Contacts of the helix formed by residues 219 - 234 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217G GLY 3.4 2.4 + - - -
218G ILE* 1.3 76.0 - - - +
220G MET* 1.3 60.0 + - - +
221G GLU 3.2 3.9 + - - -
222G ILE* 3.0 29.2 + - + +
223G SER* 2.8 27.1 + - - -
366G TRP* 5.3 0.2 - - - -
370G SER* 3.8 4.6 - - - -
371G GLU* 3.1 31.2 + - - +
372G GLU* 3.7 7.3 - - - +
405G LYS* 2.8 37.9 + - - -
419G HIS* 3.6 29.5 + - + +
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Residues in contact with MET 220 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211G GLY 5.7 0.4 - - - +
212G HIS* 3.4 55.6 - - + +
218G ILE* 3.5 16.0 + - + +
219G ASP* 1.3 71.6 - - - +
221G GLU* 1.3 62.6 + - - +
223G SER* 3.3 2.9 + - - -
224G LYS* 3.0 36.7 + - + +
372G GLU* 3.0 42.5 + - + +
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Residues in contact with GLU 221 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375F LYS* 6.5 1.6 - - + -
219G ASP* 3.2 10.0 + - - +
220G MET* 1.3 77.9 - - - +
222G ILE* 1.3 65.4 + - - +
224G LYS* 3.3 5.6 + - - +
225G ASN* 3.1 37.7 + - - +
371G GLU* 3.8 5.1 - - - +
372G GLU* 4.6 1.2 + - - -
385G LYS* 2.7 37.1 + - - +
403G MET* 3.7 20.7 - - + +
405G LYS* 2.8 21.1 + - - +
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Residues in contact with ILE 222 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218G ILE* 4.2 7.0 - - + -
219G ASP* 3.0 26.4 + - + +
221G GLU* 1.3 77.5 - - - +
223G SER* 1.3 56.1 + - - +
225G ASN* 3.2 6.0 + - - +
226G PHE* 2.9 27.6 + - + +
364G VAL* 3.8 29.8 - - + -
366G TRP* 5.7 1.1 - - + -
403G MET* 4.0 22.2 - - + +
405G LYS* 4.5 6.1 - - + -
419G HIS* 3.6 42.2 - - + +
420G ILE 4.9 1.1 - - - +
421G LEU* 4.0 23.6 - - + +
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Residues in contact with SER 223 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212G HIS* 3.4 12.5 - - - +
213G VAL* 2.5 39.2 + - - +
218G ILE* 3.9 21.3 - - - +
219G ASP 2.8 19.1 + - - -
220G MET* 3.5 9.0 - - - -
222G ILE* 1.3 75.0 - - - +
224G LYS* 1.3 57.0 + - - +
226G PHE* 3.3 4.1 + - - +
227G GLN* 3.0 29.3 + - - +
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Residues in contact with LYS 224 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376F GLU* 5.5 14.0 + - - +
211G GLY 3.7 22.6 + - - +
212G HIS* 4.8 9.0 - - + -
220G MET* 3.0 27.8 + - + +
221G GLU* 3.3 5.3 + - - +
223G SER* 1.3 76.5 - - - +
225G ASN* 1.3 69.6 + - - +
227G GLN* 2.9 32.4 + - - +
228G ARG* 3.2 22.2 + - - +
239G LEU* 4.1 4.9 - - - +
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Residues in contact with ASN 225 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221G GLU* 3.1 22.8 + - - +
222G ILE* 3.6 3.8 - - - +
224G LYS* 1.3 80.3 - - - +
226G PHE* 1.3 64.3 + - - +
228G ARG* 3.4 9.7 + - - +
229G ILE* 3.2 28.8 + - + +
402G GLY* 6.2 0.4 - - - -
403G MET* 3.6 28.0 - - - +
421G LEU* 3.4 21.7 - - + +
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Residues in contact with PHE 226 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191G VAL* 3.5 31.2 - - + -
213G VAL* 3.6 24.0 - - + -
214G GLY* 4.9 0.9 - - - -
218G ILE* 4.6 9.4 - - + -
222G ILE* 2.9 19.9 + - + +
223G SER* 3.6 4.9 - - - +
225G ASN* 1.3 77.3 - - - +
227G GLN* 1.3 61.8 + - - +
229G ILE* 3.1 6.8 + - - +
230G LEU* 3.0 42.9 + - + +
358G ILE* 3.9 17.5 - - + -
