Contacts of the helix formed by residues 215 - 225 (chain F) in PDB entry 3KQG
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 215 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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214F LYS* 1.3 76.1 - - - +
216F TRP* 1.3 66.8 + - - +
217F TYR* 3.9 3.8 + - - +
218F SER* 3.2 26.0 + - - -
219F ALA* 2.8 21.1 + - - +
252F TRP* 3.5 0.2 - - - -
311F CYS 3.5 7.4 - - - -
312F ASP* 3.4 31.9 - - + +
313F LYS 3.3 8.3 - - - -
314F THR* 3.9 11.9 - - + +
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Residues in contact with TRP 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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215F THR* 1.3 71.4 - - - +
217F TYR* 1.3 80.6 + + + +
219F ALA* 3.2 4.0 + - - +
220F GLU* 3.0 31.3 + - + -
230F LEU* 3.5 16.1 - - + +
252F TRP* 3.1 33.4 - + + +
253F ILE 2.9 25.9 + - - -
254F GLY 4.1 5.4 - - - -
255F LEU 3.1 12.0 + - - -
256F THR* 3.6 33.4 - - + -
267F VAL* 3.8 31.6 - - + -
295F CYS* 3.4 34.5 - - + -
311F CYS* 3.0 20.1 + - + +
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Residues in contact with TYR 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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215F THR* 3.2 4.2 + - - +
216F TRP* 1.3 98.9 - + + +
218F SER* 1.3 63.9 + - - +
220F GLU* 3.2 10.5 + - + -
221F GLN* 2.9 66.8 + - + +
311F CYS* 4.6 2.5 + - + +
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Residues in contact with SER 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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214F LYS* 3.7 22.3 - - - +
215F THR* 3.2 23.5 + - - +
217F TYR* 1.3 81.5 - - - +
219F ALA* 1.3 60.5 + - - +
221F GLN* 3.5 14.5 + - - +
222F PHE* 3.1 21.5 + - - +
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Residues in contact with ALA 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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214F LYS* 3.9 10.1 - - + +
215F THR 2.8 14.6 + - - +
216F TRP* 3.3 11.9 - - - +
218F SER* 1.3 74.5 - - - +
220F GLU* 1.3 60.3 + - - +
222F PHE* 3.0 7.1 + - - +
223F CYS* 2.9 29.6 + - - -
230F LEU* 4.0 8.7 - - + -
252F TRP* 4.5 2.7 - - + -
317F PHE* 3.5 37.6 - - + -
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Residues in contact with GLU 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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216F TRP* 3.0 25.6 + - + +
217F TYR* 3.2 16.8 + - + +
219F ALA* 1.3 74.5 - - - +
221F GLN* 1.3 57.9 + - - +
223F CYS* 3.2 1.1 + - - -
224F VAL* 2.9 36.5 + - + +
229F HIS* 2.7 32.5 + - - -
230F LEU* 3.0 40.0 + - + +
267F VAL* 3.4 26.7 - - + +
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Residues in contact with GLN 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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217F TYR* 2.9 58.4 + - + +
218F SER* 3.7 12.5 + - - +
220F GLU* 1.3 76.3 - - - +
222F PHE* 1.3 63.2 + - - +
224F VAL* 3.4 7.9 + - - +
225F SER* 3.0 24.4 + - - -
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Residues in contact with PHE 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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247D GLY* 4.6 15.5 - - - -
248D GLY* 5.1 1.3 - - - -
301D PRO* 6.1 4.0 - - + -
199F TRP* 6.3 0.4 - + - -
208F TYR* 3.7 36.6 - + - -
210F SER* 5.6 0.7 - - - -
212F ILE* 5.0 0.7 - - + -
214F LYS* 3.6 24.0 - - - -
218F SER 3.1 13.9 + - - +
219F ALA* 3.0 9.8 + - - +
221F GLN* 1.3 76.9 - - - +
223F CYS* 1.3 62.1 + - - +
225F SER* 2.7 24.9 + - - -
226F ARG* 3.1 60.8 - - + +
317F PHE* 3.2 26.9 - + + -
319F CYS* 4.0 5.2 - - - -
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Residues in contact with CYS 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 ALA 2.9 10.3 + - - -
220F GLU* 3.2 8.5 + - - +
222F PHE* 1.3 76.6 - - - +
224F VAL* 1.3 57.5 + - - +
226F ARG* 3.0 12.5 + - - -
228F SER* 2.6 35.8 + - - +
229F HIS* 3.8 15.0 - - - -
230F LEU* 3.5 28.5 - - - +
317F PHE* 4.0 1.8 - - - -
319F CYS* 2.0 52.9 - - - -
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Residues in contact with VAL 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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220F GLU* 2.9 41.4 + - + +
221F GLN* 3.7 7.9 - - - +
222F PHE 3.2 0.2 - - - -
223F CYS* 1.3 71.8 - - - +
225F SER* 1.3 59.9 + - - +
226F ARG 2.9 4.7 - - - -
227F ASN* 2.9 20.4 + - - -
228F SER 3.6 12.3 - - - +
229F HIS* 4.1 10.1 - - + -
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Residues in contact with SER 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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244D LYS* 3.5 18.7 + - - -
221F GLN 3.0 14.5 + - - -
222F PHE* 2.7 18.2 + - - -
224F VAL* 1.3 76.3 - - - +
226F ARG* 1.3 73.3 + - - +
227F ASN 3.5 0.9 - - - -
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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