Contacts of the helix formed by residues 219 - 234 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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217H GLY 3.6 2.2 + - - -
218H ILE* 1.3 76.1 - - - +
220H MET* 1.3 59.4 + - - +
221H GLU 3.4 4.5 + - - -
222H ILE* 3.2 33.0 + - + +
223H SER* 2.9 27.4 + - - -
370H SER* 3.9 4.4 - - - -
371H GLU* 2.9 35.7 + - - +
372H GLU* 3.3 10.4 - - - +
405H LYS* 3.0 25.4 + - - -
419H HIS* 3.6 31.1 + - + +
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Residues in contact with MET 220 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211H GLY 4.5 2.0 - - - +
212H HIS* 3.6 48.7 - - + -
218H ILE 3.4 5.5 + - - +
219H ASP* 1.3 66.8 - - - +
221H GLU* 1.3 58.1 + - - +
223H SER* 3.0 4.0 + - - -
224H LYS* 2.7 55.8 + - + +
372H GLU* 3.1 37.9 + - + +
2035H SO4 3.6 17.0 - - - +
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Residues in contact with GLU 221 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219H ASP* 3.4 10.1 + - - +
220H MET* 1.3 77.5 - - - +
222H ILE* 1.3 58.2 + - - +
224H LYS* 3.4 5.7 + - - +
225H ASN* 3.0 41.7 + - - +
371H GLU* 4.1 2.6 - - - +
372H GLU* 4.9 1.6 + - - -
385H LYS* 2.5 39.4 + - - +
403H MET* 3.9 21.4 - - + +
405H LYS* 2.6 31.7 + - + +
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Residues in contact with ILE 222 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218H ILE* 4.4 7.9 - - + -
219H ASP* 3.2 24.6 + - + +
220H MET 3.2 0.4 - - - -
221H GLU* 1.3 76.2 - - - +
223H SER* 1.3 54.3 + - - +
225H ASN* 3.4 5.3 + - - +
226H PHE* 2.8 35.0 + - - +
364H VAL* 3.8 28.7 - - + -
366H TRP* 5.7 1.1 - - + -
403H MET* 4.2 20.6 - - + -
405H LYS* 4.5 7.4 - - + -
419H HIS* 3.6 41.5 - - + +
420H ILE 5.1 0.9 - - - +
421H LEU* 4.1 24.9 - - + +
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Residues in contact with SER 223 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212H HIS* 3.4 11.2 - - - +
213H VAL* 2.6 42.1 + - - +
218H ILE* 4.1 16.6 - - - -
219H ASP 2.9 13.6 + - - -
220H MET* 3.3 13.2 - - - -
222H ILE* 1.3 72.2 - - - +
224H LYS* 1.3 62.2 + - - +
226H PHE* 3.2 6.5 + - - +
227H GLN* 2.8 31.1 + - - +
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Residues in contact with LYS 224 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211H GLY 3.8 22.7 + - - -
212H HIS* 4.7 4.0 - - - -
220H MET* 2.7 37.4 + - + +
221H GLU* 3.7 7.0 - - - +
223H SER* 1.3 73.5 - - - +
225H ASN* 1.3 63.2 + - - +
227H GLN* 3.0 33.7 + - - +
228H ARG* 3.1 51.2 + - - +
239H LEU* 4.2 3.2 - - - +
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Residues in contact with ASN 225 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221H GLU* 3.0 26.6 + - - +
222H ILE 3.8 4.0 - - - +
224H LYS* 1.3 76.8 - - - +
226H PHE* 1.3 61.8 + - - +
228H ARG* 3.4 24.7 + - - +
229H ILE* 3.2 29.1 + - + +
403H MET* 3.1 35.2 - - - +
421H LEU* 3.8 15.0 - - + +
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Residues in contact with PHE 226 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191H VAL* 3.9 17.5 - - + -
213H VAL* 3.7 24.7 - - + -
214H GLY* 5.5 0.4 - - - -
218H ILE* 5.1 3.8 - - + -
222H ILE* 2.8 20.1 + - + +
223H SER* 3.4 7.0 - - - +
224H LYS 3.2 0.2 - - - -
225H ASN* 1.3 74.5 - - - +
227H GLN* 1.3 64.6 + - - +
229H ILE* 3.2 4.5 + - - +
230H LEU* 3.0 59.0 + - + +
358H ILE* 3.9 17.5 - - + -
