Contacts of the helix formed by residues 392 - 397 (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 ASP 392 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315B GLU* 5.5 3.1 - - + +
384B TYR* 3.3 39.1 - - + +
388B MET 3.7 0.6 + - - -
389B LYS* 3.5 15.2 + - + +
390B ARG 3.6 1.2 - - - -
391B HIS* 1.3 74.6 - - - +
393B PHE* 1.3 61.9 + - - +
394B PHE* 3.4 12.3 + - - +
395B LYS* 2.7 58.8 + - + +
396B SER* 3.3 18.7 + - - -
504B LEU* 3.9 5.9 - - + +
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Residues in contact with PHE 393 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391B HIS 3.3 6.4 + - - +
392B ASP* 1.3 73.9 + - - +
394B PHE* 1.3 80.3 + + + +
396B SER* 2.8 19.6 + - - -
397B ALA* 3.1 8.9 + - + +
402B TYR* 4.1 21.1 - + + -
462B ILE* 6.3 0.2 - - + -
469B ASN 3.9 2.2 - - - -
470B GLY* 3.8 20.4 - - - -
471B ILE* 3.7 35.7 - - + -
495B ASN* 3.8 20.9 - - + -
496B THR 4.1 4.0 - - - -
497B PRO* 3.8 26.0 - - + -
503B VAL* 3.9 27.1 - - + -
504B LEU 3.4 24.6 + - - +
505B LEU* 4.8 0.7 - - + -
506B PRO* 4.4 3.4 - - + -
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Residues in contact with PHE 394 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379B GLN* 3.7 47.6 - - + -
380B CYS* 3.4 26.2 - - + +
384B TYR* 3.7 21.8 - + - -
392B ASP* 3.3 10.5 - - - +
393B PHE* 1.3 88.7 - + + +
395B LYS* 1.3 61.2 + - - +
397B ALA 3.6 5.9 + - - -
398B MET* 3.9 6.9 + - - +
402B TYR* 3.6 38.6 - + + -
462B ILE* 4.4 15.3 - - + -
471B ILE* 4.0 24.5 - - + -
495B ASN* 3.8 17.0 - - - -
511B LEU* 4.1 9.2 - - + -
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Residues in contact with LYS 395 (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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314B GLY* 3.3 12.7 - - - -
315B GLU* 3.8 37.0 - - + +
318B PHE* 3.8 25.8 - - + -
347B ALA* 3.6 21.5 - - - -
380B CYS 3.2 26.4 + - - +
382B SER 3.0 27.1 + - - -
384B TYR* 4.0 5.3 - - - +
392B ASP* 2.7 34.3 + - + +
394B PHE* 1.3 74.8 - - - +
396B SER* 1.3 65.1 + - - +
398B MET* 3.2 18.0 + - - +
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Residues in contact with SER 396 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311B SER 5.5 0.9 - - - -
312B ARG* 3.3 34.4 + - - +
315B GLU 5.4 0.2 - - - +
392B ASP 3.3 14.2 + - - -
393B PHE 2.8 19.1 + - - -
395B LYS* 1.3 80.6 - - - +
397B ALA* 1.3 58.7 + - - +
398B MET 3.5 2.8 + - - +
502B PRO 4.1 6.4 - - - +
503B VAL* 3.4 9.3 - - - +
504B LEU* 2.9 43.2 + - - -
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Residues in contact with ALA 397 (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* 3.1 23.6 + - + +
394B PHE 4.0 6.5 - - - +
395B LYS 3.2 0.6 - - - -
396B SER* 1.3 75.5 + - - +
398B MET* 1.3 62.1 + - - +
400B GLU* 3.2 10.4 - - - +
401B GLY* 2.8 42.6 + - - +
402B TYR* 4.0 13.7 - - + -
497B PRO* 4.5 4.0 - - + -
499B GLY 5.6 0.3 + - - -
503B VAL* 4.2 13.9 - - + -
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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