Contacts of the helix formed by residues 219 - 234 (chain C) in PDB entry 1ZMD
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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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217C GLY 3.6 2.4 + - - -
218C ILE* 1.3 76.8 - - - +
220C MET* 1.3 60.1 + - - +
221C GLU* 3.2 2.7 + - - +
222C ILE* 3.2 32.7 + - + +
223C SER* 2.8 27.8 + - - -
370C SER* 3.7 8.1 - - - -
371C GLU* 3.0 30.1 + - - +
372C GLU* 3.5 3.5 - - - +
405C LYS* 2.9 35.9 + - - -
407C LEU* 4.8 0.2 - - - +
419C HIS* 3.6 30.4 + - + +
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Residues in contact with MET 220 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211C GLY 4.8 2.0 - - - +
212C HIS* 3.7 40.6 - - + -
218C ILE 3.5 4.4 + - - +
219C ASP* 1.3 68.2 - - - +
221C GLU* 1.3 65.8 + - - +
223C SER* 3.6 2.1 - - - -
224C LYS* 2.9 64.4 + - + +
372C GLU* 3.0 42.2 + - + +
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Residues in contact with GLU 221 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219C ASP* 3.2 9.3 + - - +
220C MET* 1.3 76.2 - - - +
222C ILE* 1.3 65.2 + - - +
224C LYS* 3.3 6.4 + - - +
225C ASN* 3.0 31.3 + - - +
371C GLU* 4.4 0.7 - - - +
372C GLU* 4.8 1.4 + - - -
385C LYS* 2.6 31.1 + - - +
403C MET* 3.6 23.5 - - + +
405C LYS* 2.8 37.5 + - - +
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Residues in contact with ILE 222 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218C ILE* 4.5 6.1 - - + -
219C ASP* 3.2 25.5 + - + +
221C GLU* 1.3 76.4 - - - +
223C SER* 1.3 56.1 + - - +
225C ASN* 3.2 5.8 + - - +
226C PHE* 2.9 28.8 + - - +
364C VAL* 3.7 31.0 - - + -
365C ALA 6.1 0.2 - - - +
366C TRP* 5.7 1.1 - - + -
403C MET* 3.9 23.8 - - + +
405C LYS* 4.4 6.3 - - + -
419C HIS* 3.7 37.9 - - + +
420C ILE 4.9 1.3 - - - +
421C LEU* 4.0 24.7 - - + +
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Residues in contact with SER 223 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212C HIS* 3.4 12.7 - - - +
213C VAL* 2.6 39.7 + - - +
218C ILE* 4.0 21.1 - - - -
219C ASP 2.8 20.1 + - - -
220C MET* 3.6 9.9 - - - -
222C ILE* 1.3 72.9 - - - +
224C LYS* 1.3 58.0 + - - +
226C PHE* 3.4 4.8 + - - +
227C GLN* 2.9 31.7 + - - +
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Residues in contact with LYS 224 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211C GLY 3.5 19.4 + - - -
212C HIS* 4.5 2.8 - - - +
220C MET* 2.9 49.0 + - + +
221C GLU* 3.5 7.9 - - - +
223C SER* 1.3 80.0 + - - +
225C ASN* 1.3 62.8 + - - +
227C GLN* 3.3 28.8 + - - +
228C ARG* 3.2 48.8 + - - +
239C LEU* 4.2 3.4 - - - +
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Residues in contact with ASN 225 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221C GLU* 3.0 24.6 + - - +
222C ILE* 3.8 0.9 - - - +
224C LYS* 1.3 75.9 - - - +
226C PHE* 1.3 61.9 + - - +
228C ARG* 3.1 30.0 + - - +
229C ILE* 3.1 29.7 + - + +
403C MET* 3.2 31.2 - - - +
421C LEU* 3.3 21.0 - - + +
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Residues in contact with PHE 226 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191C VAL* 3.4 31.0 - - + -
213C VAL* 3.8 23.6 - - + -
214C GLY* 5.0 0.4 - - - -
218C ILE* 4.7 9.6 - - + -
222C ILE* 2.9 18.3 + - + +
223C SER* 3.5 4.3 - - - +
225C ASN* 1.3 73.2 - - - +
227C GLN* 1.3 64.3 + - - +
229C ILE* 3.1 4.9 + - - +
