Contacts of the strand formed by residues 368 - 376 (chain A) in PDB entry 1KLN
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 LEU 368 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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356A THR* 4.2 22.0 - - + -
357A GLU 3.6 9.2 - - - +
358A THR* 4.2 3.4 - - - -
366A ALA 4.1 0.8 + - - -
367A ASN* 1.3 71.6 - - - +
369A VAL* 1.3 58.4 + - - +
370A GLY 3.3 29.6 - - - +
371A LEU* 4.5 11.4 - - + -
385A VAL* 4.8 3.8 - - + -
386A ALA* 3.6 1.6 - - - +
398A ARG* 2.9 41.3 + - + -
402A LEU* 3.9 28.3 - - + -
427A ILE* 4.2 8.2 - - + +
428A LEU* 4.7 9.9 - - + -
431A TYR* 2.9 33.5 + - + +
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Residues in contact with VAL 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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357A GLU 2.8 13.6 + - - +
358A THR 3.7 3.4 - - - -
359A ASP* 3.6 27.1 - - + +
367A ASN* 3.5 12.1 - - + +
368A LEU* 1.3 76.2 - - - +
370A GLY* 1.3 58.1 + - - +
382A TYR* 3.7 3.5 + - - -
385A VAL* 3.1 11.1 + - - -
386A ALA* 3.1 28.2 + - + +
387A HIS* 3.6 19.6 - - + +
486A PHE* 4.1 7.4 - - + -
487A ASN* 3.6 39.3 - - + +
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Residues in contact with GLY 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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357A GLU* 2.9 31.7 + - - +
368A LEU* 3.3 8.7 - - - +
369A VAL* 1.3 79.5 - - - +
371A LEU* 1.3 64.3 + - - -
382A TYR* 3.5 11.1 + - - -
383A ILE 3.2 15.5 - - - -
385A VAL* 3.9 8.9 - - - +
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Residues in contact with LEU 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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354A PHE* 3.4 27.8 - - + -
355A ALA 3.4 12.1 - - - +
356A THR* 4.9 1.1 - - + -
357A GLU* 4.7 1.3 - - - +
368A LEU* 4.5 18.8 - - + -
370A GLY* 1.3 78.4 - - - +
372A SER* 1.3 61.5 + - - +
373A PHE* 4.0 21.1 - - + -
382A TYR* 3.1 7.4 - - - -
383A ILE* 3.0 43.3 + - + +
385A VAL* 5.2 7.6 - - + -
401A ALA* 5.2 3.6 - - + -
402A LEU* 5.4 5.2 - - + -
405A LEU* 3.9 24.5 - - + -
409A LEU* 4.7 11.0 - - + -
428A LEU* 4.8 8.3 - - + -
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Residues in contact with SER 372 (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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354A PHE* 3.1 5.7 - - - +
355A ALA* 2.8 48.9 + - - +
357A GLU* 4.5 0.5 + - - +
371A LEU* 1.3 75.9 - - - +
373A PHE* 1.3 67.4 + - - +
381A ALA 3.4 16.4 - - - -
382A TYR* 4.3 1.1 - - - -
498A ALA* 3.0 43.4 + - - +
499A ALA* 4.2 0.4 - - - -
502A ALA* 4.1 4.9 - - - -
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Residues in contact with PHE 373 (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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333A ILE* 6.0 0.2 - - + -
339A LEU* 5.5 0.4 - - + -
342A TRP* 4.3 22.5 - + + -
346A LEU* 4.3 25.1 - - + -
352A PHE* 4.6 7.4 - + + -
353A ALA 3.7 18.2 - - - +
354A PHE* 3.5 23.3 - + + +
371A LEU* 4.0 20.9 - - + -
372A SER* 1.3 75.2 - - - +
374A ALA* 1.3 61.6 + - - +
380A ALA* 3.2 3.5 - - - +
381A ALA* 3.0 29.3 + - + +
383A ILE* 3.5 33.0 - - + -
405A LEU* 3.8 32.3 - - + -
408A LEU* 4.8 1.6 - - + -
409A LEU* 4.3 11.7 - - + -
502A ALA* 4.0 4.0 - - - +
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Residues in contact with ALA 374 (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 TRP* 5.2 0.2 - - - -
352A PHE* 4.6 0.5 - - - +
353A ALA* 3.6 28.2 + - + +
373A PHE* 1.3 76.3 - - - +
375A ILE* 1.3 65.3 + - - +
376A GLU 4.7 1.8 - - - +
379A VAL 3.3 8.3 - - - +
380A ALA* 3.6 16.2 - - + -
502A ALA* 3.7 28.1 - - - +
503A ASP* 3.7 6.7 - - - +
506A LEU* 3.9 13.6 - - + +
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Residues in contact with ILE 375 (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 TRP* 3.8 20.0 - - + -
345A LYS* 3.9 29.8 - - + +
346A LEU* 3.8 27.6 - - + -
349A ALA* 4.9 12.1 - - + -
351A VAL 5.5 3.0 - - - +
352A PHE* 4.8 10.3 - - + +
374A ALA* 1.3 75.1 - - - +
376A GLU* 1.3 65.7 + - + +
379A VAL* 2.9 33.0 + - + +
506A LEU* 3.6 10.4 - - - +
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Residues in contact with GLU 376 (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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374A ALA* 4.7 1.2 - - - +
375A ILE* 1.3 84.9 - - + +
377A PRO* 1.3 75.3 - - + +
378A GLY 3.0 0.7 + - - -
379A VAL* 2.7 55.5 + - + +
503A ASP* 4.1 1.9 - - - +
506A LEU* 3.6 7.3 - - - +
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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