Contacts of the strand formed by residues 227 - 231 (chain C) in PDB entry 7KHC
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 LYS 227 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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221C LEU* 2.3 38.2 + - - +
222C ASP* 3.2 25.3 - - - +
225C PHE 2.9 18.3 + - - +
226C GLU* 1.3 77.8 - - - +
228C VAL* 1.3 61.5 + - - +
229C ILE* 4.8 12.6 - - + -
245C ARG* 3.0 22.2 + - - -
298C ALA* 5.0 8.6 - - + +
334C GLU* 5.5 8.7 - - + +
335C THR 3.6 7.0 - - - +
336C LEU* 3.4 24.3 - - + +
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Residues in contact with VAL 228 (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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227C LYS* 1.3 72.4 - - - +
229C ILE* 1.3 64.6 + - - +
230C PHE* 3.8 26.5 - - + -
239C MET* 4.0 15.5 - - + -
240C GLU* 4.3 7.4 - - - +
245C ARG* 3.1 42.8 - - - +
295C LYS* 5.1 5.6 - - - +
333C ILE 3.8 0.2 - - - +
334C GLU* 3.7 1.7 - - - -
335C THR* 2.9 45.9 + - + +
336C LEU 4.3 1.8 - - - +
337C PHE* 3.9 18.4 - - + +
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Residues in contact with ILE 229 (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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227C LYS* 4.8 10.8 - - + -
228C VAL* 1.3 76.7 - - - +
230C PHE* 1.3 68.4 + - - +
231C GLU* 3.5 17.3 - - + +
239C MET* 4.1 0.3 - - - +
240C GLU* 3.2 44.2 + - + +
332C ARG* 3.4 34.5 - - - +
333C ILE 3.6 3.4 - - - +
334C GLU* 3.5 31.9 - - + +
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Residues in contact with PHE 230 (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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228C VAL* 3.8 11.0 - - + -
229C ILE* 1.3 76.1 - - - +
231C GLU* 1.3 63.9 + - - +
232C ILE* 5.3 0.9 - - - +
237C LEU* 4.2 5.1 - - + +
238C GLN 3.7 10.3 - - - +
239C MET* 3.3 38.1 - - + -
287C VAL* 3.7 7.4 - - + -
291C TYR* 4.3 18.2 - + - -
292C ILE* 3.2 48.0 - - + -
295C LYS* 4.4 12.6 - - + -
331C LYS 3.3 3.1 - - - +
333C ILE* 2.8 52.3 + - + +
335C THR* 4.0 20.9 - - + -
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Residues in contact with GLU 231 (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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229C ILE* 3.5 14.9 - - + +
230C PHE* 1.3 73.7 - - - +
232C ILE* 1.3 60.3 + - - +
233C ARG* 2.4 54.0 + - - +
237C LEU* 3.9 1.3 - - - -
238C GLN 2.9 15.9 + - - +
240C GLU* 4.5 16.3 - - + +
284C LEU* 4.9 4.2 - - - +
331C LYS 3.2 5.8 - - - -
332C ARG* 3.1 53.2 + - - +
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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