230C LEU* 2.9 44.9 + - + +
358C ILE* 3.9 16.8 - - + -
360C THR* 3.2 27.4 - - - -
362C PRO* 3.9 9.4 - - + -
364C VAL* 3.5 26.7 - - + -
421C LEU* 3.6 20.6 - - + +
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Residues in contact with GLN 227 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213C VAL* 4.1 22.9 + - + +
223C SER 2.9 16.0 + - - +
224C LYS* 3.3 30.5 + - - +
226C PHE* 1.3 76.1 - - - +
228C ARG* 1.3 58.9 + - - +
230C LEU* 3.2 7.0 + - - +
231C GLN* 2.8 59.0 + - - +
237C PHE* 3.9 21.7 - - + +
239C LEU* 3.4 28.0 - - - +
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Residues in contact with ARG 228 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224C LYS* 3.2 30.0 + - - +
225C ASN* 3.1 36.9 - - - +
227C GLN* 1.3 81.2 - - - +
229C ILE* 1.3 63.2 + - + +
231C GLN* 3.3 18.1 + - - +
232C LYS* 3.1 44.5 + - - +
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Residues in contact with ILE 229 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225C ASN* 3.1 15.4 + - + +
226C PHE* 3.1 8.3 + - - +
228C ARG* 1.3 75.3 - - + +
230C LEU* 1.3 66.9 + - + +
232C LYS* 3.3 14.0 + - + +
233C GLN* 3.3 27.7 + - + +
362C PRO* 3.7 31.2 - - + -
401C ASP* 3.8 35.4 - - + +
402C GLY* 4.2 5.8 - - - +
421C LEU* 4.0 20.2 - - + -
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Residues in contact with LEU 230 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191C VAL* 3.3 29.8 - - + -
195C SER* 3.8 17.5 - - - +
213C VAL* 5.0 0.2 - - + -
226C PHE* 2.9 46.8 + - + +
227C GLN* 3.6 5.2 - - - +
229C ILE* 1.3 73.3 - - - +
231C GLN* 1.3 61.5 + - - +
233C GLN* 2.9 43.3 + - - +
235C PHE* 3.1 27.0 + - + +
237C PHE* 3.9 25.1 - - + -
360C THR* 4.5 6.1 - - + -
361C HIS 4.9 1.6 - - - +
362C PRO* 5.4 1.3 - - + -
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Residues in contact with GLN 231 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227C GLN* 2.8 48.4 + - - +
228C ARG* 3.5 21.4 - - - +
229C ILE 3.2 0.2 - - - -
230C LEU* 1.3 77.6 - - - +
232C LYS* 1.3 57.9 + - + +
234C GLY* 3.0 19.6 + - - -
235C PHE 3.2 18.3 - - - +
236C LYS* 4.9 2.9 - - - -
237C PHE* 3.8 20.2 + - + +
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Residues in contact with LYS 232 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228C ARG* 3.1 33.0 + - - +
229C ILE* 3.3 13.7 + - + +
230C LEU 3.2 0.4 - - - -
231C GLN* 1.3 77.6 - - + +
233C GLN* 1.3 60.5 + - + +
234C GLY* 3.1 1.8 + - - -
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Residues in contact with GLN 233 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64C HIS* 5.5 12.5 - - + -
195C SER* 4.5 6.2 + - - -
198C GLN* 3.0 33.4 + - - +
199C ARG* 5.3 5.8 + - - +
229C ILE* 3.3 18.6 + - + +
230C LEU* 2.9 32.7 + - - +
232C LYS* 1.3 78.2 - - - +
234C GLY* 1.3 57.4 + - - +
235C PHE* 3.5 2.7 - - + +
361C HIS* 2.7 29.5 + - - +
362C PRO* 3.7 12.3 - - - +
401C ASP* 5.2 1.8 + - - -
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Residues in contact with GLY 234 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198C GLN* 4.3 10.3 - - - +
204C VAL 4.1 0.9 + - - +
231C GLN 3.0 11.5 + - - -
232C LYS 3.1 1.8 - - - -
233C GLN* 1.3 80.6 - - - +
235C PHE* 1.3 63.8 + - - +
236C LYS* 3.3 27.0 + - - +
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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