Contacts of the strand formed by residues 379 - 384 (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 VAL 379 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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329A ASN 5.2 0.4 - - - -
342A TRP* 4.3 9.9 - - + -
345A LYS* 5.0 4.9 - - - +
374A ALA* 3.3 1.2 - - - -
375A ILE* 2.9 52.9 + - + +
376A GLU* 2.7 47.2 + - + +
377A PRO 3.2 2.2 - - - +
378A GLY* 1.3 72.5 - - - -
380A ALA* 1.3 57.3 + - - +
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Residues in contact with ALA 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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329A ASN 4.0 0.9 + - - +
330A TYR* 2.7 60.5 - - + -
331A VAL* 3.0 3.3 + - - +
342A TRP* 4.4 4.0 - - - -
373A PHE 3.2 14.8 - - - +
374A ALA* 3.6 14.1 - - + +
378A GLY 3.2 4.2 + - - -
379A VAL* 1.3 76.3 - - - +
381A ALA* 1.3 55.7 + - - +
499A ALA* 3.7 12.3 - - + +
503A ASP* 4.2 1.1 - - + -
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Residues in contact with ALA 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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330A TYR* 4.1 0.4 - - - -
331A VAL* 2.6 44.9 - - + +
333A ILE* 4.1 13.7 - - + -
342A TRP* 3.8 14.8 - - + -
372A SER* 3.4 25.8 - - - -
373A PHE* 3.0 11.6 + - + +
380A ALA* 1.3 72.8 - - - +
382A TYR* 1.3 57.9 + - - +
383A ILE* 5.2 1.5 - - + +
499A ALA* 4.2 5.5 - - - +
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Residues in contact with TYR 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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330A TYR* 5.8 0.4 - - + -
331A VAL 2.1 19.8 + - - +
332A THR* 2.4 19.7 - - + +
333A ILE 2.3 34.0 + - - -
357A GLU* 4.2 4.3 - - + -
369A VAL 3.7 1.0 + - - -
370A GLY* 3.5 17.2 + - - -
371A LEU 3.1 26.7 - - - -
372A SER* 4.3 0.2 - - - -
381A ALA 1.3 70.6 - - - +
383A ILE* 1.3 65.6 + - - +
384A PRO* 3.6 24.5 - - + -
387A HIS* 2.8 30.4 + + - -
486A PHE* 3.9 12.3 - + - -
491A LEU 4.0 3.1 - - - -
494A ALA* 4.0 3.1 - - + -
495A GLY* 3.4 43.3 - - - +
498A ALA* 3.7 24.0 - - + -
499A ALA* 4.6 2.9 - - + +
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Residues in contact with ILE 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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333A ILE* 3.3 51.4 - - + +
339A LEU* 4.0 17.9 - - + -
342A TRP* 5.9 0.4 - - + -
370A GLY* 3.2 5.9 - - - -
371A LEU* 3.0 37.6 + - + +
373A PHE* 3.5 37.5 - - + -
381A ALA* 5.2 1.8 - - + +
382A TYR* 1.3 77.5 - - - +
384A PRO* 1.3 64.7 - - - +
385A VAL* 3.8 13.4 + - + +
396A ILE* 4.6 8.5 - - + -
401A ALA* 4.9 7.0 - - + -
405A LEU* 4.7 3.8 - - + -
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Residues in contact with PRO 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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332A THR* 3.0 37.9 - - + -
333A ILE 3.4 7.0 - - - +
334A LEU* 3.1 17.9 - - + -
369A VAL 4.1 0.4 - - - +
382A TYR* 3.6 17.7 - - + +
383A ILE* 1.3 81.0 - - - +
385A VAL* 1.3 61.7 + - - +
387A HIS* 3.8 13.9 - - + -
395A GLN* 3.3 34.4 - - + +
396A ILE* 3.9 5.7 + - - +
491A LEU* 3.9 11.2 - - + -
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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