Contacts of the strand formed by residues 486 - 497 (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 VAL 486 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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478B ARG* 3.5 52.5 - - + +
479B HIS 3.3 9.2 - - - +
480B ASN* 4.1 15.5 - - - +
481B ILE* 3.6 9.7 - - - +
484B GLY 5.0 2.2 - - - +
485B SER* 1.3 84.8 + - - +
487B GLN* 1.3 65.2 + - - +
488B LEU* 4.0 6.5 + - + +
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Residues in contact with GLN 487 (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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410B PHE* 3.8 9.8 - - + +
411B LYS* 3.0 30.0 + - - +
413B ASP* 4.9 4.2 + - - +
445B ASN* 2.8 33.5 + - - +
446B ILE* 4.2 21.8 - - + +
451B LEU* 4.2 12.6 - - + -
477B ILE 3.7 1.2 - - - +
479B HIS* 2.8 40.2 + - + +
481B ILE* 3.8 16.3 - - + +
486B VAL* 1.3 73.9 - - - +
488B LEU* 1.3 80.4 + - - +
489B ALA 3.8 0.2 + - - -
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Residues in contact with LEU 488 (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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410B PHE* 3.4 3.1 - - - -
411B LYS* 3.1 60.3 + - + +
476B LYS* 4.3 27.8 - - + -
477B ILE 3.6 2.9 - - - +
478B ARG* 3.3 50.3 - - + +
486B VAL* 4.0 5.9 + - + +
487B GLN* 1.3 83.0 + - - +
489B ALA* 1.3 59.7 + - - +
490B ASP* 4.0 9.6 - - - +
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Residues in contact with ALA 489 (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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408B ILE* 4.0 3.4 - - + -
409B SER 3.6 6.5 - - - -
410B PHE* 3.7 26.9 - - + -
476B LYS* 4.5 0.9 - - - -
477B ILE* 2.8 31.3 + - + +
479B HIS* 4.0 14.1 - - + +
488B LEU* 1.3 74.8 - - - +
490B ASP* 1.3 60.2 + - - +
491B HIS* 3.0 29.9 + - + -
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Residues in contact with ASP 490 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407B THR 3.3 2.6 - - - +
408B ILE* 3.2 5.0 - - - -
409B SER* 2.8 49.3 + - - +
411B LYS* 5.8 2.9 + - - +
475B PHE 4.0 2.5 - - - +
476B LYS* 3.1 36.2 + - - +
488B LEU* 4.9 8.3 - - - +
489B ALA* 1.3 70.6 - - - +
491B HIS* 1.3 60.7 + - - +
492B TYR* 4.0 30.1 + - + -
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Residues in contact with HIS 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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369B THR 5.9 0.9 - - - -
372B THR* 2.7 29.4 + - + -
406B ARG* 3.6 20.0 - - - -
407B THR 3.6 3.1 - - - -
408B ILE* 3.3 26.8 - - + +
474B ASN* 3.5 5.3 - - - +
475B PHE* 2.8 69.7 + + + +
477B ILE* 3.4 26.9 - - + +
479B HIS* 5.7 1.3 - - - -
489B ALA* 3.0 26.3 + - + -
490B ASP* 1.3 75.5 - - - +
492B TYR* 1.3 69.8 + - - +
493B GLN 4.1 0.4 - - - -
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Residues in contact with TYR 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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405B GLU 3.7 0.5 - - - +
406B ARG* 3.1 26.9 - - - +
407B THR* 3.1 35.3 + - + +
409B SER* 5.1 6.5 - - - -
473B ALA 3.7 3.1 - - - -
474B ASN* 2.9 32.5 - - + -
490B ASP* 4.0 34.3 + - + -
491B HIS* 1.3 76.3 - - - +
493B GLN* 1.3 59.9 + - - +
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Residues in contact with GLN 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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379B GLN* 2.8 28.7 + - - +
394B PHE* 4.6 3.0 - - - -
404B GLN* 3.3 10.5 + - + -
405B GLU 3.4 4.3 - - - +
406B ARG* 2.7 45.4 + - + +
462B ILE* 5.8 0.6 - - - +
471B ILE* 4.7 4.0 - - + +
472B LYS* 3.5 6.1 - - - +
473B ALA* 2.8 49.6 + - + +
475B PHE* 3.5 13.5 - - + -
492B TYR* 1.3 74.4 - - - +
494B GLN* 1.3 68.9 + - - +
495B ASN* 2.8 24.0 + - - +
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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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403B VAL 3.7 1.7 - - - +
405B GLU* 3.1 56.2 + - + +
465B ASP* 4.5 7.6 + - + +
468B LYS* 2.9 39.6 + - + +
471B ILE 3.6 9.0 - - - +
472B LYS* 4.3 6.2 - - + +
492B TYR 5.6 0.2 - - - +
493B GLN* 1.3 79.7 - - - +
495B ASN* 1.3 62.8 + - - +
496B THR* 4.3 14.4 + - + +
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Residues in contact with ASN 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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393B PHE* 3.8 14.6 - - + -
394B PHE* 3.8 9.5 - - - -
402B TYR* 3.2 24.6 - - + -
403B VAL 3.1 4.7 - - - +
404B GLN* 2.8 29.2 + - - +
468B LYS* 5.4 0.3 - - - +
470B GLY* 3.4 3.6 - - - -
471B ILE* 2.8 50.2 + - + +
493B GLN* 2.8 27.7 + - - +
494B GLN* 1.3 78.1 - - - +
496B THR* 1.3 66.3 + - - +
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Residues in contact with THR 496 (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* 4.1 0.9 - - - -
402B TYR* 3.3 4.8 - - - +
403B VAL* 2.8 46.5 + - - +
405B GLU* 5.3 2.1 + - - +
468B LYS* 3.9 32.5 - - + +
470B GLY* 4.5 0.2 - - - -
494B GLN* 4.7 14.1 - - + +
495B ASN* 1.3 79.5 - - - +
497B PRO* 1.3 75.2 + - - +
923B SO4 4.1 15.6 + - - +
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Residues in contact with PRO 497 (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* 3.8 10.1 - - + -
397B ALA* 4.5 5.2 - - + -
401B GLY 3.9 5.4 - - - +
402B TYR* 4.2 4.9 - - + -
403B VAL* 5.3 1.2 - - - +
468B LYS 4.1 2.2 - - - +
469B ASN* 3.1 46.2 - - + +
496B THR* 1.3 94.3 + - - +
498B ILE* 1.3 62.1 + - - +
499B GLY 4.2 14.2 - - - +
501B GLY 5.6 0.2 - - - +
503B VAL* 3.8 22.7 - - + -
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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