Contacts of the strand formed by residues 567 - 578 (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 VAL 567 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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412A GLU* 3.9 19.2 - - - +
416A PHE* 3.6 6.8 - - - +
443A LEU* 4.2 13.0 - - + +
461A ILE* 4.1 14.8 - - + -
463A PHE* 3.5 27.1 - - + -
488A SER* 3.9 25.8 - - - +
489A GLU 3.4 2.7 - - - -
490A VAL* 5.0 0.4 - - + -
561A VAL* 3.8 17.3 - - + -
563A ASN 4.6 0.4 - - - +
564A PRO* 3.1 19.2 + - + +
565A ASN* 3.3 1.5 - - - -
566A GLN* 1.3 85.2 - - - +
568A ARG* 1.3 66.5 + - - +
569A MET* 4.3 7.9 - - + +
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Residues in contact with ARG 568 (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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407A VAL 5.7 1.0 + - - -
408A GLU* 4.7 18.4 + - - +
412A GLU* 3.4 21.3 - - + +
413A LYS* 3.8 53.0 - - - +
416A PHE* 3.7 23.8 - - + -
418A GLU* 5.6 2.8 + - - -
488A SER* 4.1 1.1 - - - -
489A GLU* 2.8 61.7 + - - +
567A VAL* 1.3 74.0 - - - +
569A MET* 1.3 73.7 + - - +
570A ARG* 3.5 20.7 + - - +
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Residues in contact with MET 569 (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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367A CYS* 4.6 0.2 - - - -
407A VAL* 3.1 32.9 - - + +
408A GLU* 5.0 1.6 - - - -
409A LYS* 3.7 34.3 + - + -
412A GLU* 2.8 23.4 + - - +
438A ILE* 3.8 31.9 - - - +
439A LEU* 4.4 9.9 - - + -
442A GLY* 4.1 3.1 - - - -
443A LEU* 4.6 7.6 - - + +
486A LEU* 3.7 30.5 - - + -
488A SER* 3.6 19.9 + - - +
567A VAL* 4.2 6.7 - - + -
568A ARG* 1.3 81.9 + - - +
570A ARG* 1.3 60.3 + - - +
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Residues in contact with ARG 570 (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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378A GLU* 6.2 0.2 - - - +
406A GLU* 3.4 34.7 + - - +
407A VAL* 2.8 29.8 + - - +
425A LEU* 4.3 9.6 - - + -
487A LEU 2.8 14.8 + - - +
489A GLU* 4.0 27.3 + - + +
532A ASN* 4.2 15.8 - - - +
568A ARG* 3.9 28.1 - - - +
569A MET* 1.3 80.8 - - - +
571A TYR* 1.3 102.2 + - + +
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Residues in contact with TYR 571 (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 LEU* 3.8 29.8 - - + -
378A GLU* 4.0 11.3 - - + +
382A ILE* 3.7 28.7 - - + -
404A LEU* 4.0 13.0 - - + -
405A PHE 3.3 10.8 - - - +
406A GLU* 4.3 1.3 - - + -
407A VAL* 3.8 4.5 - - - -
425A LEU* 4.3 7.4 - - + -
485A LEU 3.9 0.7 - - - +
486A LEU* 3.4 7.4 - - - +
487A LEU* 2.7 51.9 + - + -
531A LEU* 3.6 24.9 - - + +
532A ASN* 4.0 10.0 + - - -
570A ARG* 1.3 125.8 + - + +
572A LEU* 1.3 59.7 + - - +
573A LEU* 4.1 4.0 - - + -
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Residues in contact with LEU 572 (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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241A LEU* 3.9 28.5 - - + -
369A LEU* 4.4 4.5 - - + -
404A LEU* 3.6 1.8 - - - -
405A PHE* 2.8 49.0 + - + +
407A VAL* 3.6 13.2 - - + +
435A TRP* 4.4 12.8 - - + -
439A LEU* 4.1 23.8 - - + -
484A LEU* 4.1 33.9 - - + -
