Contacts of the helix formed by residues 219 - 233 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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217D GLY 3.4 2.4 + - - -
218D ILE* 1.3 75.1 - - - +
220D MET* 1.3 56.7 + - - +
221D GLU 3.3 14.2 + - - -
222D ILE* 3.2 15.5 + - + +
223D SER* 2.8 33.9 + - - -
366D TRP* 5.3 0.6 - - - -
370D SER* 3.8 4.9 - - - -
371D GLU* 3.0 36.4 + - - +
372D GLU* 3.4 9.6 - - - +
405D LYS* 2.6 35.1 + - - -
419D HIS* 3.6 27.5 + - + +
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Residues in contact with MET 220 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211D GLY 4.8 4.7 - - - +
212D HIS* 3.7 46.4 - - + +
218D ILE 3.5 4.4 + - - +
219D ASP* 1.3 73.1 - - - +
221D GLU* 1.3 56.9 + - - +
223D SER* 3.2 2.4 + - - -
224D LYS* 2.9 67.1 + - + +
372D GLU* 3.1 39.4 + - + +
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Residues in contact with GLU 221 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219D ASP* 3.3 10.6 + - - +
220D MET* 1.3 78.9 - - - +
222D ILE* 1.3 62.7 + - - +
224D LYS* 3.5 11.3 + - - +
225D ASN* 3.2 36.7 + - - +
371D GLU* 3.9 4.1 - - - +
372D GLU* 4.8 0.8 + - - -
383D VAL* 5.7 0.2 - - - +
385D LYS* 3.3 23.9 + - - -
403D MET* 4.0 15.7 - - + +
405D LYS* 2.6 34.4 + - - +
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Residues in contact with ILE 222 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218D ILE* 4.4 6.3 - - + -
219D ASP* 3.2 24.5 + - + +
221D GLU* 1.3 77.5 - - - +
223D SER* 1.3 58.4 + - - +
225D ASN* 3.3 5.5 + - - +
226D PHE* 2.9 27.8 + - + +
364D VAL* 3.7 30.3 - - + -
366D TRP* 5.8 1.3 - - + -
403D MET* 3.7 28.3 - - + -
405D LYS* 4.6 1.8 - - + -
419D HIS* 3.7 39.9 - - + +
420D ILE 4.8 1.8 - - - +
421D LEU* 4.1 24.4 - - + +
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Residues in contact with SER 223 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212D HIS* 3.3 21.3 - - - +
213D VAL* 2.6 31.7 + - - +
218D ILE* 3.8 21.1 - - - +
219D ASP 2.8 21.1 + - - -
220D MET* 3.5 9.0 - - - -
222D ILE* 1.3 73.1 - - - +
224D LYS* 1.3 59.0 + - - +
226D PHE* 3.1 5.1 + - - +
227D GLN* 2.9 30.8 + - - +
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Residues in contact with LYS 224 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212D HIS* 5.9 1.3 - - + -
220D MET* 2.9 54.8 + - + +
221D GLU* 3.9 9.4 - - - +
223D SER* 1.3 76.7 - - - +
225D ASN* 1.3 62.4 + - - +
227D GLN* 3.4 12.3 + - - +
228D ARG* 3.1 42.4 + - - +
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Residues in contact with ASN 225 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221D GLU* 3.2 39.8 + - - +
222D ILE* 3.8 1.1 - - - +
224D LYS* 1.3 77.9 - - - +
226D PHE* 1.3 61.4 + - - +
228D ARG* 3.0 31.2 + - - +
229D ILE* 3.1 29.1 + - + +
403D MET* 4.4 15.6 - - - +
421D LEU* 3.5 21.6 - - + +
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Residues in contact with PHE 226 (chain D).
