Contacts of the helix formed by residues 246 - 254 (chain D) in PDB entry 1KPH
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 ASN 246 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24A ARG* 3.2 33.2 + - - +
29A PRO* 3.4 32.4 + - - +
25D LEU* 2.8 46.3 - - + +
242D ALA 3.1 13.4 + - - +
243D LEU 2.9 9.0 + - - +
245D ALA* 1.3 76.6 + - - +
247D LYS* 1.3 62.5 + - - +
248D GLY 3.3 2.7 - - - -
249D GLN* 3.1 5.2 + - - +
250D ALA* 2.8 21.2 + - - +
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Residues in contact with LYS 247 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A GLU* 5.5 10.7 + - - +
243D LEU 3.0 1.2 + - - -
244D GLN* 2.9 18.4 + - + +
245D ALA 3.3 1.8 - - - +
246D ASN* 1.3 75.4 - - - +
248D GLY* 1.3 64.1 + - - +
250D ALA* 3.2 1.6 + - - +
251D ILE* 2.9 45.2 + - + +
256D GLU* 4.6 7.9 + - - -
259D TYR* 3.4 47.8 - - + +
260D GLU* 5.0 4.1 + - - -
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Residues in contact with GLY 248 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A LEU* 5.2 14.3 - - - +
109A ASN* 6.1 3.6 - - - -
245D ALA 5.1 1.0 + - - -
246D ASN 3.3 1.0 - - - -
247D LYS* 1.3 80.3 - - - +
249D GLN* 1.3 61.1 + - - +
251D ILE* 3.4 6.8 + - - +
252D ALA* 3.0 22.9 + - - +
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Residues in contact with GLN 249 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A ASP* 4.9 7.7 + - - -
24A ARG* 3.6 43.4 - - - +
102A HIS* 5.6 7.8 - - + -
25D LEU* 3.6 25.6 - - + -
246D ASN* 3.1 9.1 + - + +
248D GLY* 1.3 75.8 - - - +
250D ALA* 1.3 58.7 + - - +
252D ALA* 3.7 11.5 - - - +
253D LEU* 2.9 56.6 + - + +
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Residues in contact with ALA 250 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22D PHE* 4.0 14.6 - - + -
25D LEU* 3.5 21.5 - - + +
243D LEU* 4.1 4.9 - - + -
246D ASN 2.8 17.5 + - - +
247D LYS 3.4 5.4 - - - +
249D GLN* 1.3 77.2 - - - +
251D ILE* 1.3 57.4 + - - +
253D LEU* 4.1 0.7 - - - +
254D GLN* 3.0 32.7 + - - +
255D SER 3.7 2.3 + - - +
259D TYR* 3.7 24.5 - - + -
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Residues in contact with ILE 251 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A ASN* 6.5 1.3 - - - -
247D LYS* 2.9 42.9 + - + +
248D GLY* 3.9 5.6 - - - +
250D ALA* 1.3 73.2 - - - +
252D ALA* 1.3 66.3 + - - +
254D GLN 3.3 17.3 - - - +
255D SER* 3.4 7.5 + - - -
256D GLU* 3.7 53.6 - - + +
259D TYR* 4.1 11.2 - - + -
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Residues in contact with ALA 252 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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248D GLY 3.0 17.5 + - - +
249D GLN* 3.3 15.9 + - - +
251D ILE* 1.3 80.8 - - - +
253D LEU* 1.3 64.7 + - + +
254D GLN 4.3 2.4 - - - +
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Residues in contact with LEU 253 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D SER* 5.6 1.8 - - - +
21D ASP* 3.8 48.9 - - + +
22D PHE* 4.2 4.5 - - + +
25D LEU* 4.0 9.9 - - + -
249D GLN* 2.9 48.9 + - + +
250D ALA* 4.1 1.8 - - - +
252D ALA* 1.3 79.0 - - + +
254D GLN* 1.3 78.3 + - + +
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Residues in contact with GLN 254 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D LEU* 3.5 40.3 + - + +
19D SER* 3.9 11.7 - - - -
22D PHE* 3.6 27.4 - - + -
250D ALA 3.0 12.5 + - - +
251D ILE 3.3 8.3 - - - +
252D ALA 4.3 2.3 - - - +
253D LEU* 1.3 90.2 + - - +
255D SER* 1.3 66.7 + - - +
258D VAL* 3.8 27.4 - - + +
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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