Contacts of the helix formed by residues 245 - 251 (chain C) in PDB entry 3KYS
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 ARG 245 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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243C ASP* 2.7 34.9 + - - +
244C ILE* 1.3 73.6 - - - +
246C GLN* 1.3 62.9 + - + +
247C ILE 3.0 6.0 + - - -
248C TYR* 3.7 24.4 + - + +
249C ASP* 5.0 1.9 + - - -
410C LYS* 3.6 35.2 - - + +
411C ASP* 4.3 29.0 + - - -
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Residues in contact with GLN 246 (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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243C ASP* 2.9 31.9 + - + +
245C ARG* 1.3 79.0 - - - +
247C ILE* 1.3 60.4 + - + +
249C ASP* 4.2 4.9 - - - +
89D ARG* 3.2 39.9 + - - +
90D LYS* 3.3 60.7 + - - +
91D LEU* 4.4 17.5 - - + -
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Residues in contact with ILE 247 (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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242C VAL* 4.5 12.6 - - + -
244C ILE* 2.8 12.7 + - + +
246C GLN* 1.3 87.6 - - + +
248C TYR* 1.3 67.4 + - - +
249C ASP* 3.1 4.9 - - - -
250C LYS* 2.8 26.0 + - + +
251C PHE* 3.7 27.7 - - + -
258C LEU* 3.8 11.7 - - + -
272C LEU* 4.2 32.8 - - + -
389C ALA* 4.8 3.1 - - + -
391C VAL* 5.2 1.8 - - + -
408C LEU* 5.2 4.0 - - + -
86D MET* 3.8 33.4 - - + -
91D LEU* 4.8 4.3 - - + -
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Residues in contact with TYR 248 (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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244C ILE* 3.0 33.0 + - + +
245C ARG* 3.7 29.3 + - + +
247C ILE* 1.3 75.1 - - - +
249C ASP* 1.3 61.8 - - - +
250C LYS 3.2 0.5 + - - -
251C PHE 3.2 12.5 + - - +
253C GLU* 2.9 40.3 - - + +
258C LEU* 3.8 10.1 - - + -
259C LYS* 3.4 49.1 + - + +
262C PHE* 3.6 17.7 - - - +
410C LYS* 3.0 38.2 + - - -
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Residues in contact with ASP 249 (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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245C ARG 5.0 2.1 + - - -
246C GLN 4.2 4.9 - - - +
247C ILE 2.9 5.0 + - - +
248C TYR* 1.3 78.4 - - - +
250C LYS* 1.3 92.8 + - - +
251C PHE 3.3 3.3 + - - +
253C GLU* 5.5 0.9 - - - -
314C PHE 4.7 2.4 - - - +
315C GLY* 3.8 10.9 + - - -
83D THR* 3.5 10.0 + - - +
84D VAL* 5.7 1.2 - - - +
89D ARG* 2.4 33.4 + - - -
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Residues in contact with LYS 250 (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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247C ILE* 2.8 16.3 + - + +
249C ASP* 1.3 100.1 + - - +
251C PHE* 1.3 64.9 + - + +
314C PHE 5.4 0.2 - - - -
315C GLY* 3.3 17.8 + - - +
367C LEU 5.6 0.2 - - - -
368C GLU* 2.2 40.9 + - - -
369C ASN* 4.3 6.9 - - - +
370C PHE 5.0 1.1 - - - -
371C THR* 2.9 46.9 + - + +
391C VAL* 4.5 6.5 - - + -
83D THR* 5.1 6.0 - - + +
86D MET* 3.4 41.1 - - + +
89D ARG* 4.3 7.6 - - - +
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Residues in contact with PHE 251 (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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247C ILE* 3.7 33.0 - - + -
248C TYR 3.2 14.3 + - - +
249C ASP 3.3 3.2 - - - +
250C LYS* 1.3 84.2 - - + +
252C PRO* 1.4 75.4 - - + +
253C GLU* 3.1 5.2 + - - +
258C LEU* 3.8 28.3 - - + -
272C LEU* 5.1 0.2 - - + -
312C CYS* 4.8 1.1 - - - -
315C GLY 3.1 8.5 - - - +
371C THR* 3.5 34.1 - - + -
372C ILE 3.4 23.6 - - - -
373C LEU* 3.6 24.2 - - + -
389C ALA* 3.5 21.5 - - + -
390C CYS 3.6 9.9 - - - -
391C VAL* 4.9 6.1 - - + -
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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