Contacts of the helix formed by residues 214 - 234 (chain F) in PDB entry 7KHI
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 PRO 214 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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152F GLU* 5.5 0.2 - - - +
158F LEU* 3.9 28.3 - - + -
213F ASP* 1.3 85.3 - - + +
215F GLU* 1.3 78.5 + - - +
217F ALA* 3.3 7.7 + - + +
218F ARG* 2.9 51.8 + - - +
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Residues in contact with GLU 215 (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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213F ASP* 3.9 11.2 - - + +
214F PRO* 1.3 94.8 - - - +
216F LEU* 1.3 64.2 + - - +
218F ARG* 3.3 23.0 + - - +
219F GLU* 3.0 27.7 + - - +
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Residues in contact with LEU 216 (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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165F PHE* 6.3 1.1 - - + -
167F ASP 5.1 9.4 - - - +
213F ASP* 3.1 23.0 + - + +
215F GLU* 1.3 77.9 - - - +
217F ALA* 1.3 62.2 + - - +
219F GLU* 2.9 34.0 - - - +
220F LYS* 2.9 59.3 + - + +
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Residues in contact with ALA 217 (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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148F TYR* 3.0 19.5 + - + +
152F GLU* 5.7 0.4 - - - +
158F LEU* 6.6 0.4 - - + -
162F ILE* 5.9 0.7 - - + -
165F PHE* 3.4 29.2 - - + -
213F ASP 3.2 9.2 + - - +
214F PRO* 3.3 11.0 + - + +
216F LEU* 1.3 79.2 - - - +
218F ARG* 1.3 63.2 + - - +
220F LYS* 3.3 13.3 + - - +
221F PHE* 2.9 24.6 + - - -
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Residues in contact with ARG 218 (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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148F TYR* 2.9 15.1 + - + +
152F GLU* 3.1 34.6 + - - +
158F LEU* 4.6 6.9 - - - +
214F PRO* 2.9 38.2 + - - +
215F GLU* 3.3 39.0 + - - +
217F ALA* 1.3 75.7 - - - +
219F GLU* 1.3 58.2 + - - +
221F PHE* 3.3 2.1 + - - +
222F ALA* 2.9 27.5 + - - +
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Residues in contact with GLU 219 (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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215F GLU* 3.0 15.9 + - - +
216F LEU* 2.9 50.3 - - + +
218F ARG* 1.3 77.0 - - - +
220F LYS* 1.3 64.3 + - + +
222F ALA* 3.1 9.1 + - - +
223F GLU* 3.0 27.1 + - - +
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Residues in contact with LYS 220 (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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165F PHE* 3.2 50.8 - - - +
167F ASP 5.3 3.1 + - - +
216F LEU* 2.9 59.4 + - + +
217F ALA* 3.4 14.5 - - - +
219F GLU* 1.3 77.4 - - + +
221F PHE* 1.3 58.8 + - + +
223F GLU* 3.0 25.3 - - - +
224F LEU* 2.9 27.2 + - - +
255F VAL* 6.6 0.2 - - + -
258F GLN* 3.6 22.9 - - - +
259F PHE* 4.4 18.9 - - + -
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Residues in contact with PHE 221 (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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144F LEU* 3.6 42.4 - - + -
145F LEU* 3.4 29.4 - - + +
148F TYR* 3.3 55.9 - + + -
162F ILE* 4.9 3.6 - - + -
165F PHE* 4.0 22.9 - + - -
217F ALA* 2.9 25.2 + - - +
218F ARG 3.9 1.6 - - - +
220F LYS* 1.3 77.7 - - + +
222F ALA* 1.3 58.6 + - - +
224F LEU* 3.5 7.7 - - + +
225F ARG* 2.9 29.3 + - - +
259F PHE* 3.9 23.1 - + - -
261F LEU* 6.0 0.7 - - + -
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Residues in contact with ALA 222 (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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218F ARG 2.9 14.1 + - - +
219F GLU* 3.4 12.6 - - - +
221F PHE* 1.3 75.5 - - - +
223F GLU* 1.3 63.0 + - - +
225F ARG* 3.2 9.3 + - - +
226F ALA* 3.0 21.4 + - - +
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Residues in contact with GLU 223 (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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219F GLU* 3.0 13.4 + - - +
220F LYS* 3.0 45.2 - - - +
222F ALA* 1.3 75.5 - - - +
224F LEU* 1.3 57.6 + - - +
226F ALA* 3.4 8.1 + - - +
227F GLN* 2.9 30.8 + - - +
255F VAL* 5.0 15.5 - - + +
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Residues in contact with LEU 224 (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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141F ILE* 3.6 20.2 - - + -
144F LEU* 4.5 1.3 - - + -
145F LEU* 3.5 28.7 - - + -
