Contacts of the strand formed by residues 470 - 480 (chain B) in PDB entry 1KP5
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 470 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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393B PHE* 3.8 13.0 - - - -
464B ALA 3.7 0.2 - - - -
465B ASP* 2.8 27.6 + - - +
468B LYS* 3.1 5.2 - - - -
469B ASN* 1.3 80.4 - - - +
471B ILE* 1.3 70.3 + - - +
495B ASN 3.4 13.7 - - - -
497B PRO* 4.3 1.3 - - - -
505B LEU* 3.6 8.2 - - - +
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Residues in contact with ILE 471 (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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393B PHE* 3.7 33.0 - - + -
394B PHE* 4.0 18.6 - - + -
462B ILE* 4.1 16.4 - - + -
463B THR 3.4 10.5 - - - +
464B ALA* 4.3 0.2 - - - -
465B ASP* 4.1 5.7 - - - +
470B GLY* 1.3 81.5 - - - +
472B LYS* 1.3 68.5 + - - +
493B GLN* 4.7 3.6 - - - +
494B GLN* 3.6 2.9 - - - +
495B ASN* 2.8 54.8 + - + +
506B PRO* 3.4 37.5 - - + -
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Residues in contact with LYS 472 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462B ILE* 3.8 3.5 - - - +
463B THR* 2.9 61.7 + - - +
464B ALA 3.1 18.4 + - - -
465B ASP* 3.9 23.4 - - + +
471B ILE* 1.3 78.0 - - - +
473B ALA* 1.3 66.0 + - - +
474B ASN* 5.2 7.9 - - - +
493B GLN 3.5 14.4 - - - +
494B GLN* 4.3 6.5 - - + +
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Residues in contact with ALA 473 (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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460B VAL* 4.1 12.6 - - + -
461B TYR 3.4 17.3 - - - +
462B ILE* 4.0 15.3 - - + -
463B THR* 6.2 0.7 - - - -
471B ILE* 5.3 0.7 - - + -
472B LYS* 1.3 78.3 - - - +
474B ASN* 1.3 70.0 + - - +
475B PHE* 4.4 1.8 - - + -
491B HIS 4.6 0.2 - - - -
493B GLN* 2.8 57.2 + - + +
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Residues in contact with ASN 474 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461B TYR* 4.1 18.1 + - - +
472B LYS* 5.1 8.5 - - - +
473B ALA* 1.3 82.5 + - - +
475B PHE* 1.3 70.8 + - - +
491B HIS 3.5 7.0 - - - +
492B TYR* 2.9 40.3 - - + -
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Residues in contact with PHE 475 (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 THR* 4.3 0.9 - - + -
376B GYS 3.9 20.9 - + - -
406B ARG* 3.8 15.3 - - - -
458B HIS* 5.5 2.0 - - + -
459B ASN 4.1 17.3 - - - +
460B VAL* 3.8 26.0 - - + -
473B ALA* 4.6 0.2 - - + -
474B ASN* 1.3 86.2 - - - +
476B LYS* 1.3 65.7 + - - +
477B ILE* 3.8 25.4 - - + -
490B ASP* 3.8 0.6 - - - -
491B HIS* 2.8 74.3 + + + +
493B GLN* 3.5 26.0 - - + -
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Residues in contact with LYS 476 (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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458B HIS* 3.2 17.3 - - - -
475B PHE* 1.3 75.3 - - - +
477B ILE* 1.3 62.5 + - - +
478B ARG* 4.0 11.0 + - + +
488B LEU* 4.3 32.8 - - + -
489B ALA 3.7 4.0 - - - +
490B ASP* 3.1 38.2 + - - +
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Residues in contact with ILE 477 (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 THR* 4.0 0.2 - - + -
376B GYS 3.8 18.6 - - + +
455B TYR* 3.5 22.2 - - + +
458B HIS* 3.4 33.7 - - + +
475B PHE* 3.8 12.3 + - + -
476B LYS* 1.3 72.1 - - - +
478B ARG* 1.3 64.6 + - - +
479B HIS* 3.5 34.7 + - + +
487B GLN 3.7 0.9 - - - +
488B LEU* 3.6 2.8 - - - -
489B ALA* 2.8 35.0 + - + +
491B HIS* 3.4 32.1 - - + +
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Residues in contact with ARG 478 (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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456B ASN* 3.1 29.5 + - + +
458B HIS* 3.1 17.1 + - + +
476B LYS* 4.8 13.4 - - + +
477B ILE* 1.3 74.2 - - - +
479B HIS* 1.3 62.0 + - - +
486B VAL* 3.5 25.5 - - + +
487B GLN 3.8 3.1 - - - -
488B LEU* 3.3 37.7 - - + +
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Residues in contact with HIS 479 (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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368B PRO* 3.3 42.2 - - + +
369B THR* 3.9 11.2 + - - +
410B PHE* 4.2 9.0 - + - -
451B LEU* 3.7 31.4 - - + -
454B ASN 5.4 2.3 + - - -
455B TYR* 3.8 12.1 - + - -
477B ILE* 3.5 27.8 - - + +
478B ARG* 1.3 73.6 + - - +
480B ASN* 1.3 64.3 + - - +
486B VAL* 3.3 3.9 - - - -
487B GLN* 2.8 48.5 + - + +
489B ALA* 4.0 17.7 - - + +
491B HIS* 5.7 1.0 - - - -
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Residues in contact with ASN 480 (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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451B LEU* 3.6 6.1 - - - +
452B GLU* 2.9 47.6 + - - +
454B ASN* 3.7 21.9 + - - +
456B ASN* 3.6 28.3 + - - -
478B ARG 4.0 0.8 + - - -
479B HIS* 1.3 75.6 - - - +
481B ILE* 1.3 61.8 + - - +
484B GLY 6.2 0.2 - - - -
485B SER 3.8 4.0 + - - +
486B VAL* 4.1 17.0 - - - +
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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