Contacts of the helix formed by residues 366 - 371 (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 PRO 366 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363B LEU* 4.2 0.6 - - - +
365B VAL* 1.3 91.7 - - + +
367B TRP* 1.3 64.9 + - - +
368B PRO* 3.9 8.5 - - + -
369B THR* 2.6 36.1 + - + +
370B LEU* 4.0 0.7 + - - +
445B ASN 4.1 6.3 - - - +
446B ILE* 3.0 39.3 - - + +
449B HIS* 4.1 11.9 - - - -
451B LEU* 4.1 22.2 - - + -
921B SO4 3.5 19.5 - - - +
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Residues in contact with TRP 367 (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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339B VAL* 4.1 5.8 - - + -
356B PHE* 3.7 25.4 - - + -
357B ILE 4.0 5.6 - - - -
358B CYS* 3.7 30.1 - - + -
363B LEU* 3.4 24.0 - - + +
365B VAL 3.6 2.0 + - - -
366B PRO* 1.3 70.3 - - - +
368B PRO* 1.3 71.2 - - + +
370B LEU* 3.0 17.3 + - + +
371B VAL 3.6 6.1 + - - -
374B PHE* 3.7 26.0 - + - -
453B TYR* 4.0 3.6 - + + -
519B LYS* 4.1 9.9 - - - -
526B ASP* 3.1 46.7 + - - -
527B HIS* 3.4 18.5 + - - -
528B MET* 3.4 37.5 - - + +
921B SO4 2.9 29.0 + - - +
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Residues in contact with PRO 368 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366B PRO* 3.3 9.2 - - + -
367B TRP* 1.3 94.8 - - + +
369B THR* 1.3 60.7 + - - +
370B LEU 3.2 1.2 + - - -
371B VAL* 3.3 15.8 + - + -
451B LEU* 4.8 8.1 - - + +
452B GLU 3.5 23.6 - - - +
453B TYR* 4.3 6.1 - - + -
454B ASN 4.3 9.6 - - - +
455B TYR* 3.3 15.1 + - + -
479B HIS* 3.3 29.3 - - + +
517B LEU* 4.0 16.4 - - + -
528B MET* 4.1 1.3 - - + -
921B SO4 3.5 9.9 - - - +
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Residues in contact with THR 369 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365B VAL* 3.8 7.1 - - - +
366B PRO* 2.6 29.9 + - + +
368B PRO* 1.3 76.5 - - - +
370B LEU* 1.3 59.0 + - - +
371B VAL 3.5 0.2 - - - -
372B THR* 4.5 8.4 + - - -
373B THR* 4.7 1.9 + - - -
408B ILE* 4.9 2.9 - - - +
410B PHE* 3.8 26.3 - - + -
416B TYR* 3.0 36.4 + - - +
446B ILE* 4.5 4.0 - - + -
451B LEU* 3.5 29.4 - - + -
479B HIS* 3.9 10.2 + - - +
491B HIS* 5.9 0.7 - - - -
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Residues in contact with LEU 370 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328B LEU* 5.4 1.6 - - + -
337B PHE* 4.2 11.4 - - + -
363B LEU* 3.9 25.1 - - + -
365B VAL* 3.8 22.2 - - + -
366B PRO 4.4 0.4 - - - +
367B TRP 3.0 7.1 + - - +
369B THR* 1.3 83.2 - - - +
371B VAL* 1.3 66.4 + - - +
372B THR 3.3 2.2 - - - -
373B THR* 3.0 10.1 + - + +
374B PHE* 2.9 57.2 + - + -
416B TYR* 3.9 16.4 - - + -
435B LEU* 3.6 31.4 - - + -
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Residues in contact with VAL 371 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367B TRP 3.6 1.0 + - - -
368B PRO* 3.3 13.5 + - + +
370B LEU* 1.3 75.7 - - - +
372B THR* 1.3 61.0 + - - +
374B PHE* 3.8 7.5 - - - +
376B GYS 2.9 30.6 + - + -
455B TYR* 3.6 37.9 - - + -
515B SER* 4.6 0.7 - - - +
517B LEU* 3.9 6.7 - - + -
528B MET* 3.8 33.4 - - + -
530B LEU* 4.3 15.7 - - + +
532B GLU* 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
------------------------------------------------------------
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