Contacts of the strand formed by residues 239 - 246 (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 ALA 239 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96I LYS 5.0 4.9 - - - +
98I VAL* 3.9 15.0 - - + -
233I SER* 3.6 4.3 - - - -
234I TYR* 3.1 45.5 + - + +
235I GLU 4.9 2.4 + - - +
237I ASP 4.9 0.2 - - - +
238I GLN* 1.3 79.6 + - - +
240I SER* 1.3 66.9 + - - +
371I LEU* 4.4 2.5 - - + -
372I LYS 3.3 5.4 - - - -
373I ILE* 3.5 26.0 - - + -
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Residues in contact with SER 240 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231I GLU* 3.5 35.3 + - - -
232I MET 3.5 7.4 - - - -
233I SER* 4.2 8.0 - - - -
234I TYR* 4.0 6.2 - - - -
237I ASP 5.8 1.0 - - - -
238I GLN 4.8 2.8 + - - -
239I ALA* 1.3 79.1 + - - +
241I MET* 1.3 60.7 + - - +
242I ILE 3.5 0.9 + - - -
370I GLU 3.4 1.9 - - - +
371I LEU* 3.5 1.4 - - - +
372I LYS* 2.8 49.5 + - - +
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Residues in contact with MET 241 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180I PHE* 5.3 2.0 - - + -
184I TRP* 3.6 32.1 - - + -
230I ILE 3.5 2.4 - - - +
231I GLU* 3.5 5.1 - - - -
232I MET* 2.7 34.1 + - + +
234I TYR* 3.6 22.6 - - - +
240I SER* 1.3 69.4 - - - +
242I ILE* 1.3 62.3 + - - +
243I ILE* 3.7 20.2 + - + -
281I LEU* 5.6 1.1 - - + -
284I PHE* 3.8 16.4 - - + -
333I ILE* 4.4 7.9 - - + -
335I VAL* 3.4 34.1 - - + -
369I PHE* 4.3 19.1 - - + -
370I GLU 3.7 10.3 - - - +
371I LEU* 4.9 3.8 - - - +
379I PHE* 6.2 1.1 - - - -
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Residues in contact with ILE 242 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229I MET* 4.0 37.0 - - + -
230I ILE 3.8 1.6 - - - +
231I GLU* 3.2 41.7 - - + +
240I SER 4.5 3.6 - - - +
241I MET* 1.3 71.2 - - - +
243I ILE* 1.3 61.0 + - - +
244I ILE* 4.1 11.9 - - + -
265I LEU* 4.8 0.4 - - + -
269I GLU* 4.5 7.2 - - - +
368I TYR* 3.7 0.8 - - + +
369I PHE* 2.9 8.8 - - - +
370I GLU* 2.7 65.5 + - - +
372I LYS* 4.1 22.9 - - + -
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Residues in contact with ILE 243 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229I MET* 3.3 3.6 - - - +
230I ILE* 2.9 56.0 + - + +
232I MET* 3.5 28.0 - - + -
241I MET* 3.7 15.0 + - + -
242I ILE* 1.3 77.9 - - - +
244I ILE* 1.3 66.2 + - - +
245I LEU* 4.4 0.9 - - + +
281I LEU* 3.5 28.7 - - + -
284I PHE* 5.5 0.4 - - + -
363I ILE* 4.1 13.2 - - + -
367I PHE* 3.9 29.6 - - + -
368I TYR 3.5 2.2 - - - -
369I PHE* 4.4 10.1 - - + -
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Residues in contact with ILE 244 (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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222I VAL* 6.0 1.1 - - + -
225I LEU* 4.1 18.2 - - + -
227I ALA* 3.5 24.9 - - + -
228I LYS 3.1 7.4 - - - +
229I MET* 3.7 26.0 - - + -
242I ILE* 4.1 5.6 - - + -
243I ILE* 1.3 76.2 - - - +
245I LEU* 1.3 58.8 + - - +
246I PRO* 3.4 11.4 - - - +
255I LEU* 3.8 17.6 - - + +
259I LEU* 4.6 5.4 - - + -
265I LEU* 3.6 30.7 - - + -
367I PHE* 3.9 0.2 - - - +
368I TYR* 3.0 46.4 + - + -
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Residues in contact with LEU 245 (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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227I ALA* 3.1 2.6 - - - -
228I LYS* 2.6 57.1 + - + +
230I ILE* 4.6 2.5 - - + -
243I ILE* 3.9 2.1 - - + -
244I ILE* 1.3 72.6 - - - +
246I PRO* 1.4 68.9 - - + +
247I ASN* 3.6 1.6 + - - +
361I VAL* 5.4 2.9 - - + -
362I HIS 3.3 25.4 - - - +
363I ILE* 3.8 31.0 - - + -
364I ASP* 4.8 0.4 - - - +
365I ARG* 3.4 50.9 - - + +
367I PHE* 3.8 12.3 - - + -
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Residues in contact with PRO 246 (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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225I LEU 5.4 0.7 - - - +
226I ASP* 3.5 10.3 - - - +
227I ALA* 3.7 3.8 - - + -
244I ILE 3.4 11.2 - - - +
245I LEU* 1.4 85.2 - - + +
247I ASN* 1.3 57.6 + - - +
248I GLN 3.1 10.9 + - - +
249I VAL 5.4 0.9 - - - +
251I GLY* 3.5 37.0 - - - +
252I ILE* 4.0 5.2 - - - +
255I LEU* 4.0 13.9 - - + -
365I ARG* 3.0 29.8 - - - -
366I PRO 3.4 26.7 - - - +
367I PHE* 4.4 0.4 - - - -
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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