Contacts of the helix formed by residues 219 - 234 (chain F) in PDB entry 1ZMC
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 ASP 219 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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217F GLY 3.4 2.0 + - - -
218F ILE* 1.3 74.5 - - - +
220F MET* 1.3 61.1 + - - +
221F GLU 3.1 16.3 + - - -
222F ILE* 3.1 16.0 + - + +
223F SER* 2.7 30.7 + - - -
370F SER* 3.8 6.9 - - - -
371F GLU* 3.1 36.5 + - - +
372F GLU* 3.4 10.8 - - - +
405F LYS* 2.7 30.7 + - - -
419F HIS* 3.8 24.4 + - + +
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Residues in contact with MET 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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211F GLY 4.5 4.7 - - - +
212F HIS* 3.8 44.9 - - + +
218F ILE 3.5 5.0 + - - +
219F ASP* 1.3 71.6 - - - +
221F GLU* 1.3 58.9 + - - +
223F SER* 3.6 1.5 - - - -
224F LYS* 2.8 59.0 + - + +
372F GLU* 3.2 36.8 + - + +
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Residues in contact with GLU 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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219F ASP* 3.1 10.2 + - - +
220F MET* 1.3 79.1 - - - +
222F ILE* 1.3 62.8 + - - +
224F LYS* 4.1 4.0 - - - +
225F ASN* 3.2 37.3 + - - +
371F GLU* 3.8 4.4 - - - +
372F GLU* 5.1 0.6 + - - -
385F LYS* 2.7 32.6 + - - +
403F MET* 3.9 14.5 - - + +
405F LYS* 2.7 33.7 + - - +
375G LYS* 6.3 3.4 - - + -
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Residues in contact with ILE 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 ILE* 4.6 6.5 - - + -
219F ASP* 3.1 25.2 + - + +
221F GLU* 1.3 75.3 - - - +
223F SER* 1.3 58.4 + - - +
225F ASN* 3.3 5.6 + - - +
226F PHE* 3.0 27.4 + - - +
364F VAL* 3.6 30.7 - - + -
366F TRP* 5.6 1.3 - - + -
403F MET* 3.7 26.9 - - + +
405F LYS* 4.4 5.2 - - + -
419F HIS* 3.7 39.7 - - + +
420F ILE 4.6 1.1 - - - +
421F LEU* 4.0 23.0 - - + +
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Residues in contact with SER 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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212F HIS* 3.5 11.6 - - - +
213F VAL* 2.6 38.9 + - - +
218F ILE* 3.9 21.7 - - - +
219F ASP 2.7 21.1 + - - -
220F MET* 3.6 8.5 - - - -
222F ILE* 1.3 71.3 - - - +
224F LYS* 1.3 65.8 + - - +
226F PHE* 3.4 5.8 + - - +
227F GLN* 3.1 24.3 + - - +
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Residues in contact with LYS 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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211F GLY 4.7 8.8 + - - +
212F HIS* 5.4 2.0 - - + -
220F MET* 2.8 47.3 + - + +
221F GLU* 4.1 4.0 - - - +
223F SER* 1.3 75.1 - - - +
225F ASN* 1.3 66.7 + - - +
227F GLN* 3.3 32.5 + - - +
228F ARG* 3.1 35.4 + - - +
239F LEU* 4.8 6.3 - - - +
376G GLU* 3.6 33.6 + - - -
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Residues in contact with ASN 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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221F GLU* 3.2 30.5 + - - +
222F ILE* 3.8 0.6 - - - +
224F LYS* 1.3 76.4 - - - +
226F PHE* 1.3 64.3 + - - +
228F ARG* 2.8 35.0 + - - +
229F ILE* 3.2 28.8 + - + +
403F MET* 3.8 25.3 - - - +
421F LEU* 3.8 17.2 - - + +
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Residues in contact with PHE 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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191F VAL* 3.7 18.4 - - + -
213F VAL* 4.4 15.3 - - + -
218F ILE* 5.1 7.4 - - + -
222F ILE* 3.0 19.0 + - + +
223F SER* 3.6 6.5 - - - +
225F ASN* 1.3 73.3 - - - +
227F GLN* 1.3 61.9 + - - +
229F ILE* 3.1 4.2 + - - +
230F LEU* 2.8 66.8 + - + +
358F ILE* 4.0 22.0 - - + -
