Contacts of the helix formed by residues 244 - 257 (chain F) 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 THR 244 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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243F ALA* 1.3 79.6 - - - +
245F ALA* 1.3 60.2 + - - +
247F GLU* 2.9 27.5 + - + +
248F GLU* 2.9 25.6 + - + +
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Residues in contact with ALA 245 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231F THR* 3.4 31.0 - - + +
234F THR* 3.5 29.8 - - - +
235F ILE* 3.6 5.8 - - - +
243F ALA 3.2 0.8 - - - +
244F THR* 1.3 78.3 - - - +
246F GLN* 1.3 57.0 + - - +
248F GLU* 3.2 13.0 + - - +
249F ILE* 2.9 30.8 + - - +
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Residues in contact with GLN 246 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235F ILE* 3.5 35.2 + - + +
243F ALA* 3.1 15.8 + - - +
245F ALA* 1.3 78.6 - - - +
247F GLU* 1.3 56.5 + - - +
249F ILE* 3.1 12.4 + - - +
250F LEU* 2.9 42.1 + - + +
353F LEU* 5.2 16.8 - - - +
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Residues in contact with GLU 247 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243F ALA 3.7 1.8 + - - +
244F THR* 2.9 21.3 + - + +
246F GLN* 1.3 78.5 - - - +
248F GLU* 1.3 62.7 + - - +
250F LEU* 3.2 13.4 + - + +
251F LYS* 2.9 52.0 + - - +
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Residues in contact with GLU 248 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227F GLN* 2.5 32.7 + - - +
231F THR* 3.4 28.9 - - + -
244F THR* 2.9 27.0 + - + +
245F ALA* 3.2 7.2 + - - +
247F GLU* 1.3 78.9 - - - +
249F ILE* 1.3 58.6 + - - +
251F LYS* 3.1 16.9 + - - +
252F LEU 2.8 15.8 + - - -
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Residues in contact with ILE 249 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135F ALA 4.8 12.2 - - - +
136F GLU* 5.2 6.5 - - - +
141F ILE* 5.0 4.0 - - + -
227F GLN* 4.4 2.0 - - - +
228F TYR* 3.4 42.2 - - + +
231F THR* 3.0 25.4 - - - +
232F ARG* 4.9 1.6 - - - +
235F ILE* 3.7 16.8 - - + -
245F ALA 2.9 18.3 + - - +
246F GLN* 3.1 18.6 + - - +
248F GLU* 1.3 73.7 - - - +
250F LEU* 1.3 63.5 + - + +
252F LEU* 3.2 6.6 + - + +
253F SER* 2.9 26.2 + - - -
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Residues in contact with LEU 250 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132F CYS* 6.2 0.7 - - - -
136F GLU* 3.0 46.7 - - + +
246F GLN* 2.9 37.3 + - + +
247F GLU* 3.2 21.1 + - + +
249F ILE* 1.3 79.1 - - + +
251F LYS* 1.3 58.0 + - + +
253F SER* 3.1 7.7 + - - -
254F GLU* 3.0 40.3 + - + +
364F ARG* 4.4 11.2 - - - +
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Residues in contact with LYS 251 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227F GLN* 4.5 1.6 - - - +
247F GLU* 2.9 47.9 + - - +
248F GLU* 3.1 23.1 + - - +
250F LEU* 1.3 75.0 - - - +
252F LEU* 1.3 60.4 + - - +
254F GLU* 3.1 27.5 + - - +
255F VAL* 2.9 38.3 + - + +
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Residues in contact with LEU 252 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135F ALA* 5.1 0.4 - - - -
141F ILE* 5.4 6.7 - - + -
223F GLU* 4.4 6.5 - - - +
224F LEU* 3.4 29.4 - - + +
227F GLN* 3.1 43.4 - - + +
228F TYR* 3.4 38.1 - - + -
248F GLU 2.8 7.5 + - - +
249F ILE* 3.2 11.2 + - + +
251F LYS* 1.3 75.8 - - - +
253F SER* 1.3 57.5 + - - +
255F VAL* 3.1 21.2 - - + +
256F PHE* 2.9 32.2 + - + +
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Residues in contact with SER 253 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132F CYS* 2.0 56.1 + - - -
135F ALA* 3.3 12.5 - - - +
136F GLU* 3.0 24.7 + - - +
249F ILE 2.9 13.3 + - - -
250F LEU 3.1 10.5 + - - -
252F LEU* 1.3 77.2 - - - +
254F GLU* 1.3 57.0 + - - +
256F PHE* 3.4 1.7 + - - +
257F LYS 2.9 22.0 + - - -
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Residues in contact with GLU 254 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129F GLN* 4.9 5.2 + - - +
132F CYS* 3.2 24.3 - - - -
166F VAL* 4.2 8.7 - - - +
167F ASP* 4.8 7.6 - - - +
250F LEU* 3.0 21.5 + - - +
251F LYS* 3.1 33.4 + - + +
253F SER* 1.3 78.4 - - - +
255F VAL* 1.3 59.7 + - + +
257F LYS* 2.9 32.4 - - + +
364F ARG* 5.1 11.1 + - - +
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Residues in contact with VAL 255 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167F ASP* 5.8 4.7 - - - +
220F LYS* 4.6 10.7 - - - +
223F GLU* 4.4 9.2 - - - +
224F LEU* 4.4 11.4 - - + -
251F LYS* 2.9 21.6 + - + +
252F LEU* 3.1 39.5 - - + +
254F GLU* 1.3 76.0 - - + +
256F PHE* 1.3 63.0 + - - +
258F GLN* 3.1 40.1 + - - +
259F PHE* 4.5 4.8 - - - -
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Residues in contact with PHE 256 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131F GLN* 3.2 59.0 - - + -
134F VAL* 5.7 0.4 - - + -
135F ALA* 3.5 18.6 - - + -
144F LEU* 3.4 46.9 - - + -
221F PHE* 4.7 2.9 - + - -
224F LEU* 4.2 15.5 - - + -
252F LEU* 2.9 18.1 + - + +
253F SER 3.9 0.7 - - - +
255F VAL* 1.3 73.3 - - - +
257F LYS* 1.3 55.2 + - - +
258F GLN 2.8 5.8 - - - -
259F PHE* 2.5 66.6 + + + +
261F LEU* 4.2 7.2 - - + -
266F PHE* 4.7 2.2 - + - -
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Residues in contact with LYS 257 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125F ASP* 3.0 29.4 + - - +
128F ASN* 2.7 74.4 - - - +
129F GLN* 3.9 22.7 - - - +
131F GLN* 4.3 0.4 - - - -
132F CYS* 3.6 17.7 - - + +
166F VAL* 3.4 27.6 - - + +
167F ASP* 5.2 2.7 - - - +
253F SER 2.9 14.2 + - - +
254F GLU* 2.9 29.6 - - + +
255F VAL 3.2 0.2 - - - -
256F PHE* 1.3 74.8 - - - +
258F GLN* 1.3 49.4 + - - +
259F PHE 3.2 2.6 + - - +
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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