Contacts of the strand formed by residues 423 - 429 (chain A) in PDB entry 3KCZ
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 ARG 423 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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416A PHE* 3.6 34.8 - - + -
417A ARG 5.1 0.6 + - - -
418A GLU* 2.9 43.1 + - - +
420A LEU 4.7 12.4 + - - +
421A HIS 3.4 1.0 - - - -
422A ASN* 1.3 75.9 - - - +
424A MET* 1.3 59.1 + - - +
489A GLU* 4.4 9.5 + - + -
490A VAL 3.3 13.5 - - - +
491A ALA* 4.6 2.9 - - - +
532A ASN 4.6 3.6 + - - -
533A GLY* 3.5 27.0 + - - +
534A SER* 3.1 23.1 - - - +
535A THR* 2.9 26.7 + - - -
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Residues in contact with MET 424 (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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422A ASN* 3.6 21.3 - - - +
423A ARG* 1.3 75.3 - - - +
425A LEU* 1.3 60.0 + - - +
426A LEU* 3.5 18.7 + - + -
465A ASP* 5.4 0.2 - - - +
488A SER 3.4 1.7 - - - +
489A GLU* 3.5 0.3 - - - -
490A VAL* 2.8 38.9 + - - +
492A LEU* 3.5 24.0 - - + -
528A PHE* 4.8 8.5 - - + -
534A SER* 4.3 4.7 - - - -
535A THR* 3.4 19.7 - - + +
537A PRO* 3.9 35.2 - - + -
559A TYR* 4.0 25.6 - - - +
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Residues in contact with LEU 425 (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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381A VAL* 6.2 0.2 - - + -
382A ILE* 5.1 2.5 - - + -
385A TYR* 2.7 37.0 + - + -
424A MET* 1.3 69.8 - - - +
426A LEU* 1.3 57.8 + - - +
487A LEU* 4.2 28.7 - - + -
488A SER 3.3 26.2 - - - +
489A GLU* 4.0 16.2 - - + +
531A LEU* 4.1 21.3 - - + +
534A SER* 4.1 8.8 - - - -
535A THR 2.8 15.7 + - - +
536A VAL* 4.1 22.9 - - + -
537A PRO* 3.6 4.5 - - - +
570A ARG* 4.3 10.8 - - + -
571A TYR* 4.3 7.6 - - + -
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Residues in contact with LEU 426 (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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385A TYR* 3.9 7.6 - - - +
424A MET* 3.8 32.5 - - + +
425A LEU* 1.3 83.5 - - - +
427A TRP* 1.3 62.3 + - - +
463A PHE* 3.8 23.2 - - + -
464A ALA 3.8 13.7 - - - +
465A ASP* 4.0 15.5 - - + -
486A LEU 3.6 0.2 - - - +
487A LEU* 3.4 9.1 - - - -
488A SER* 2.9 30.5 + - - +
490A VAL* 4.1 20.9 - - + -
492A LEU* 4.5 3.1 - - + -
537A PRO* 4.5 0.2 - - + -
559A TYR* 3.7 36.1 - - + -
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Residues in contact with TRP 427 (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 ILE 4.6 1.8 - - - -
385A TYR* 3.2 49.0 - + - -
386A LEU* 3.7 21.5 - - + -
389A THR* 3.5 0.6 + - - -
426A LEU* 1.3 72.5 - - - +
428A HIS* 1.3 62.1 - - - +
463A PHE* 3.2 12.7 - - - -
464A ALA 2.9 44.9 + - - +
465A ASP 3.8 2.2 - - - -
466A MET 3.7 3.6 - - - -
467A SER* 3.4 39.6 - - - +
470A SER* 3.2 20.0 + - - +
485A LEU* 3.9 24.2 - - + -
486A LEU 3.4 8.1 - - - -
487A LEU* 3.4 31.6 - - + -
573A LEU* 3.8 28.5 - - + -
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Residues in contact with HIS 428 (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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1A 3AB 3.3 22.0 + - - -
426A LEU 5.4 0.2 - - - +
427A TRP* 1.3 76.7 - - - +
429A GLY* 1.3 71.8 + - - +
430A SER* 4.4 11.2 + - - -
435A TRP* 3.9 7.7 - + - -
438A ILE* 4.7 2.2 - - + +
443A LEU* 3.6 37.4 - - + +
461A ILE* 5.1 2.2 - - + -
462A TYR* 2.8 30.5 + - + -
463A PHE* 4.2 12.8 - - + -
470A SER* 3.9 2.7 - - - -
485A LEU* 3.9 1.7 - - - +
486A LEU* 2.9 44.1 + - + +
488A SER* 5.5 0.2 - - - +
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Residues in contact with GLY 429 (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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1A 3AB 2.8 29.8 + - - -
428A HIS* 1.3 81.0 + - - +
430A SER* 1.3 63.6 + - - -
435A TRP* 4.4 2.0 - - - -
470A SER* 3.4 19.6 - - - -
473A TYR* 3.7 9.0 - - - +
474A CYS* 4.3 4.9 - - - -
485A LEU* 3.9 10.3 - - - -
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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