220F LYS 2.9 18.5 + - - +
221F PHE* 3.5 15.0 - - + +
223F GLU* 1.3 75.3 - - - +
225F ARG* 1.3 63.4 + - - +
227F GLN* 3.3 5.0 + - - +
228F TYR* 2.8 40.0 + - + +
252F LEU* 4.3 11.3 - - + +
255F VAL* 5.7 9.0 - - + -
256F PHE* 4.7 8.5 - - + -
259F PHE* 3.2 39.5 - - + -
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Residues in contact with ARG 225 (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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145F LEU* 3.7 33.5 - - - +
149F ASP* 2.8 40.0 + - - -
221F PHE 2.9 13.6 + - - +
222F ALA* 3.2 10.3 + - - +
224F LEU* 1.3 79.3 - - - +
226F ALA* 1.3 63.4 + - - +
228F TYR* 3.7 5.6 - - - +
229F VAL* 2.9 43.9 + - + +
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Residues in contact with ALA 226 (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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222F ALA 3.0 12.5 + - - +
223F GLU* 3.6 11.2 - - - +
224F LEU 3.2 0.2 - - - -
225F ARG* 1.3 77.3 - - - +
227F GLN* 1.3 63.2 + - - +
229F VAL* 3.9 3.3 - - - +
230F VAL* 3.0 33.7 + - + +
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Residues in contact with GLN 227 (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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223F GLU 2.9 20.5 + - - +
224F LEU* 3.9 3.8 - - - +
226F ALA* 1.3 72.6 - - - +
228F TYR* 1.3 55.6 + - - +
230F VAL* 2.9 21.5 - - - +
231F THR* 2.6 40.9 + - - +
248F GLU* 4.1 13.9 + - - +
251F LYS* 3.0 40.4 + - - +
252F LEU* 3.7 26.0 - - + -
255F VAL* 5.5 5.6 - - + -
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Residues in contact with TYR 228 (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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138F PRO* 3.1 29.0 + - + +
141F ILE* 3.7 44.6 - - + -
142F THR* 4.5 13.0 + - - -
145F LEU* 5.8 0.7 - - + -
224F LEU* 2.8 26.7 + - + +
225F ARG* 3.7 8.3 - - - +
227F GLN* 1.3 74.2 - - - +
229F VAL* 1.3 69.3 + - + +
231F THR* 3.3 3.1 + - - -
232F ARG* 2.9 61.9 + - + +
252F LEU* 3.2 21.0 - - + +
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Residues in contact with VAL 229 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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225F ARG* 2.9 36.9 + - + +
226F ALA* 4.0 3.4 - - - +
228F TYR* 1.3 84.5 - - + +
230F VAL* 1.3 60.4 + - + +
232F ARG* 3.3 20.9 + - - +
233F ASP* 2.9 48.9 + - - +
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Residues in contact with VAL 230 (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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226F ALA* 3.0 21.5 + - + +
227F GLN* 2.9 39.7 - - - +
229F VAL* 1.3 80.6 - - + +
231F THR* 1.3 57.2 + - - +
233F ASP* 3.4 7.1 + - - +
234F THR* 2.6 39.4 + - - +
248F GLU* 4.7 2.2 - - - +
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Residues in contact with THR 231 (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* 2.6 41.9 + - - +
228F TYR* 3.8 4.9 - - - -
230F VAL* 1.3 75.5 - - - +
232F ARG* 1.3 63.0 + - - +
234F THR 3.8 3.1 - - - -
235F ILE* 3.5 15.2 + - - -
245F ALA* 3.8 6.0 - - - +
248F GLU* 3.3 36.1 + - + +
249F ILE* 3.5 33.9 - - + +
252F LEU* 4.5 4.1 - - + +
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Residues in contact with ARG 232 (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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138F PRO* 6.6 0.2 - - + -
228F TYR* 2.9 48.5 + - + +
229F VAL* 3.8 22.9 + - - +
230F VAL 3.2 0.2 - - - -
231F THR* 1.3 76.8 - - - +
233F ASP* 1.3 67.2 + - - +
235F ILE* 3.2 27.5 + - + +
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Residues in contact with ASP 233 (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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229F VAL* 2.9 37.4 + - - +
230F VAL* 3.7 6.4 - - - +
232F ARG* 1.3 81.0 + - - +
234F THR* 1.3 57.1 + - - +
235F ILE* 3.0 13.2 + - - +
236F LYS* 4.3 2.3 + - - +
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Residues in contact with THR 234 (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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230F VAL* 2.6 23.9 + - - +
231F THR 3.8 3.6 - - - -
232F ARG 3.4 0.2 - - - -
233F ASP* 1.3 73.0 - - - +
235F ILE* 1.3 65.5 + - - +
236F LYS* 3.1 10.0 + - - -
244F THR* 3.6 13.9 + - - +
245F ALA* 3.3 8.5 - - - +
248F GLU* 3.3 33.2 + - - +
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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