485A LEU 3.7 17.3 - - - +
486A LEU* 4.0 17.3 - - + -
571A TYR* 1.3 74.0 - - - +
573A LEU* 1.3 61.9 + - - +
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Residues in contact with LEU 573 (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* 3.7 17.9 - - + -
386A LEU* 4.3 16.8 - - + -
401A LEU* 3.6 24.5 - - + -
403A ASP 3.7 4.0 - - - -
404A LEU* 3.7 20.9 - - + -
427A TRP* 3.8 22.7 - - + -
484A LEU* 3.2 11.8 - - - +
485A LEU* 2.7 41.7 + - + +
487A LEU* 3.9 26.7 - - + -
571A TYR* 4.2 5.2 - - + +
572A LEU* 1.3 73.1 - - - +
574A LYS* 1.3 60.4 + - - +
575A VAL* 3.6 8.8 + - + +
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Residues in contact with LYS 574 (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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240A GLU* 4.7 20.4 + - - +
241A LEU* 5.6 5.6 - - + +
244A LEU* 4.1 15.8 - - + +
401A LEU* 3.6 4.0 - - - +
402A LEU* 2.8 52.4 + - + -
403A ASP* 2.9 30.7 + - + +
405A PHE* 4.7 11.4 - - + -
482A THR* 4.0 25.4 - - + -
484A LEU* 3.6 20.0 - - + -
572A LEU 4.0 1.0 + - - -
573A LEU* 1.3 69.8 - - - +
575A VAL* 1.3 54.9 + - - +
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Residues in contact with VAL 575 (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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386A LEU* 4.7 4.9 - - + -
399A MET* 3.7 31.0 - - + -
400A THR 3.5 6.5 - - - +
401A LEU* 4.3 7.0 - - + -
402A LEU* 4.4 4.3 - - - -
481A ASN 3.7 0.3 - - - +
482A THR* 3.4 5.7 - - - +
483A GLY 2.8 42.1 + - - +
485A LEU* 4.3 19.5 - - + +
573A LEU* 3.9 26.7 - - + +
574A LYS* 1.3 78.5 - - - +
576A GLN* 1.3 75.7 + - - +
577A PHE* 3.9 12.9 - - + -
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Residues in contact with GLN 576 (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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399A MET* 3.3 5.2 - - - -
400A THR* 2.8 56.5 + - - +
402A LEU* 3.8 30.6 - - + +
481A ASN* 3.6 25.5 + - - +
482A THR* 4.8 1.8 - - - +
575A VAL* 1.3 74.2 - - - +
577A PHE* 1.3 61.3 + - - +
578A ASN* 2.7 25.5 + - - +
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Residues in contact with PHE 577 (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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397A TYR* 3.5 35.7 - + + -
398A THR 3.6 3.1 - - - -
399A MET* 4.2 8.7 - - + +
471A ALA* 3.8 28.3 - - + -
474A CYS* 3.9 12.8 - - + -
476A ALA* 3.5 23.6 - - + -
481A ASN* 2.8 41.7 + - - +
483A GLY* 3.8 22.0 - - - -
485A LEU* 5.7 1.1 - - + -
575A VAL* 3.9 15.9 - - + -
576A GLN* 1.3 73.2 - - - +
578A ASN* 1.3 59.9 - - - +
579A PHE* 3.4 23.8 + + + -
580A GOL 3.7 17.7 - - - -
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Residues in contact with ASN 578 (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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397A TYR* 3.2 4.9 - - - -
398A THR* 2.7 64.0 + - - +
399A MET 3.8 3.2 - - - -
400A THR* 2.9 23.0 + - - +
481A ASN* 5.5 0.3 + - - -
576A GLN* 2.7 33.5 + - - +
577A PHE* 1.3 72.1 - - - +
579A PHE* 1.3 64.2 + - - +
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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