Contacts of the helix formed by residues 231 - 236 (chain C) in PDB entry 5KKR
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 SER 231 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229C TYR 3.7 1.8 + - - -
230C MET* 1.3 77.4 - - - +
232C PRO* 1.3 72.3 - - - +
233C GLU* 3.1 25.8 + - - -
234C ARG* 3.0 23.3 + - - +
235C LEU* 3.2 11.0 + - - +
244C SER* 2.5 33.3 + - - -
247C TRP* 3.5 17.9 - - - -
248C SER* 4.9 1.0 + - - -
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Residues in contact with PRO 232 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230C MET 3.9 0.4 - - - -
231C SER* 1.3 86.3 - - - +
233C GLU* 1.3 66.3 + - - +
235C LEU* 3.5 13.9 + - + +
236C GLN* 3.3 33.6 + - - +
247C TRP* 3.5 44.9 - - + -
317C ILE* 3.7 21.1 - - + +
318C VAL* 4.3 10.8 - - + +
344C LYS* 4.4 19.5 - - + +
349C ARG* 4.2 0.4 - - - +
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Residues in contact with GLU 233 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231C SER* 3.1 22.2 + - - +
232C PRO* 1.3 77.4 - - - +
234C ARG* 1.3 66.6 + - + +
236C GLN* 3.5 9.5 + - - +
237C GLY 3.4 3.1 + - - -
238C THR* 2.7 45.2 + - - +
239C HIS 4.5 10.8 - - - +
240C TYR* 4.6 4.7 - - + -
243C GLN 4.8 0.2 - - - -
244C SER* 3.5 9.9 + - - -
344C LYS 4.4 0.8 + - - +
346C PRO* 3.5 26.2 - - + +
349C ARG* 2.9 43.2 + - - -
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Residues in contact with ARG 234 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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877B GLN* 5.6 0.3 - - - +
878B PRO* 3.3 31.3 - - + +
881B ALA* 3.4 17.4 - - + +
187C MET* 5.4 0.4 - - - +
189C ARG* 2.7 39.4 + - - +
230C MET* 3.7 31.1 - - + +
231C SER* 3.0 19.8 + - - +
233C GLU* 1.3 74.0 - - + +
235C LEU* 1.3 64.8 + - - +
236C GLN 3.1 1.8 - - - -
237C GLY* 3.2 11.9 + - - +
238C THR 4.4 4.7 - - - -
240C TYR* 3.6 54.3 + - + -
244C SER* 3.3 20.1 + - - +
245C ASP* 5.1 1.6 + - - -
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Residues in contact with LEU 235 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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880B GLU* 3.6 34.5 - - + +
881B ALA* 3.8 8.4 - - - +
884B TRP* 3.1 22.5 - - + +
885B GLN* 3.3 13.1 - - - +
230C MET* 3.7 25.1 - - + -
231C SER 3.2 12.2 + - - +
232C PRO* 3.8 7.0 - - + +
233C GLU 3.4 0.4 - - - -
234C ARG* 1.3 75.8 - - - +
236C GLN* 1.3 58.5 + - - +
237C GLY 3.3 0.2 - - - -
314C LEU* 3.6 35.7 - - + +
317C ILE* 4.0 28.7 - - + -
318C VAL* 4.2 12.1 - - + -
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Residues in contact with GLN 236 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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884B TRP* 3.8 27.3 - - + -
885B GLN* 3.8 11.6 - - - +
890B MET* 4.0 13.8 - - + +
232C PRO* 3.3 22.3 + - - +
233C GLU* 3.9 12.5 - - - +
234C ARG 3.1 0.4 - - - -
235C LEU* 1.3 77.2 - - - +
237C GLY* 1.3 59.1 + - - +
238C THR* 3.3 18.0 + - + +
318C VAL* 3.3 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