Contacts of the strand formed by residues 394 - 400 (chain A) in PDB entry 1KIT
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 ASN 394 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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388A ILE* 3.6 29.5 - - + +
390A ASP 4.0 2.8 - - - +
392A ALA* 2.9 22.9 + - - +
393A ALA* 1.3 75.3 - - - +
395A GLN* 1.3 60.8 + - - +
408A THR* 3.6 0.2 - - - -
409A LEU* 2.8 40.6 + - - +
479A GLY 3.2 7.4 - - - +
480A ASN* 3.6 6.4 + - - +
487A GLY* 3.1 24.7 - - - -
488A ARG* 3.3 14.5 + - - +
489A LEU* 3.8 26.0 - - + -
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Residues in contact with GLN 395 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367A LEU* 5.3 5.8 - - + -
386A ILE* 5.8 0.7 - - - -
393A ALA* 3.0 26.9 + - - +
394A ASN* 1.3 75.7 - - - +
396A ILE* 1.3 62.4 + - - +
397A GLN* 5.5 2.6 - - + +
406A VAL* 3.8 16.8 - - + +
407A VAL 3.3 12.3 - - - +
408A THR* 3.1 20.6 + - - +
409A LEU* 5.9 1.6 - - - -
477A GLN 4.0 0.2 - - - +
478A PHE* 3.2 7.3 - - - +
479A GLY 2.7 39.6 + - - +
481A ALA* 2.8 37.0 - - + +
489A LEU* 4.6 7.4 - - - +
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Residues in contact with ILE 396 (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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382A SER* 5.6 2.9 - - - +
384A ALA* 4.4 20.6 - - + -
386A ILE* 4.4 20.2 - - + -
395A GLN* 1.3 72.9 - - - +
397A GLN* 1.3 63.8 + - - +
398A VAL* 4.3 7.9 - - + -
405A TYR 3.7 0.9 - - - +
406A VAL* 3.2 6.4 - - - +
407A VAL* 2.9 61.1 + - + +
409A LEU* 5.0 6.3 - - + -
443A TYR* 5.3 9.2 - - + -
445A LEU* 5.1 6.4 - - + +
476A ILE* 3.9 19.3 - - + -
477A GLN 3.5 15.3 - - - +
478A PHE* 4.2 11.2 - - + -
494A ILE* 5.3 5.2 - - + -
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Residues in contact with GLN 397 (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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369A ARG* 5.5 0.4 - - - +
395A GLN* 5.5 3.4 - - + +
396A ILE* 1.3 75.9 - - - +
398A VAL* 1.3 64.0 + - - +
399A ALA* 4.0 6.0 - - - +
404A LYS* 3.7 25.5 - - + +
405A TYR 3.3 2.7 - - - +
406A VAL* 3.3 27.7 - - + +
473A GLU* 3.9 9.2 + - - -
475A ASN* 3.5 31.7 + - - +
476A ILE* 3.4 5.3 - - - +
477A GLN* 2.7 73.5 + - + +
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Residues in contact with VAL 398 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A LEU* 4.3 12.3 - - + -
380A TRP* 4.0 22.2 - - + -
382A SER* 3.1 29.6 - - - +
396A ILE* 5.0 4.0 - - + -
397A GLN* 1.3 76.3 - - - +
399A ALA* 1.3 60.1 + - - +
400A ASP 4.3 0.2 - - - -
403A ARG 4.0 0.9 - - - +
404A LYS* 3.6 1.6 - - - +
405A TYR* 2.7 40.4 + - + +
445A LEU* 3.8 23.3 - - + -
475A ASN 3.3 7.2 - - - +
476A ILE* 4.7 7.2 - - + -
496A LEU* 3.9 22.9 - - + -
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Residues in contact with ALA 399 (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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372A THR* 3.9 0.7 + - - -
374A LEU* 4.5 3.9 - - - +
397A GLN* 4.0 7.0 - - - +
398A VAL* 1.3 75.6 - - - +
400A ASP* 1.3 58.5 - - - +
403A ARG 3.3 9.9 - - - +
404A LYS* 4.5 9.0 - - + -
471A SER* 4.6 0.2 - - - +
473A GLU* 3.0 38.4 - - + +
474A ASN* 3.1 3.6 + - - -
475A ASN* 2.4 49.2 + - + +
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Residues in contact with ASP 400 (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 LEU* 3.4 30.6 - - + +
376A SER* 3.3 29.9 - - - -
380A TRP* 2.9 32.6 + - + +
398A VAL 4.3 0.2 - - - -
399A ALA* 1.3 71.9 - - - +
401A GLY* 1.3 55.0 + - - +
402A SER* 3.0 9.5 + - - -
403A ARG* 3.0 30.4 + - - +
405A TYR* 5.0 1.7 - - - -
447A TYR* 4.1 11.1 - - - -
473A GLU 3.1 0.2 + - - -
474A ASN* 3.7 13.8 - - - +
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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