360G THR* 3.3 27.8 - - - -
362G PRO* 4.1 7.9 - - + -
364G VAL* 3.4 28.0 - - + -
421G LEU* 3.8 19.5 - - + +
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Residues in contact with GLN 227 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213G VAL* 3.6 20.6 + - + +
223G SER 3.0 15.5 + - - +
224G LYS* 2.9 36.0 + - - +
226G PHE* 1.3 79.2 - - - +
228G ARG* 1.3 56.1 + - - +
230G LEU* 3.3 7.1 + - - +
231G GLN* 2.8 59.3 + - - +
237G PHE* 3.6 24.8 + - + +
239G LEU* 3.5 26.2 - - - +
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Residues in contact with ARG 228 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224G LYS 3.2 15.6 + - - +
225G ASN* 3.7 9.0 - - - +
226G PHE 3.2 0.2 - - - -
227G GLN* 1.3 79.4 - - - +
229G ILE* 1.3 63.4 + - + +
231G GLN* 3.4 14.9 + - - +
232G LYS* 3.0 28.7 + - + +
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Residues in contact with ILE 229 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225G ASN* 3.2 17.5 + - + +
226G PHE* 3.1 7.2 + - - +
228G ARG* 1.3 81.4 - - + +
230G LEU* 1.3 63.5 + - + +
232G LYS* 3.3 20.3 + - - +
233G GLN* 3.2 27.5 + - - +
362G PRO* 3.7 23.3 - - + -
401G ASP* 3.7 46.4 - - + +
402G GLY* 4.2 6.5 - - - +
421G LEU* 3.9 24.9 - - + -
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Residues in contact with LEU 230 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191G VAL* 3.5 32.1 - - + -
195G SER* 4.9 4.7 - - - +
226G PHE* 3.0 44.0 + - + +
227G GLN* 3.6 7.9 - - - +
229G ILE* 1.3 75.4 - - - +
231G GLN* 1.3 64.0 + - - +
233G GLN* 3.0 35.9 + - - +
234G GLY 3.2 0.5 + - - -
235G PHE* 3.0 33.9 + - + +
237G PHE* 4.0 24.0 - - + -
360G THR* 4.7 12.8 - - + -
361G HIS 4.8 2.2 - - - +
362G PRO* 5.1 2.5 - - + -
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Residues in contact with GLN 231 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227G GLN* 2.8 49.8 + - - +
228G ARG* 3.7 14.4 - - - +
230G LEU* 1.3 76.1 - - - +
232G LYS* 1.3 59.1 + - - +
234G GLY* 2.9 20.1 + - - -
235G PHE 3.1 19.2 - - - +
236G LYS* 5.1 0.7 - - - -
237G PHE* 3.7 20.1 + - + +
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Residues in contact with LYS 232 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228G ARG* 3.0 15.1 + - + +
229G ILE* 3.5 26.5 - - - +
230G LEU 3.2 0.4 - - - -
231G GLN* 1.3 77.7 - - - +
233G GLN* 1.3 62.7 + - - +
234G GLY 3.2 0.6 + - - -
401G ASP* 3.2 27.3 + - - -
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Residues in contact with GLN 233 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64G HIS* 5.5 13.5 - - + -
195G SER* 4.4 9.7 + - - -
198G GLN* 2.9 29.0 + - - +
199G ARG* 5.4 4.2 + - - +
229G ILE* 3.2 20.7 + - + +
230G LEU* 3.0 28.3 + - - +
232G LYS* 1.3 81.2 - - + +
234G GLY* 1.3 57.1 + - - +
235G PHE* 3.6 1.6 - - + +
361G HIS* 2.8 27.4 + - - +
362G PRO* 3.6 13.1 - - - +
401G ASP* 4.7 3.2 + - - -
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Residues in contact with GLY 234 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198G GLN* 3.8 16.1 + - - +
204G VAL 4.3 2.4 + - - +
231G GLN 2.9 11.2 + - - -
232G LYS 3.2 0.8 - - - -
233G GLN* 1.3 80.6 - - - +
235G PHE* 1.3 63.5 + - - +
236G LYS* 3.4 26.3 + - - +
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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