Contacts of the strand formed by residues 390 - 397 (chain A) in PDB entry 1CJT
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 390 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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387A HIS* 4.1 16.6 - - + +
388A ASP 3.2 19.3 - - - +
389A ASN* 1.3 77.2 - - - +
391A SER* 1.3 65.3 + - - +
392A ILE* 4.3 5.2 - - + +
445A VAL* 5.3 3.6 - - + -
446A SER 3.3 13.5 - - - +
447A GLY 3.9 22.0 - - - +
448A LEU* 4.8 4.3 - - + -
455A HIS* 3.9 3.4 - - - -
489A SER* 3.2 4.0 - - - -
490A GLY 2.9 40.4 + - - +
492A VAL* 3.5 33.2 - - + -
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Residues in contact with SER 391 (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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390A VAL* 1.3 72.5 - - - +
392A ILE* 1.3 65.1 + - - +
445A VAL* 3.2 10.6 - - - +
446A SER 3.1 27.9 + - - -
455A HIS* 2.9 26.9 + - - -
456A ALA* 3.4 10.4 - - - -
459A CYS* 3.5 23.3 - - - -
487A ILE* 4.8 2.7 - - - -
488A HIS 3.5 4.7 - - - -
489A SER* 2.8 20.9 + - - -
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Residues in contact with ILE 392 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390A VAL* 4.3 6.7 - - + +
391A SER* 1.3 80.6 - - - +
393A LEU* 1.3 65.1 + - - +
394A PHE* 3.6 31.9 - - + -
443A TYR* 5.2 1.8 - - + -
444A CYS 3.8 3.6 - - - +
445A VAL* 3.8 20.6 - - + -
459A CYS* 4.4 2.5 - - - -
486A GLY 3.7 0.7 - - - +
487A ILE* 3.3 6.1 - - - +
488A HIS 2.9 37.9 + - - +
490A GLY 4.9 1.8 - - - +
492A VAL* 3.5 31.0 - - + -
506A VAL* 5.2 1.6 - - + -
510A ASP* 4.6 9.9 - - + +
511A VAL* 4.1 25.4 - - + +
514A ALA* 3.8 10.5 - - + +
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Residues in contact with LEU 393 (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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392A ILE* 1.3 74.6 - - - +
394A PHE* 1.3 80.6 + - - +
395A ALA* 4.2 2.5 - - + +
442A TYR* 4.9 2.2 - - + +
443A TYR* 3.1 9.1 - - - +
444A CYS* 3.0 40.7 + - - +
459A CYS* 3.2 40.6 - - + +
462A MET* 3.8 21.8 - - + -
463A GLY* 3.9 10.5 - - - +
466A MET* 4.1 17.9 - - + -
485A VAL* 3.8 15.7 - - + -
486A GLY 3.3 5.8 - - - +
487A ILE* 4.0 7.9 - - + -
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Residues in contact with PHE 394 (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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101A FOK 3.5 37.9 - - + -
392A ILE* 3.6 29.2 - - + -
393A LEU* 1.3 79.1 - - - +
395A ALA* 1.3 59.7 + - - +
441A CYS* 3.7 16.8 - - - -
442A TYR 3.7 2.0 - - - -
443A TYR* 3.6 32.3 - + + -
485A VAL* 3.4 3.1 - - - -
486A GLY 2.9 30.9 + - - +
511A VAL* 3.8 17.0 - - + -
514A ALA* 3.8 6.5 - - + +
515A ASN* 3.6 36.6 - - + -
518A GLU* 3.8 21.7 - - + +
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Residues in contact with ALA 395 (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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393A LEU* 4.3 1.6 - - + -
394A PHE* 1.3 77.6 - - - +
396A ASP* 1.3 62.1 + - - +
441A CYS* 3.3 5.1 - - - -
442A TYR* 2.7 42.6 + - + +
466A MET* 3.4 33.0 - - + -
483A MET* 3.5 15.2 - - + +
484A ARG 3.2 11.4 - - - +
485A VAL* 4.6 2.9 - - + -
518A GLU* 4.3 1.3 - - - -
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Residues in contact with ASP 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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102A DAD 2.8 8.2 + - - -
395A ALA* 1.3 76.5 - - - +
397A ILE* 1.3 64.5 + - - +
398A GLU 3.8 0.5 + - - -
440A ASP* 2.9 8.6 - - - +
441A CYS* 3.3 16.2 - - - +
483A MET* 3.1 9.4 - - - +
484A ARG* 3.1 35.2 + - - +
518A GLU* 3.4 29.1 - - - +
581A MG 2.4 21.6 - - - -
582A MN 2.0 34.7 + - - -
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Residues in contact with ILE 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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102A DAD 2.9 2.3 + - - -
396A ASP* 1.3 77.4 + - - +
398A GLU* 1.3 70.9 + - - +
400A PHE* 4.0 17.0 - - + +
403A LEU* 5.0 6.5 - - + -
416A LEU* 4.4 17.0 - - + -
419A LEU* 4.1 25.4 - - + -
420A PHE* 5.1 0.7 - - + -
440A ASP* 3.0 35.2 + - + +
481A VAL* 4.4 19.5 - - + -
482A ASN 3.4 15.0 - - - +
483A MET* 3.8 12.1 - - + -
484A ARG* 4.7 0.7 - - - -
582A MN 2.2 35.0 + - - -
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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