Contacts of the helix formed by residues 219 - 232 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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217A GLY 3.5 1.8 + - - -
218A ILE* 1.3 76.3 - - - +
220A MET* 1.3 61.3 + - - +
221A GLU* 3.2 15.7 + - - +
222A ILE* 3.2 15.7 + - + +
223A SER* 2.9 26.9 + - - -
366A TRP* 5.1 0.6 - - - -
370A SER* 3.8 4.0 - - - -
371A GLU* 2.8 36.8 + - - +
372A GLU* 3.4 8.2 - - - +
405A LYS* 2.6 32.0 + - - -
419A HIS* 3.7 29.3 + - + +
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Residues in contact with MET 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212A HIS* 3.5 52.0 - - + +
217A GLY 6.3 0.4 - - - +
218A ILE* 3.4 26.1 + - + +
219A ASP* 1.3 71.5 - - - +
221A GLU* 1.3 63.9 + - - +
223A SER* 3.1 2.8 + - - -
224A LYS* 3.0 32.9 + - + +
372A GLU* 3.0 42.2 + - + +
2003A SO4 3.9 9.6 - - - +
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Residues in contact with GLU 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219A ASP* 3.2 3.0 + - - -
220A MET* 1.3 78.5 - - - +
222A ILE* 1.3 64.3 + - - +
224A LYS* 3.2 4.1 + - - +
225A ASN* 3.0 39.2 + - - +
371A GLU* 4.2 3.0 - - - +
372A GLU* 4.7 0.8 + - - -
385A LYS* 3.1 37.2 + - - +
403A MET* 3.8 15.5 - - + +
405A LYS* 3.0 29.5 + - + +
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Residues in contact with ILE 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218A ILE* 4.6 7.0 - - + -
219A ASP* 3.2 21.3 + - + +
221A GLU* 1.3 76.1 - - - +
223A SER* 1.3 53.5 + - - +
225A ASN* 3.3 5.9 + - - +
226A PHE* 2.8 37.4 + - + +
364A VAL* 3.8 28.9 - - + -
366A TRP* 5.6 1.8 - - + -
403A MET* 3.8 25.6 - - + -
405A LYS* 4.6 2.5 - - + -
419A HIS* 3.6 41.3 - - + +
420A ILE 4.9 1.3 - - - +
421A LEU* 3.8 25.1 - - + +
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Residues in contact with SER 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212A HIS* 3.3 11.5 - - - +
213A VAL* 2.5 41.4 + - - +
218A ILE* 3.7 21.3 - - - -
219A ASP 2.9 12.8 + - - -
220A MET* 3.5 11.7 - - - -
222A ILE* 1.3 78.2 - - - +
224A LYS* 1.3 56.9 + - - +
226A PHE* 3.4 4.0 + - - +
227A GLN* 2.9 29.1 + - - +
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Residues in contact with LYS 224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211A GLY 4.6 14.3 + - - +
212A HIS* 4.9 6.1 - - + -
220A MET* 3.0 25.4 + - + +
221A GLU* 3.9 4.7 - - - +
223A SER* 1.3 77.7 - - - +
225A ASN* 1.3 66.0 + - - +
227A GLN* 3.2 28.3 + - - +
228A ARG* 2.9 40.8 + - - +
239A LEU* 5.1 1.6 - - - -
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Residues in contact with ASN 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221A GLU* 3.0 40.2 + - - +
222A ILE* 3.8 0.4 - - - +
224A LYS* 1.3 78.5 - - - +
226A PHE* 1.3 58.4 + - - +
228A ARG* 2.9 33.1 + - - +
229A ILE* 3.0 31.5 + - + +
403A MET* 4.0 19.0 - - - +
421A LEU* 3.6 18.5 - - + +
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Residues in contact with PHE 226 (chain A).
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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191A VAL* 3.8 19.1 - - + -
213A VAL* 4.5 13.2 - - + -
214A GLY* 5.4 0.9 - - - -
218A ILE* 4.9 8.1 - - + -
222A ILE* 2.8 20.3 + - + +
223A SER* 3.6 6.3 - - - +
225A ASN* 1.3 75.6 - - - +
227A GLN* 1.3 65.4 - - - +
229A ILE* 3.2 5.0 + - - +
230A LEU* 3.0 58.2 + - + +
358A ILE* 4.0 19.1 - - + -
360A THR* 3.3 28.9 - - + -
362A PRO* 3.9 10.8 - - + -
364A VAL* 3.4 25.8 - - + -
421A LEU* 3.7 19.9 - - + +
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Residues in contact with GLN 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213A VAL* 3.5 23.4 + - + +
223A SER 2.9 16.6 + - - +
224A LYS* 3.5 26.9 - - - +
226A PHE* 1.3 74.6 - - - +
228A ARG* 1.3 65.0 + - - +
230A LEU* 3.0 9.3 + - - +
231A GLN* 2.8 53.8 + - - +
237A PHE* 3.7 17.5 - - + +
239A LEU* 3.3 35.8 - - - +
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Residues in contact with ARG 228 (chain A).
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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224A LYS* 2.9 28.0 + - - +
225A ASN* 2.9 40.4 + - - +
227A GLN* 1.3 77.2 - - - +
229A ILE* 1.3 65.4 + - + +
231A GLN* 3.3 11.0 + - - +
232A LYS* 3.0 26.2 + - + +
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Residues in contact with ILE 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225A ASN* 3.0 19.1 - - + +
226A PHE* 3.2 6.5 + - - +
228A ARG* 1.3 78.5 - - + +
230A LEU* 1.3 60.5 + - + +
232A LYS* 3.4 10.3 + - + +
233A GLN* 3.1 34.0 + - + +
362A PRO* 3.9 29.6 - - + -
401A ASP* 3.1 42.6 - - - +
402A GLY* 4.5 8.1 - - - +
421A LEU* 4.1 18.8 - - + -
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Residues in contact with LEU 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191A VAL* 3.7 17.0 - - + -
195A SER* 4.8 7.9 - - - +
213A VAL* 4.8 0.9 - - + -
226A PHE* 3.0 61.3 + - + +
227A GLN* 3.0 7.2 + - - +
229A ILE* 1.3 74.2 - - - +
231A GLN* 1.3 66.1 + - - +
233A GLN* 3.0 34.3 + - - +
235A PHE* 3.1 34.0 + - + +
237A PHE* 3.8 24.7 - - + -
360A THR* 4.9 6.7 - - - -
361A HIS 5.3 2.5 - - - +
362A PRO* 5.5 2.0 - - + -
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Residues in contact with GLN 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227A GLN* 2.8 48.0 + - - +
228A ARG* 3.8 10.6 - - - +
230A LEU* 1.3 70.7 - - - +
232A LYS* 1.3 59.2 + - - +
233A GLN 2.9 10.0 + - - -
234A GLY* 3.0 14.2 + - - -
235A PHE 3.1 19.5 - - - +
236A LYS* 4.8 1.1 - - - -
237A PHE* 3.6 25.8 + - + +
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Residues in contact with LYS 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228A ARG* 3.0 18.4 + - + +
229A ILE* 3.6 11.7 - - + +
230A LEU 3.2 0.2 - - - -
231A GLN* 1.3 75.7 - - - +
233A GLN* 1.3 60.0 + - + +
2000A SO4 5.4 5.5 + - - -
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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