Contacts of the strand formed by residues 353 - 356 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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333D GLY* 3.9 13.2 - - - +
334D VAL* 3.4 32.3 - - + -
347D CYS* 4.0 15.7 - - - -
349D SER* 4.8 2.5 - - - -
351D SER 4.8 0.7 - - - +
352D SER* 1.3 78.1 - - - +
354D PHE* 1.3 72.1 + - - +
355D VAL* 4.0 21.8 - - + -
373D LYS* 3.5 1.6 - - - +
374D ILE* 2.7 42.9 + - + +
414D MET* 4.2 11.0 - - - -
415D SER 3.4 13.0 - - - +
416D PHE* 3.7 27.4 - - + -
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Residues in contact with PHE 354 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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463C SER* 4.4 8.1 - - - -
352D SER* 4.2 9.4 - - - -
353D ILE* 1.3 78.9 - - - +
355D VAL* 1.3 64.0 + - - +
371D VAL* 3.7 20.9 - - + -
372D CYS 3.2 4.0 - - - -
373D LYS* 3.5 41.3 - - + -
414D MET* 2.8 26.5 - - - +
415D SER* 2.8 27.6 + - - +
417D VAL 3.1 27.4 - - - -
418D LYS 3.5 13.7 - - - -
419D GLY* 3.5 16.6 - - - -
420D TRP* 3.8 6.9 - - + -
424D TYR* 3.5 33.7 - + - -
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Residues in contact with VAL 355 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353D ILE* 4.0 1.6 - - + -
354D PHE* 1.3 74.7 - - - +
356D GLN* 1.3 67.0 + - - +
357D SER* 3.9 5.6 + - - +
360D CYS* 6.2 0.7 - - + -
370D THR 4.1 0.5 - - - +
371D VAL* 3.6 2.5 - - - -
372D CYS* 2.7 46.9 + - + +
374D ILE* 3.4 29.4 - - + -
380D LEU* 5.0 2.5 - - + -
382D ILE* 4.1 18.2 - - + -
412D ILE* 3.5 28.0 - - + -
413D ARG 3.5 2.0 - - - +
414D MET* 3.3 34.3 - - + -
420D TRP* 4.8 0.2 - - - -
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Residues in contact with GLN 356 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355D VAL* 1.3 74.4 - - - +
357D SER* 1.3 60.4 + - - +
358D ARG* 4.3 9.8 + - - +
361D ASN* 4.7 0.4 - - - +
368D PRO 4.6 6.5 - - - +
369D THR* 2.7 42.8 + - - +
370D THR 3.5 15.3 - - - +
371D VAL* 4.2 5.7 - - + +
411D THR 4.6 1.9 - - - +
412D ILE* 3.7 2.8 - - - +
413D ARG* 2.8 46.0 + - + +
420D TRP* 3.7 33.2 + - + +
429D VAL* 5.7 0.5 - - - +
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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