360F THR* 3.1 29.6 - - + -
362F PRO* 3.7 10.1 - - + -
364F VAL* 3.5 25.6 - - + -
421F LEU* 3.9 18.8 - - + +
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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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212F HIS* 5.0 0.5 - - - -
213F VAL* 3.7 25.2 + - + +
223F SER 3.1 13.7 + - - +
224F LYS* 3.4 34.4 + - - +
226F PHE* 1.3 78.8 - - - +
228F ARG* 1.3 58.6 + - - +
230F LEU* 3.2 11.3 + - - +
231F GLN* 2.8 58.0 + - - +
237F PHE* 3.9 11.1 + - + +
239F LEU* 3.4 31.0 - - - +
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Residues in contact with ARG 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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224F LYS* 3.1 21.8 + - - +
225F ASN* 2.8 45.0 + - - +
226F PHE 3.2 0.4 - - - -
227F GLN* 1.3 77.5 - - + +
229F ILE* 1.3 62.2 + - + +
231F GLN* 3.2 17.2 + - - +
232F LYS* 2.9 37.0 + - + +
376G GLU* 5.7 4.7 - - - -
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Residues in contact with ILE 229 (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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225F ASN* 3.2 17.9 + - + +
226F PHE* 3.1 6.4 + - - +
228F ARG* 1.3 76.7 - - + +
230F LEU* 1.3 63.3 + - + +
232F LYS* 3.2 24.5 + - - +
233F GLN* 3.1 27.7 + - - +
362F PRO* 3.7 24.0 - - + -
401F ASP* 3.6 42.6 - - + +
402F GLY* 4.2 6.7 - - - +
421F LEU* 4.0 21.3 - - + -
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Residues in contact with LEU 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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191F VAL* 3.9 13.0 - - + -
195F SER* 4.6 7.6 - - - +
213F VAL* 4.8 1.3 - - + -
226F PHE* 2.8 65.4 + - + +
227F GLN* 3.5 6.1 - - - +
228F ARG 3.2 0.2 - - - -
229F ILE* 1.3 77.5 - - - +
231F GLN* 1.3 56.6 + - - +
233F GLN* 3.0 40.3 + - - +
235F PHE* 3.1 33.2 + - + +
237F PHE* 3.9 26.0 - - + -
360F THR* 4.8 7.4 - - + -
361F HIS 5.2 1.6 - - - +
362F PRO* 5.4 1.8 - - + -
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Residues in contact with GLN 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* 2.8 48.2 + - - +
228F ARG* 3.6 17.4 - - - +
230F LEU* 1.3 73.9 - - - +
232F LYS* 1.3 65.1 + - - +
234F GLY* 3.0 14.0 + - - -
235F PHE 3.2 19.5 - - - +
236F LYS* 4.8 4.2 - - + +
237F PHE* 3.9 19.3 + - + +
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Residues in contact with LYS 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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228F ARG* 2.9 20.8 + - + +
229F ILE* 3.2 32.4 + - - +
231F GLN* 1.3 76.5 - - + +
233F GLN* 1.3 61.3 + - - +
234F GLY 3.5 0.5 + - - -
401F ASP* 4.5 10.3 + - - -
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Residues in contact with GLN 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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64F HIS* 5.3 15.0 - - + -
195F SER* 4.2 10.0 + - - -
198F GLN* 3.0 29.3 + - - +
199F ARG* 5.2 4.3 + - - +
229F ILE* 3.1 21.9 + - - +
230F LEU* 3.0 27.3 + - - +
232F LYS* 1.3 79.3 - - + +
234F GLY* 1.3 56.2 + - - +
235F PHE* 3.6 2.1 - - + +
361F HIS* 3.0 27.6 + - - +
362F PRO* 3.6 14.5 - - - +
401F ASP* 4.7 3.0 + - - -
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Residues in contact with GLY 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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198F GLN* 4.1 14.7 - - - +
203F ASP* 5.8 0.2 - - - -
204F VAL 4.0 2.1 + - - +
231F GLN 3.0 11.9 + - - -
232F LYS 3.3 1.0 - - - -
233F GLN* 1.3 79.0 - - - +
235F PHE* 1.3 64.3 + - - +
236F LYS* 3.4 24.6 + - - +
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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