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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191D VAL* 3.3 32.8 - - + -
213D VAL* 3.8 22.4 - - + -
214D GLY* 5.2 0.7 - - - -
218D ILE* 4.8 6.7 - - + -
222D ILE* 2.9 19.0 + - + +
223D SER* 3.4 4.3 - - - +
225D ASN* 1.3 73.8 - - - +
227D GLN* 1.3 65.6 + - - +
229D ILE* 3.1 4.5 + - + +
230D LEU* 2.9 42.8 + - + +
358D ILE* 3.8 16.4 - - + -
360D THR* 3.1 28.5 - - - -
362D PRO* 3.8 10.5 - - + -
364D VAL* 3.4 28.5 - - + -
421D LEU* 3.9 19.9 - - + +
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Residues in contact with GLN 227 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212D HIS* 4.8 1.6 - - - -
213D VAL* 4.1 23.1 + - + +
223D SER* 2.9 13.2 + - - +
224D LYS* 3.5 14.4 - - - +
226D PHE* 1.3 76.2 - - - +
228D ARG* 1.3 58.1 + - - +
230D LEU* 3.0 8.1 + - - +
231D GLN* 2.8 61.8 + - - +
237D PHE* 3.8 17.3 - - + +
239D LEU* 3.3 32.4 - - - +
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Residues in contact with ARG 228 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224D LYS* 3.1 26.2 + - - +
225D ASN* 3.0 37.4 + - - +
227D GLN* 1.3 82.0 - - + +
229D ILE* 1.3 62.9 + - + +
231D GLN* 3.3 18.3 + - - +
232D LYS* 3.1 28.5 + - + +
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Residues in contact with ILE 229 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225D ASN* 3.1 15.2 + - + +
226D PHE* 3.1 8.5 + - + +
228D ARG* 1.3 77.5 - - + +
230D LEU* 1.3 64.0 + - + +
232D LYS* 3.3 17.3 + - + +
233D GLN* 3.2 22.9 + - + +
362D PRO* 3.5 38.6 - - + -
401D ASP* 3.7 38.1 - - + +
402D GLY 4.2 5.2 - - - +
421D LEU* 4.1 18.6 - - + -
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Residues in contact with LEU 230 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191D VAL* 3.6 16.2 - - + -
195D SER* 4.6 7.2 - - - +
213D VAL* 5.0 0.9 - - + -
226D PHE* 2.9 58.1 + - + +
227D GLN* 3.5 7.0 - - - +
229D ILE* 1.3 73.2 - - - +
231D GLN* 1.3 61.5 + - - +
233D GLN* 2.8 44.2 + - - +
235D PHE* 3.1 32.2 + - + +
237D PHE* 3.9 26.2 - - + -
360D THR* 4.7 9.2 - - + -
361D HIS 4.9 2.0 - - - +
362D PRO* 5.4 1.8 - - + -
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Residues in contact with GLN 231 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227D GLN* 2.8 50.4 + - - +
228D ARG* 3.3 21.6 + - - +
230D LEU* 1.3 71.6 - - - +
232D LYS* 1.3 58.7 + - + +
234D GLY* 2.9 20.8 + - - -
235D PHE 3.1 18.3 - - - +
236D LYS* 5.2 0.7 - - - -
237D PHE* 3.7 21.3 + - + +
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Residues in contact with LYS 232 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228D ARG* 3.1 16.3 + - + +
229D ILE* 3.5 15.0 - - + +
231D GLN* 1.3 76.2 - - + +
233D GLN* 1.3 59.7 + - + +
234D GLY* 3.2 1.3 + - - -
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Residues in contact with GLN 233 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64D HIS* 5.9 10.9 - - + -
195D SER* 4.3 9.2 + - - -
198D GLN* 3.0 34.0 + - - +
199D ARG* 5.4 2.8 + - - +
229D ILE* 3.2 20.6 - - + +
230D LEU* 2.8 30.6 + - - +
232D LYS* 1.3 79.0 - - + +
234D GLY* 1.3 56.9 + - - +
235D PHE* 3.5 2.8 - - + +
361D HIS* 2.8 28.9 + - - +
362D PRO* 3.8 11.3 - - - +
401D ASP* 5.2 2.0 + - - -
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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