Contacts of the strand formed by residues 489 - 495 (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 ARG 489 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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488A SER* 1.3 81.8 - - - +
490A LEU* 1.3 74.5 + - - +
491A VAL* 3.5 25.1 - - + +
528A GLY 4.8 11.1 + - - -
529A THR* 4.9 3.4 + - - +
531A HIS* 5.4 11.5 + - - -
534A ASP* 5.8 0.4 + - - -
565A PHE 3.5 0.5 - - - +
566A LYS* 3.3 3.8 - - - +
567A ILE* 2.7 53.9 + - + +
569A PRO* 4.4 21.1 - - + +
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Residues in contact with LEU 490 (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* 6.1 0.2 - - - +
489A ARG* 1.3 82.6 + - - +
491A VAL* 1.3 64.9 + - - +
564A THR* 4.0 19.7 - - + -
565A PHE 3.4 3.1 - - - +
566A LYS* 3.8 34.8 - - + +
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Residues in contact with VAL 491 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489A ARG* 3.5 28.9 - - - +
490A LEU* 1.3 80.9 - - - +
492A GLN* 1.3 65.8 + - - +
529A THR* 2.9 49.4 - - - +
530A LEU* 4.7 1.6 - - + -
563A ILE 3.9 0.3 - - - +
564A THR* 3.3 3.1 - - - +
565A PHE* 2.7 48.4 + - + +
567A ILE* 3.8 24.7 - - + -
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Residues in contact with GLN 492 (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* 1.3 82.8 - - - +
493A PHE* 1.3 86.2 + - - +
494A GLN* 2.8 32.8 + - - +
529A THR* 4.6 2.8 + - - -
562A SER* 3.1 20.0 + - - +
563A ILE 3.3 6.1 - - - +
564A THR* 3.6 18.6 - - + +
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Residues in contact with PHE 493 (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* 1.3 91.0 + - - +
494A GLN* 1.3 72.5 + - - +
495A LYS* 3.8 11.2 - - + -
501A MET* 3.3 30.7 - - + -
523A MET* 3.4 29.2 - - + -
524A ILE* 4.0 12.1 - - + -
527A GLN* 3.6 20.2 - - - +
529A THR* 4.4 11.4 - - + +
563A ILE* 3.0 50.2 + - + +
565A PHE* 3.1 39.3 - + - -
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Residues in contact with GLN 494 (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* 2.8 24.7 + - - +
493A PHE* 1.3 86.0 - - - +
495A LYS* 1.3 59.2 + - - +
496A ASN* 3.7 20.7 + - - +
523A MET* 3.7 9.2 - - - +
527A GLN* 4.7 5.9 + - - +
561A GLY* 3.5 23.9 - - - -
562A SER* 3.2 16.8 + - - +
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Residues in contact with LYS 495 (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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493A PHE* 3.8 7.6 - - + -
494A GLN* 1.3 72.7 - - - +
496A ASN* 1.3 56.5 + - - +
497A THR 3.2 14.0 + - - +
498A ASP 4.7 1.0 + - - -
499A GLU 3.1 25.7 + - - -
500A PRO* 4.5 2.0 - - - +
501A MET* 4.4 21.4 - - + +
523A MET* 4.6 11.2 - - + +
556A LEU 4.2 12.3 - - - +
557A ARG* 4.3 4.7 + - - +
559A MET 3.1 24.7 - - - +
560A ARG* 3.2 29.7 - - - +
561A GLY 2.9 25.7 + - - +
563A ILE* 3.7 26.9 - - + -
574B PHE 4.9 1.6 + - - -
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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