Contacts of the helix formed by residues 218 - 229 (chain D) in PDB entry 3NZG
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 218 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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235A TYR* 4.7 0.2 + - - -
259A ARG* 2.8 31.6 + - - -
308A ASN 5.6 0.7 - - - +
310A GLN* 3.4 26.9 + - - +
336A PRO* 6.3 0.4 - - + -
216D PHE* 4.6 0.4 - - - +
217D THR* 1.3 80.6 + - - +
219D TRP* 1.3 72.6 + - - +
220D TYR* 3.2 14.9 + - - +
221D GLU* 3.1 28.2 + - + +
222D VAL* 3.1 13.3 + - - +
241D LEU* 3.8 2.7 - - - +
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Residues in contact with TRP 219 (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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282A HIS* 3.5 36.1 - + - +
308A ASN* 3.7 37.5 + - + +
217D THR 4.0 1.4 + - - -
218D ASP* 1.3 78.5 + - - +
220D TYR* 1.3 74.7 + + + +
222D VAL* 3.2 3.2 + - - -
223D ALA* 2.7 45.3 + - + +
241D LEU* 3.7 20.5 - - + +
245D ASP* 5.6 0.4 + - - -
248D GLY* 3.8 21.3 - - - +
251D LYS* 3.5 39.6 - - + +
252D LEU* 3.6 6.3 - - + +
255D ASN* 3.4 39.0 - - + -
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Residues in contact with TYR 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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234A LEU 4.8 1.0 + - - -
235A TYR 5.0 0.2 - - - -
257A ARG* 2.4 35.8 + - - -
258A SER* 3.6 7.8 - - - -
259A ARG* 3.4 58.7 + - + +
282A HIS* 4.0 17.5 - + + -
218D ASP* 3.2 14.6 + - - +
219D TRP* 1.3 105.1 - + + +
221D GLU* 1.3 64.6 + - - +
223D ALA* 3.2 3.8 + - + +
224D ARG* 3.0 61.6 + - + +
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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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259A ARG* 4.7 3.8 - - - +
188D THR* 3.6 30.6 - - + +
216D PHE* 3.8 19.7 - - + +
217D THR 5.5 0.5 + - - -
218D ASP* 3.1 28.7 + - + +
220D TYR* 1.3 81.9 - - - +
222D VAL* 1.3 62.7 + - + +
224D ARG* 3.3 9.4 + - - +
225D LEU* 3.1 20.4 + - - +
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Residues in contact with VAL 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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216D PHE* 3.3 48.5 - - + -
218D ASP 3.1 10.2 + - - +
219D TRP* 3.6 7.0 - - - +
221D GLU* 1.3 78.3 - - - +
223D ALA* 1.3 61.5 + - - +
225D LEU* 3.1 8.0 + - + +
226D LEU* 3.0 34.4 + - + +
240D THR* 3.9 15.7 - - + +
241D LEU* 3.9 10.8 - - + -
252D LEU* 3.5 27.6 - - + -
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Residues in contact with ALA 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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219D TRP* 2.7 38.5 + - + +
220D TYR* 3.2 6.3 + - + +
222D VAL* 1.3 74.4 - - - +
224D ARG* 1.3 62.1 + - - +
226D LEU* 3.5 0.3 + - - -
227D ASN* 2.9 37.6 + - - +
252D LEU* 3.6 5.3 - - + +
255D ASN* 4.5 4.3 - - + +
256D THR* 3.7 25.4 - - + -
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Residues in contact with ARG 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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207A ASP* 5.5 3.4 + - - -
230A GLU 5.6 0.4 + - - -
233A GLU* 3.4 55.0 + - - +
234A LEU 3.3 20.0 + - - -
235A TYR* 5.3 2.0 - - - +
259A ARG* 5.1 4.4 - - - +
220D TYR* 3.0 52.4 + - + +
221D GLU* 3.5 12.6 - - - +
223D ALA* 1.3 75.7 - - - +
225D LEU* 1.3 62.8 + - - +
227D ASN* 4.0 6.0 - - - +
228D SER* 3.1 25.2 + - - -
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Residues in contact with LEU 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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188D THR* 3.5 32.8 - - + +
189D LYS* 5.7 0.9 - - + +
191D VAL* 4.0 17.9 - - + -
192D ALA* 3.9 24.0 - - + +
212D TYR* 4.1 9.6 - - + -
216D PHE* 3.5 35.7 - - + -
221D GLU 3.1 12.2 + - - +
222D VAL* 3.1 12.4 + - + +
224D ARG* 1.3 74.0 - - - +
226D LEU* 1.3 73.0 + - + +
228D SER* 2.6 25.3 + - - +
229D ILE* 3.4 13.6 + - + +
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Residues in contact with LEU 226 (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 TYR* 3.6 29.2 - - + +
222D VAL* 3.0 34.6 + - + +
223D ALA 4.1 2.0 - - - +
225D LEU* 1.3 83.4 - - + +
227D ASN* 1.3 63.6 + - - +
229D ILE* 3.1 26.5 + - + +
230D GLU* 3.5 10.4 + - - +
234D LEU* 6.0 0.4 - - + -
237D ALA* 4.0 17.7 - - + -
240D THR* 4.7 0.9 - - + -
252D LEU* 4.4 6.7 - - + -
256D THR* 4.5 9.0 - - + +
258D SER* 3.5 25.7 + - - +
260D ILE* 3.8 29.2 - - + -
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Residues in contact with ASN 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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257A ARG* 3.6 29.8 - - - +
223D ALA* 2.9 26.4 + - - +
224D ARG* 4.0 5.3 - - - +
226D LEU* 1.3 77.0 - - - +
228D SER* 1.3 60.9 + - - +
229D ILE 3.2 1.0 + - - -
230D GLU* 3.6 33.0 + - - +
255D ASN 3.1 20.2 + - - -
256D THR* 3.3 24.5 - - - -
257D ARG* 4.0 1.0 + - - +
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Residues in contact with SER 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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189D LYS* 3.8 24.6 + - - -
192D ALA* 4.2 2.8 - - - +
196D ARG* 3.0 21.1 + - - -
224D ARG* 3.1 14.3 + - - -
225D LEU* 2.6 23.3 + - - +
227D ASN* 1.3 75.6 - - - +
229D ILE* 1.3 65.4 + - - +
230D GLU 3.6 0.4 - - - -
231D ASP* 3.6 3.6 - - - +
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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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192D ALA* 4.0 23.3 - - + +
195D LEU* 3.8 18.8 - - + -
196D ARG* 4.2 8.1 - - - +
212D TYR* 3.9 7.9 - - - +
225D LEU* 3.6 12.6 - - + +
226D LEU* 3.1 21.7 + - + +
228D SER* 1.3 94.0 + - - +
230D GLU* 1.3 63.3 + - - +
231D ASP* 3.2 7.6 - - - -
232D LEU* 3.1 34.4 + - + +
233D GLU 4.2 1.0 + - - -
234D LEU* 3.7 29.2 + - + +
258D SER* 5.9 0.4 - - - +
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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