Contacts of the strand formed by residues 489 - 495 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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549A VAL* 4.1 17.8 - - - +
550A GLU* 4.5 21.4 + - - +
553A GLN* 5.2 2.2 - - - +
487B ARG 3.8 10.5 + - - +
488B SER* 1.3 82.1 - - - +
490B LEU* 1.3 62.1 + - - +
491B VAL* 3.7 7.4 - - + -
529B THR 5.0 6.6 + - - -
531B HIS* 5.6 2.0 + - - -
534B ASP* 5.0 0.8 + - - -
565B PHE 3.5 0.3 - - - +
566B LYS* 3.5 5.0 - - - +
567B ILE* 2.8 58.8 + - + +
569B PRO* 3.7 23.1 - - - +
572B ARG* 3.4 23.0 - - - +
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Residues in contact with LEU 490 (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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489B ARG* 1.3 72.2 - - - +
491B VAL* 1.3 61.9 + - - +
492B GLN* 3.8 2.8 + - - +
538B GLU* 5.8 0.9 - - - +
564B THR* 3.3 27.8 - - + +
565B PHE 3.6 0.2 - - - -
566B LYS* 3.8 31.6 - - + +
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Residues in contact with VAL 491 (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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489B ARG* 4.4 7.2 - - + -
490B LEU* 1.3 71.9 - - - +
492B GLN* 1.3 67.5 + - - +
493B PHE* 4.5 11.3 - - + -
529B THR* 3.1 38.6 - - + +
530B LEU* 3.9 18.2 - - + -
563B ILE 3.6 1.0 - - - +
564B THR* 3.1 3.1 - - - -
565B PHE* 2.8 42.6 + - + +
567B ILE* 3.8 32.3 - - + -
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Residues in contact with GLN 492 (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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490B LEU 3.8 4.4 + - - +
491B VAL* 1.3 79.7 - - - +
493B PHE* 1.3 89.1 + - - +
494B GLN* 3.5 15.0 + - - +
527B GLN* 5.5 1.2 - - - +
529B THR* 5.1 2.9 + - - +
562B SER* 3.0 28.5 + - - +
563B ILE 3.2 6.7 - - - +
564B THR* 3.7 14.8 - - + +
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Residues in contact with PHE 493 (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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491B VAL* 4.5 12.6 - - + -
492B GLN* 1.3 92.8 - - - +
494B GLN* 1.3 69.4 + - - +
495B LYS* 4.2 9.2 - - + -
501B MET* 3.8 22.7 - - + -
523B MET* 4.4 13.2 - - - -
524B ILE* 4.1 18.2 - - + -
527B GLN* 4.3 26.7 - - + +
530B LEU* 5.6 1.3 - - + -
561B GLY 3.8 0.2 - - - +
563B ILE* 2.8 74.0 + - + +
565B PHE* 3.7 28.9 - + - -
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Residues in contact with GLN 494 (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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492B GLN* 3.5 11.9 + - - +
493B PHE* 1.3 78.1 - - - +
495B LYS* 1.3 60.6 + - - +
496B ASN* 3.3 31.5 + - - +
523B MET* 4.6 8.0 - - - +
527B GLN* 5.4 4.0 + - - -
561B GLY* 3.6 6.0 - - - -
562B SER* 3.1 36.8 + - - +
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Residues in contact with LYS 495 (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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493B PHE* 4.0 7.4 + - + -
494B GLN* 1.3 75.3 - - - +
496B ASN* 1.3 59.4 + - - +
497B THR 2.8 27.9 + - - +
498B ASP* 3.8 3.8 - - - +
499B GLU 2.7 31.1 + - - +
500B PRO* 5.3 0.2 - - - -
501B MET* 3.8 26.9 - - + +
523B MET* 3.8 16.5 - - + +
556B LEU 4.1 14.6 - - - +
557B ARG* 4.6 3.4 + - - +
559B MET 3.8 14.4 - - - +
560B ARG* 3.1 14.3 - - - +
561B GLY 2.8 31.4 + - - -
563B ILE* 3.6 25.4 - - + -
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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