357C SER* 4.0 4.6 + - - -
370C THR 4.0 1.0 - - - +
371C VAL* 3.5 3.9 - - - -
372C CYS* 2.6 49.3 + - + +
374C ILE* 3.5 32.8 - - + -
380C LEU* 5.4 0.7 - - + -
382C ILE* 4.1 19.7 - - + -
412C ILE* 3.8 26.0 - - + -
413C ARG 3.7 3.4 - - - +
414C MET* 3.8 20.6 - - + -
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Residues in contact with GLN 356 (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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355C VAL* 1.3 73.1 - - - +
357C SER* 1.3 62.1 + - - +
358C ARG* 4.3 11.6 + - + +
368C PRO 4.5 6.3 - - - +
369C THR* 2.9 40.6 + - - +
370C THR 3.8 14.1 - - - +
371C VAL* 4.3 5.5 - - + +
411C THR 4.8 0.3 - - - +
412C ILE* 3.4 5.9 - - - +
413C ARG* 2.9 44.8 + - + +
420C TRP* 3.6 35.2 + - + +
429C VAL* 5.8 0.3 - - - +
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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