Contacts of the strand formed by residues 561 - 568 (chain A) in PDB entry 1KWA
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 GLY 561 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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494A GLN* 3.5 14.6 - - - -
495A LYS* 2.9 36.1 + - - -
496A ASN* 4.7 4.1 - - - +
560A ARG* 1.3 75.3 - - - +
562A SER* 1.3 64.9 + - - -
563A ILE* 3.5 4.3 + - - +
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Residues in contact with SER 562 (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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492A GLN* 3.1 26.5 + - - +
493A PHE 3.9 0.4 - - - -
494A GLN* 3.2 20.8 - - - +
540A ASN* 3.6 14.8 + - - +
560A ARG 4.1 2.3 + - - +
561A GLY* 1.3 71.7 - - - -
563A ILE* 1.3 62.8 + - - +
564A THR* 4.2 3.7 + - - -
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Residues in contact with ILE 563 (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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491A VAL 3.9 0.5 - - - +
492A GLN* 3.3 3.4 - - - -
493A PHE* 3.0 50.1 + - + +
495A LYS* 3.7 36.1 - - + -
501A MET* 5.1 3.8 - - - -
539A ILE* 4.1 17.5 - - + -
540A ASN* 3.6 5.8 - - - +
556A LEU* 5.1 3.1 - - + +
559A MET* 3.9 26.2 - - + +
560A ARG 5.1 1.8 - - - +
561A GLY 3.8 8.3 - - - +
562A SER* 1.3 80.2 + - - +
564A THR* 1.3 64.3 + - - +
565A PHE* 3.7 30.9 + - + -
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Residues in contact with THR 564 (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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490A LEU* 4.0 31.6 - - + -
491A VAL 3.3 10.8 - - - +
492A GLN* 3.6 18.7 - - + +
538A GLU 3.7 0.5 - - - +
539A ILE* 3.4 4.5 - - - +
540A ASN* 2.7 47.1 + - - +
541A GLY 4.8 1.2 + - - +
562A SER* 4.5 3.1 + - - -
563A ILE* 1.3 76.9 - - - +
565A PHE* 1.3 64.4 + - - +
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Residues in contact with PHE 565 (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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489A ARG 3.5 0.9 - - - +
490A LEU* 3.4 3.5 - - - -
491A VAL* 2.7 43.0 + - + +
493A PHE* 3.1 33.4 - + - -
501A MET* 3.6 22.9 - - + -
503A ILE* 5.2 0.4 - - + -
529A THR* 4.8 5.2 - - - -
530A LEU* 4.7 15.7 - - + -
536A ILE* 3.8 33.4 - - + -
538A GLU 3.3 1.8 - - - +
539A ILE* 3.9 22.7 - - + -
556A LEU* 3.9 21.8 - - + -
563A ILE* 3.7 13.0 - - + -
564A THR* 1.3 77.4 - - - +
566A LYS* 1.3 61.4 + - - +
567A ILE* 3.6 18.0 + - + -
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Residues in contact with LYS 566 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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488A SER* 2.9 36.1 + - - +
489A ARG 3.3 6.7 - - - +
490A LEU* 3.8 19.5 - - + +
536A ILE* 3.8 0.3 - - - -
537A ARG* 2.7 46.8 + - + +
538A GLU* 2.9 52.4 + - + +
564A THR 4.2 0.4 + - - -
565A PHE* 1.3 71.0 - - - +
567A ILE* 1.3 56.6 + - - +
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Residues in contact with ILE 567 (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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488A SER* 3.4 6.3 - - - -
489A ARG* 2.7 62.0 + - + +
491A VAL* 3.8 24.0 - - + -
529A THR 4.8 0.9 - - - +
530A LEU* 4.0 15.5 - - + -
534A ASP* 3.9 27.6 - - + +
535A GLU 3.0 13.2 - - - +
536A ILE* 4.1 10.1 - - + -
537A ARG* 4.5 0.7 - - - +
565A PHE* 3.8 22.7 - - + +
566A LYS* 1.3 80.0 - - - +
568A VAL* 1.3 63.9 + - - +
569A PRO* 3.4 9.1 - - + +
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Residues in contact with VAL 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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487A ARG 5.1 5.4 - - - +
488A SER* 4.8 10.3 - - - +
533A GLY 4.7 0.3 - - - +
534A ASP* 3.6 0.7 - - - -
535A GLU* 2.8 48.8 + - + +
537A ARG* 4.1 24.2 - - + +
567A ILE* 1.3 76.0 - - - +
569A PRO* 1.3 73.0 - - + +
570A SER* 4.5 0.5 - - - -
572A ARG* 6.1 0.2 - - - +
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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