360H THR* 3.3 27.8 - - - -
362H PRO* 3.7 12.1 - - + -
364H VAL* 3.3 28.0 - - + -
421H LEU* 3.6 18.1 - - + +
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Residues in contact with GLN 227 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212H HIS* 5.0 0.9 - - - -
213H VAL* 4.1 18.2 - - + +
223H SER 2.8 13.4 + - - +
224H LYS* 3.0 37.8 + - - +
226H PHE* 1.3 77.2 - - - +
228H ARG* 1.3 63.0 + - - +
230H LEU* 3.3 6.8 + - - +
231H GLN* 2.8 54.0 + - - +
237H PHE* 3.9 19.2 + - + +
239H LEU* 3.3 26.2 - - - +
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Residues in contact with ARG 228 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224H LYS* 3.1 42.8 + - - +
225H ASN* 3.5 27.7 + - - +
226H PHE 3.2 0.2 - - - -
227H GLN* 1.3 77.4 - - + +
229H ILE* 1.3 64.3 + - + +
231H GLN* 3.3 14.6 + - - +
232H LYS* 3.2 23.2 + - - +
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Residues in contact with ILE 229 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225H ASN* 3.4 15.0 - - + +
226H PHE* 3.2 7.6 + - - +
228H ARG* 1.3 76.3 - - + +
230H LEU* 1.3 62.5 + - - +
232H LYS* 3.3 19.7 + - + +
233H GLN* 3.1 22.9 + - - +
362H PRO* 3.6 26.2 - - + -
401H ASP* 3.3 44.6 - - + +
402H GLY* 4.2 6.5 - - - +
421H LEU* 3.9 21.3 - - + -
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Residues in contact with LEU 230 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191H VAL* 3.5 31.0 - - + -
195H SER* 4.9 7.0 - - - +
213H VAL* 5.1 0.9 - - + -
226H PHE* 3.0 51.3 + - + +
227H GLN* 3.7 4.5 - - - +
229H ILE* 1.3 73.6 - - - +
231H GLN* 1.3 66.7 + - - +
233H GLN* 3.0 32.6 + - - +
234H GLY 3.1 0.5 + - - -
235H PHE* 2.9 34.5 + - + +
237H PHE* 3.9 24.7 - - + -
360H THR* 4.9 7.6 - - + -
361H HIS 5.0 0.7 - - - +
362H PRO* 4.9 4.5 - - + -
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Residues in contact with GLN 231 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227H GLN* 2.8 49.2 + - - +
228H ARG* 3.6 13.7 + - - +
230H LEU* 1.3 75.7 - - - +
232H LYS* 1.3 56.1 + - - +
234H GLY* 2.8 26.2 + - - -
235H PHE 3.0 18.8 - - - +
236H LYS* 4.7 2.4 - - - +
237H PHE* 3.8 22.8 + - + +
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Residues in contact with LYS 232 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228H ARG 3.2 13.9 + - - +
229H ILE* 3.3 37.0 - - + +
231H GLN* 1.3 78.3 - - - +
233H GLN* 1.3 73.3 + - - +
234H GLY* 3.1 1.5 + - - -
401H ASP* 3.6 16.0 + - - -
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Residues in contact with GLN 233 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64H HIS* 5.4 16.0 - - + -
195H SER* 4.3 10.6 + - - -
198H GLN* 3.1 27.2 + - - +
199H ARG* 5.2 4.0 + - - +
229H ILE* 3.1 21.2 + - - +
230H LEU* 3.0 24.4 + - - +
232H LYS* 1.3 94.1 - - - +
234H GLY* 1.3 55.9 + - - +
235H PHE* 3.7 1.6 - - + +
361H HIS* 2.8 29.7 + - - +
362H PRO* 3.3 17.0 - - - +
401H ASP* 4.5 1.6 + - - -
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Residues in contact with GLY 234 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198H GLN* 4.0 15.1 - - - +
204H VAL 4.1 1.4 + - - +
231H GLN 2.8 12.2 + - - -
232H LYS 3.1 1.6 - - - -
233H GLN* 1.3 80.6 - - - +
235H PHE* 1.3 62.8 + - - +
236H LYS* 3.3 25.2 + - - +
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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