Contacts of the strand formed by residues 515 - 521 (chain A) in PDB entry 1KCW
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 CYS 515 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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508A PRO* 5.0 0.2 - - - -
513A PRO* 3.4 6.7 - - - +
514A VAL* 1.3 80.9 - - - +
516A LEU* 1.3 65.1 + - - +
539A LYS* 3.9 7.9 - - + -
540A ILE 3.4 4.0 - - - -
541A CYS* 2.0 47.1 - - - -
545A SER* 4.3 1.1 - - - -
546A LEU* 4.2 1.3 - - - -
552A GLN* 3.7 31.6 - - - +
626A TYR* 3.4 22.0 - - + +
665A THR* 3.1 27.7 + - - +
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Residues in contact with LEU 516 (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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291A ARG* 4.5 16.4 - - + +
507A GLY* 4.8 1.6 - - - -
508A PRO* 3.8 37.7 - - + -
512A ASP* 4.0 15.0 - - - +
513A PRO* 3.7 31.6 - - + -
515A CYS* 1.3 73.5 - - - +
517A ALA* 1.3 67.0 + - - +
518A LYS* 3.2 34.9 + - + +
539A LYS* 3.7 4.3 - - - -
540A ILE* 3.0 27.9 + - + +
626A TYR* 4.6 1.6 - - - -
665A THR* 3.6 3.8 - - - +
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Residues in contact with ALA 517 (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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516A LEU* 1.3 72.5 - - - +
518A LYS* 1.3 71.7 + - - +
538A MET 4.2 2.5 - - - -
626A TYR* 3.6 32.6 - - + -
627A LEU 3.8 11.2 - - - +
628A PHE* 5.2 2.2 - - + -
663A SER* 3.3 16.8 + - - -
664A LEU 3.2 31.4 - - - +
665A THR* 2.9 9.7 + - - +
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Residues in contact with LYS 518 (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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291A ARG* 5.1 9.7 + - - +
293A ASP* 4.0 33.1 - - - +
459A ILE* 3.8 21.3 - - + +
460A GLY* 4.1 16.8 + - - -
506A VAL 4.9 5.9 + - - -
516A LEU* 3.7 35.0 - - + +
517A ALA* 1.3 82.0 - - - +
519A MET* 1.3 65.5 + - - +
538A MET* 2.9 43.5 + - + +
540A ILE* 4.3 17.4 - - + +
560A TYR* 6.1 0.2 - - - -
628A PHE* 3.4 17.6 - - - -
663A SER* 4.2 8.7 - - - +
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Residues in contact with MET 519 (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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459A ILE* 3.0 46.9 + - + +
518A LYS* 1.3 80.7 - - - +
520A TYR* 1.3 61.6 + - - +
521A TYR* 4.0 12.3 - - + -
535A ILE* 3.4 26.5 - - + -
536A GLY 3.2 13.7 - - - +
538A MET* 3.0 14.8 - - - +
628A PHE* 4.4 24.0 - - + -
629A SER 3.8 24.0 - - - +
630A ALA* 4.2 12.3 - - + -
661A GLN* 4.5 19.3 - - - +
662A THR 5.3 0.4 - - - +
663A SER* 5.7 3.4 - - - -
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Residues in contact with TYR 520 (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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357A ILE* 4.3 3.2 - - + +
406A TYR* 3.5 37.5 - + - +
431A GLY* 3.7 2.9 - - - -
432A PRO* 3.2 39.5 + - - +
434A ILE* 3.4 29.2 - - + -
456A ILE* 4.4 14.4 - - + -
457A GLU 3.0 18.2 - - - +
458A PRO* 3.9 3.6 - - + -
459A ILE 4.6 0.2 - - - +
500A TRP* 5.2 0.9 - - + -
519A MET* 1.3 73.8 - - - +
521A TYR* 1.3 65.1 + - - +
535A ILE* 3.0 3.5 - - - +
536A GLY* 2.7 50.7 + - - -
537A PRO 3.3 19.7 - - - -
538A MET* 3.3 26.7 - - + -
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Residues in contact with TYR 521 (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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279A PHE* 4.4 3.5 - - - -
281A HIS* 5.8 0.5 + - - -
320A GLN* 3.9 13.8 + - - -
406A TYR* 3.6 6.7 - - - -
456A ILE* 4.4 0.2 - - - -
457A GLU* 2.6 51.7 + - + +
459A ILE* 3.1 40.9 - - + +
519A MET* 4.0 10.1 - - + -
520A TYR* 1.3 78.8 - - - +
522A SER* 1.3 69.2 + - - +
523A ALA* 4.3 9.2 - - + -
526A PRO* 4.3 20.4 - - + -
530A ILE* 3.6 31.2 - - + -
534A LEU 3.0 17.9 - - - +
535A ILE* 3.6 17.3 - - + -
661A GLN* 3.5 17.6 + - - -
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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