Contacts of the strand formed by residues 527 - 537 (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 HIS 527 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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355B LYS* 3.9 8.3 - - - -
356B PHE 2.9 17.7 - - - +
357B ILE* 4.2 7.2 - - + -
367B TRP* 3.4 10.4 + - - -
519B LYS* 2.9 48.6 + - + +
520B ASP* 2.6 49.6 + - + +
523B GLU* 3.4 30.9 - - + +
525B ARG 3.0 14.3 + - - +
526B ASP* 1.3 77.8 + - - +
528B MET* 1.3 67.4 + - - +
529B VAL* 4.2 8.1 - - + -
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Residues in contact with MET 528 (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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355B LYS* 3.4 1.4 - - - -
356B PHE* 2.7 50.7 + - + -
367B TRP* 3.4 61.5 - - + +
368B PRO 3.8 0.2 - - - -
371B VAL* 3.8 16.6 - - + -
374B PHE* 5.0 3.8 - - - -
453B TYR* 3.3 19.3 - - + +
517B LEU* 3.3 39.9 - - + -
518B SER 4.2 0.9 - - - -
527B HIS* 1.3 80.8 - - - +
529B VAL* 1.3 71.4 + - - +
530B LEU* 4.6 3.6 - - - +
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Residues in contact with VAL 529 (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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353B THR* 5.6 7.2 - - + -
354B LEU 3.4 8.1 - - - +
355B LYS* 4.1 23.3 - - + -
516B ALA 3.8 0.5 - - - +
517B LEU* 3.5 6.2 - - - -
518B SER* 3.1 51.7 + - - +
519B LYS 4.3 0.9 - - - -
520B ASP* 4.1 26.2 - - + +
527B HIS* 4.2 3.1 - - + -
528B MET* 1.3 79.4 - - - +
530B LEU* 1.3 66.8 + - - +
531B LEU* 6.0 1.8 - - + -
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Residues in contact with LEU 530 (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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352B LEU* 3.7 2.0 - - + +
353B THR* 3.5 6.6 - - - +
354B LEU* 2.6 46.2 + - + +
356B PHE* 4.0 26.5 - - + -
371B VAL* 4.3 16.8 - - + +
376B GYS 3.4 27.6 - - - +
515B SER* 4.0 14.1 - - - -
516B ALA 3.7 1.6 - - - +
517B LEU* 3.6 26.5 - - + -
528B MET* 4.0 2.9 + - + -
529B VAL* 1.3 76.4 - - - +
531B LEU* 1.3 68.2 + - - +
532B GLU* 4.0 20.9 - - + +
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Residues in contact with LEU 531 (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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351B LYS* 4.0 26.5 - - + -
352B LEU 3.5 12.1 - - - +
353B THR* 4.1 10.5 - - + +
514B GLN 3.9 0.2 - - - +
515B SER* 3.4 2.9 - - - -
516B ALA* 2.8 53.7 + - + +
529B VAL* 4.3 2.2 - - + -
530B LEU* 1.3 73.0 - - - +
532B GLU* 1.3 61.7 + - - +
533B PHE* 4.4 20.4 - - + -
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Residues in contact with GLU 532 (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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350B GLY 3.4 1.6 - - - +
351B LYS* 3.5 2.8 - - - +
352B LEU* 2.8 60.2 + - + +
371B VAL* 3.8 8.7 - - - +
376B GYS 2.7 46.5 + - - -
513B THR* 4.0 15.7 - - + +
514B GLN 3.2 10.1 - - - +
515B SER* 2.6 31.8 + - - +
530B LEU* 4.0 9.1 - - + +
531B LEU* 1.3 76.5 - - - +
533B PHE* 1.3 66.7 + - - +
534B VAL* 4.2 4.7 - - + +
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Residues in contact with PHE 533 (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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349B TYR* 4.0 14.6 - - + -
350B GLY 3.3 1.1 - - - -
351B LYS* 3.3 57.0 - - + -
512B SER 3.6 1.6 - - - +
513B THR* 3.5 1.4 - - - -
514B GLN* 2.9 52.4 + - + +
531B LEU* 4.4 23.6 - - + -
532B GLU* 1.3 74.3 - - - +
534B VAL* 1.3 60.4 + - - +
535B THR* 5.9 1.1 - - - -
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Residues in contact with VAL 534 (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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350B GLY* 3.0 18.6 + - - +
352B LEU* 5.1 14.6 - - + -
378B VAL 6.1 0.2 - - - +
379B GLN* 5.8 7.0 - - + -
381B PHE 4.3 2.7 - - - +
382B SER* 3.3 35.4 - - - +
383B ARG 2.9 21.1 + - - -
511B LEU* 3.8 17.9 - - + -
512B SER 3.1 5.8 - - - +
513B THR* 3.6 26.0 - - + +
532B GLU* 5.2 4.5 - - - +
533B PHE* 1.3 76.7 - - - +
535B THR* 1.3 62.9 + - - +
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Residues in contact with THR 535 (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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383B ARG* 3.6 30.5 + - - +
385B PRO* 4.7 3.1 - - - +
511B LEU* 4.4 3.6 - - - -
512B SER* 2.8 54.9 + - - +
533B PHE 5.9 0.7 - - - -
534B VAL* 1.3 75.9 - - - +
536B ALA* 1.3 70.2 + - - +
537B ALA* 3.8 1.9 + - + +
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Residues in contact with ALA 536 (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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383B ARG 2.8 19.5 + - - +
384B TYR* 3.8 28.5 - - + -
385B PRO* 3.9 9.2 - - - +
388B MET* 3.8 19.3 - - + +
509B HIS* 4.3 0.7 - - + -
510B TYR 3.4 7.0 - - - +
511B LEU* 3.7 19.5 - - + +
535B THR* 1.3 78.7 + - - +
537B ALA* 1.3 64.2 + - - +
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Residues in contact with ALA 537 (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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388B MET* 4.0 8.7 - - - +
509B HIS* 3.3 6.8 - - - +
510B TYR* 2.9 55.7 + - + +
512B SER* 5.5 3.1 - - - -
535B THR* 4.6 4.5 - - + +
536B ALA* 1.3 78.8 - - - +
538B GLY* 1.3 64.7 + - - +
539B LEU 3.4 2.5 - - - +
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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