Contacts of the helix formed by residues 292 - 298 (chain I) in PDB entry 1K9O
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 LEU 292 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30I MET* 4.1 26.0 - - - -
50I VAL* 3.8 32.5 - - + -
174I LEU* 4.7 8.3 - - + -
176I ASN* 4.1 7.9 - - + +
290I THR* 3.3 10.2 + - + -
291I ASP* 1.3 69.7 - - - +
293I LYS* 1.3 59.3 + - - +
295I VAL* 4.1 3.6 - - + -
296I LEU* 2.7 48.0 + - + +
327I ALA* 2.8 26.8 + - + +
328I ILE 3.6 20.0 - - - +
329I GLN* 3.9 25.8 - - + -
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Residues in contact with LYS 293 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291I ASP* 3.1 13.9 + - - +
292I LEU* 1.3 77.8 - - - +
294I GLU* 1.3 57.4 + - - +
297I SER* 2.8 39.5 + - - +
305I PHE* 3.8 52.4 + - + -
324I VAL 4.7 0.4 + - - -
325I ASP* 3.2 32.4 + - - +
326I ALA* 4.7 1.6 - - - -
327I ALA* 3.5 11.5 + - + +
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Residues in contact with GLU 294 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33I GLU 5.1 0.2 - - - +
37I ALA* 3.4 28.1 - - - +
291I ASP* 3.3 34.0 + - - +
293I LYS* 1.3 82.4 - - - +
295I VAL* 1.3 69.5 + - - +
297I SER* 3.7 4.5 - - - -
298I ASN* 3.0 40.7 + - - +
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Residues in contact with VAL 295 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30I MET* 4.0 30.3 - - + +
33I GLU* 3.7 31.9 - - + +
34I VAL* 4.5 7.6 - - + -
37I ALA* 5.1 1.3 - - + -
290I THR* 3.7 18.6 - - + -
291I ASP 2.9 21.0 + - - +
292I LEU* 4.1 5.2 - - - -
294I GLU* 1.3 85.8 - - - +
296I LEU* 1.3 61.6 + - + +
298I ASN* 3.0 22.0 + - - +
299I MET* 3.2 22.5 + - - +
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Residues in contact with LEU 296 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26I PHE* 3.8 34.1 - - + -
30I MET* 4.3 11.7 - - - -
50I VAL* 4.3 9.9 - - + -
54I LEU* 3.8 28.3 - - + -
174I LEU* 5.4 2.5 - - + -
292I LEU* 2.7 42.7 + - + +
295I VAL* 1.3 74.3 - - - +
297I SER* 1.3 57.0 + - - +
299I MET* 2.8 31.4 + - + +
301I ILE* 3.3 24.3 + - + +
305I PHE* 3.7 24.7 - - + -
327I ALA* 5.4 0.7 - - + -
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Residues in contact with SER 297 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293I LYS* 2.8 28.2 + - - +
294I GLU* 3.7 5.8 - - - -
296I LEU* 1.3 76.2 - - - +
298I ASN* 1.3 58.6 + - - +
299I MET 3.2 2.8 + - - -
300I ASN 3.8 1.0 + - - -
301I ILE 3.4 19.9 + - - -
302I LYS* 3.3 39.3 + - - +
305I PHE* 3.5 12.8 - - - +
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Residues in contact with ASN 298 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33I GLU* 3.4 32.3 + - - +
294I GLU* 3.0 32.7 + - - +
295I VAL 3.0 11.2 + - - +
297I SER* 1.3 78.2 - - - +
299I MET* 1.3 61.4 + - - +
300I ASN* 3.6 1.9 - - - +
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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
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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