Contacts of the strand formed by residues 567 - 578 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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412B GLU* 3.8 21.5 - - - +
416B PHE* 3.7 6.4 - - - -
443B LEU* 4.4 13.5 - - + +
461B ILE* 4.1 15.3 - - + -
463B PHE* 3.8 25.6 - - + -
488B SER* 3.9 25.4 - - - +
489B GLU 3.5 2.7 - - - -
490B VAL* 5.1 0.2 - - + -
561B VAL* 3.8 17.5 - - + -
564B PRO* 3.0 20.3 + - + +
565B ASN* 3.2 2.2 - - - -
566B GLN* 1.3 84.9 - - - +
568B ARG* 1.3 67.9 + - - +
569B MET* 4.3 6.3 - - + +
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Residues in contact with ARG 568 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408B GLU* 4.8 10.9 + - - +
412B GLU* 3.6 16.6 - - + +
413B LYS* 4.0 49.2 - - - +
416B PHE* 3.7 24.4 - - + -
488B SER* 4.0 2.2 - - - -
489B GLU* 2.8 63.4 + - + +
567B VAL* 1.3 75.2 - - - +
569B MET* 1.3 72.1 + - - +
570B ARG* 3.0 40.1 + - - +
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Residues in contact with MET 569 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367B CYS* 4.6 0.2 - - - -
407B VAL* 3.3 32.8 - - + +
408B GLU* 5.0 1.4 - - - -
409B LYS* 3.7 32.7 + - + -
412B GLU* 2.8 24.6 + - - +
438B ILE* 3.7 30.5 - - - +
439B LEU* 4.1 12.8 - - - +
442B GLY* 4.0 7.2 - - - -
443B LEU* 4.7 4.7 - - + +
486B LEU* 3.8 28.7 - - + -
488B SER* 3.6 18.8 - - - +
567B VAL* 4.7 6.1 - - + -
568B ARG* 1.3 78.0 + - - +
570B ARG* 1.3 63.8 + - - +
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Residues in contact with ARG 570 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406B GLU* 3.3 39.0 + - - +
407B VAL* 2.8 49.0 + - - +
408B GLU* 4.6 9.7 + - - +
425B LEU* 4.4 4.9 - - + -
487B LEU 2.9 9.1 + - - +
489B GLU* 3.5 34.4 + - + +
532B ASN* 5.4 6.9 - - - +
568B ARG* 3.0 47.3 + - - +
569B MET* 1.3 80.8 + - - +
571B TYR* 1.3 95.8 + - + +
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Residues in contact with TYR 571 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372B LEU* 4.0 24.7 - - + -
378B GLU* 4.1 11.8 - - + +
382B ILE* 3.5 34.5 - - + -
404B LEU* 4.2 8.7 - - + -
405B PHE 3.2 12.1 - - - +
406B GLU* 4.3 9.2 - - + -
407B VAL* 3.7 3.8 - - - +
425B LEU* 4.1 9.2 - - + -
485B LEU 3.9 0.2 - - - +
486B LEU* 3.4 7.6 - - - +
487B LEU* 2.8 51.4 + - + -
531B LEU* 3.6 27.8 - - + +
532B ASN* 4.1 12.8 + - - -
570B ARG* 1.3 109.2 + - + +
572B LEU* 1.3 61.9 + - - +
573B LEU* 4.2 2.7 - - + -
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Residues in contact with LEU 572 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241B LEU* 4.1 26.5 - - + -
369B LEU* 4.6 6.1 - - + -
404B LEU* 3.6 2.8 - - - +
405B PHE* 2.8 45.8 + - + +
407B VAL* 3.6 13.0 - - + +
435B TRP* 4.1 17.7 - - + -
439B LEU* 4.4 21.8 - - + -
484B LEU* 4.0 36.3 - - + -
485B LEU 3.5 12.8 - - - +
486B LEU* 4.1 15.9 - - + -
571B TYR* 1.3 75.3 - - - +
573B LEU* 1.3 62.0 + - - +
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Residues in contact with LEU 573 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382B ILE* 3.7 23.3 - - + -
386B LEU* 4.2 16.6 - - + -
401B LEU* 3.5 25.4 - - + -
403B ASP 3.7 4.7 - - - -
404B LEU* 3.7 20.0 - - + -
427B TRP* 3.7 30.5 - - + -
484B LEU* 3.1 11.3 - - - +
485B LEU* 2.8 41.1 + - + +
487B LEU* 4.2 12.6 - - + -
571B TYR* 4.3 4.7 - - + +
572B LEU* 1.3 75.6 - - - +
574B LYS* 1.3 60.3 + - - +
575B VAL* 3.6 8.7 + - + +
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Residues in contact with LYS 574 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237B ARG 5.7 0.4 + - - -
240B GLU* 4.4 23.6 + - - +
241B LEU* 5.1 5.9 - - + +
244B LEU* 4.4 13.8 - - + +
401B LEU* 3.7 2.4 - - - +
402B LEU* 2.8 48.9 + - + +
403B ASP* 3.0 29.6 + - + +
405B PHE* 4.6 12.9 - - + -
482B THR* 4.0 25.1 - - + -
484B LEU* 3.5 20.6 - - + -
572B LEU 4.0 1.6 + - - -
573B LEU* 1.3 71.7 - - - +
575B VAL* 1.3 60.2 + - - +
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Residues in contact with VAL 575 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386B LEU* 4.7 4.5 - - + -
399B MET* 3.7 30.7 - - + -
400B THR 3.5 6.5 - - - +
401B LEU* 4.4 5.6 - - + -
402B LEU* 4.4 3.4 - - - -
481B ASN 3.6 0.2 - - - +
482B THR* 3.4 6.8 - - - +
483B GLY 2.8 38.8 + - - +
485B LEU* 4.4 21.3 - - + +
573B LEU* 3.8 28.0 - - + +
574B LYS* 1.3 79.4 - - - +
576B GLN* 1.3 75.1 + - - +
577B PHE* 3.8 13.1 + - + -
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Residues in contact with GLN 576 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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399B MET* 3.3 4.5 - - - -
400B THR* 2.7 55.6 + - - +
402B LEU* 3.6 34.0 - - + +
481B ASN* 3.6 22.2 - - - +
482B THR* 4.8 1.6 - - - +
575B VAL* 1.3 72.8 - - - +
577B PHE* 1.3 62.1 + - - +
578B ASN* 2.7 26.5 + - - +
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Residues in contact with PHE 577 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397B TYR* 3.6 37.2 - + + -
398B THR 3.6 3.1 - - - +
399B MET* 4.2 6.7 - - + +
471B ALA* 3.7 36.1 - - + -
474B CYS* 3.9 12.6 - - + -
476B ALA* 3.6 19.3 - - + -
481B ASN* 2.7 46.6 + - - +
483B GLY* 3.8 21.3 - - - -
485B LEU* 5.6 1.1 - - + -
575B VAL* 3.9 17.0 - - + -
576B GLN* 1.3 74.6 - - - +
578B ASN* 1.3 61.7 + - - +
579B PHE* 3.4 22.8 + + + -
580B GOL 3.7 10.1 - - - -
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Residues in contact with ASN 578 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397B TYR* 3.2 6.2 - - - +
398B THR* 2.6 60.2 + - - +
399B MET 3.9 0.6 - - - -
400B THR* 2.8 27.7 + - - +
481B ASN* 5.4 0.3 + - - -
576B GLN* 2.7 34.0 + - - +
577B PHE* 1.3 70.0 - - - +
579B 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