Contacts of the helix formed by residues 385 - 391 (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 385 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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383B ARG* 3.5 41.3 - - + +
384B TYR* 1.3 88.4 - - - +
386B ASP* 1.3 61.4 + - - +
387B HIS* 3.2 25.8 - - + +
388B MET* 2.8 32.0 + - + -
389B LYS* 3.4 5.0 + - - +
535B THR* 4.7 2.9 - - - +
536B ALA 3.9 18.2 - - - +
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Residues in contact with ASP 386 (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* 5.4 1.2 - - - +
384B TYR 3.7 0.2 + - - -
385B PRO* 1.3 71.9 - - - +
387B HIS* 1.3 58.8 + - - +
388B MET 3.0 5.2 + - - -
389B LYS* 3.2 37.8 + - - +
544B THR* 2.7 34.6 + - - -
545B GLY* 3.4 9.4 + - - -
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Residues in contact with HIS 387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301B THR* 3.5 9.0 - - - -
385B PRO* 3.1 25.3 + - + +
386B ASP* 1.3 77.2 + - - +
388B MET* 1.3 72.2 + - + +
389B LYS 3.7 0.4 - - - -
539B LEU* 3.2 32.5 + - + +
541B PRO* 3.5 32.8 - - + +
543B GLY 4.1 11.7 - - - +
544B THR* 4.5 1.8 - - - +
545B GLY 3.2 27.5 - - - +
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Residues in contact with MET 388 (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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384B TYR* 3.6 19.3 - - + -
385B PRO* 2.8 18.6 + - + +
387B HIS* 1.3 108.0 - - + +
389B LYS* 1.3 61.1 + - - +
390B ARG 3.1 2.9 - - - -
391B HIS* 2.8 32.1 + - + +
509B HIS* 3.8 34.8 - - + +
536B ALA* 3.8 31.4 - - + +
537B ALA* 4.0 8.3 - - - +
539B LEU* 3.6 30.3 - - + -
545B GLY 4.3 0.4 - - - -
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Residues in contact with LYS 389 (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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311B SER* 4.1 9.5 + - - +
315B GLU* 3.9 31.7 - - + +
348B THR* 6.3 0.4 - - - +
383B ARG* 5.7 3.6 - - - +
384B TYR* 2.7 36.8 + - + +
385B PRO* 3.4 2.2 + - - +
386B ASP* 3.2 41.1 + - - +
387B HIS 3.7 0.6 - - - -
388B MET* 1.3 77.1 - - - +
390B ARG* 1.3 57.5 + - - +
391B HIS 3.1 3.5 + - - -
392B ASP* 3.5 10.2 + - + +
504B LEU* 3.3 16.5 - - - +
545B GLY* 4.9 3.6 - - - -
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Residues in contact with ARG 390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301B THR 3.0 25.5 - - - +
302B GLY* 5.1 1.8 - - - -
307B HIS* 3.6 18.1 + - + +
308B HIS 3.9 2.5 + - - -
309B HIS* 3.0 25.8 - - - +
310B HIS* 2.7 46.2 + - - +
311B SER* 4.2 3.8 - - - +
388B MET 3.0 1.4 + - - -
389B LYS* 1.3 76.0 - - + +
391B HIS* 1.3 64.7 + - + +
392B ASP 3.6 0.9 - - - -
504B LEU* 3.6 28.4 - - + +
505B LEU 4.4 5.7 - - - +
544B THR 4.2 6.7 + - - -
545B GLY* 3.3 28.5 + - - +
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Residues in contact with HIS 391 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301B THR* 3.6 27.5 + - - -
302B GLY* 4.7 3.8 - - - -
307B HIS* 6.2 0.9 - - + -
384B TYR* 3.6 15.4 + - + -
388B MET* 2.8 19.8 + - + +
390B ARG* 1.3 82.7 + - + +
392B ASP* 1.3 58.1 + - - +
393B PHE 3.3 5.4 + - - -
504B LEU* 4.8 1.6 - - - -
505B LEU 4.5 1.3 + - - -
506B PRO* 3.1 31.8 - - + +
507B ASP* 3.1 50.0 + - + -
509B HIS* 3.8 5.8 - - + +
539B LEU* 3.4 28.3 - - + +
545B GLY 3.6 15.3 + - - -
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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