Contacts of the helix formed by residues 216 - 231 (chain A) in PDB entry 2Z1Z
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 THR 216 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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214A ALA 5.1 1.2 + - - -
215A ALA* 1.3 76.3 - - - +
217A ARG* 1.3 64.2 + - - +
218A GLU* 3.1 16.8 - - + +
219A GLN* 2.9 46.1 + - + +
220A LEU* 3.0 23.7 + - - +
248A ASN* 3.6 18.3 + - - +
249A PRO* 4.0 1.3 - - - -
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Residues in contact with ARG 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216A THR* 1.3 73.5 - - - +
218A GLU* 1.3 56.7 + - - +
221A THR* 2.8 37.4 + - - +
247A ASP 5.5 5.8 + - - +
248A ASN* 4.4 3.8 - - - +
249A PRO* 3.6 29.6 - - + +
254A GLU* 3.7 43.1 + - - +
255A ILE* 3.7 9.2 - - + +
256A PRO* 5.7 2.0 - - - +
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Residues in contact with GLU 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216A THR* 3.1 10.3 - - + +
217A ARG* 1.3 77.6 - - - +
219A GLN* 1.3 57.8 + - + +
221A THR* 3.3 20.4 - - - +
222A GLN* 3.0 46.3 + - - +
225A GLU* 5.4 1.2 - - - +
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Residues in contact with GLN 219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187A ASN 5.1 2.2 + - - -
188A GLY* 4.8 8.6 + - - +
190A PHE* 3.2 63.8 - - + +
214A ALA 4.4 1.9 - - - +
215A ALA* 3.3 11.2 - - + +
216A THR* 2.9 47.4 + - + +
218A GLU* 1.3 75.9 - - + +
220A LEU* 1.3 56.2 + - - +
222A GLN* 3.2 12.9 + - - +
223A LEU 3.0 21.7 + - - -
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Residues in contact with LEU 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190A PHE* 5.0 0.2 - - + -
204A PHE* 4.0 18.4 - - + -
215A ALA* 3.4 33.4 - - + +
216A THR 3.0 16.7 + - - +
219A GLN* 1.3 72.3 - - - +
221A THR* 1.3 61.2 + - - +
223A LEU* 3.4 16.5 - - + +
224A VAL* 2.8 35.7 + - - +
236A TYR* 3.7 25.4 - - + +
249A PRO* 3.9 26.5 - - + +
251A SER 4.9 1.8 - - - +
252A ILE* 4.0 14.3 - - + +
255A ILE* 3.8 17.7 - - + -
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Residues in contact with THR 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217A ARG* 2.8 27.5 + - - +
218A GLU* 3.3 23.4 + - - +
220A LEU* 1.3 76.4 - - - +
222A GLN* 1.3 61.3 + - - +
224A VAL* 3.5 2.8 + - - +
225A GLU* 3.1 43.4 + - - +
255A ILE* 3.8 23.9 - - + +
256A PRO* 5.9 0.9 - - - +
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Residues in contact with GLN 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190A PHE* 4.0 13.3 - - - -
191A PRO 5.4 0.3 - - - +
193A LEU* 3.9 24.7 + - + +
218A GLU* 3.0 38.4 + - - +
219A GLN* 3.3 16.2 - - - +
221A THR* 1.3 72.7 - - - +
223A LEU* 1.3 59.9 + - - +
225A GLU* 3.3 13.7 + - - +
226A PHE* 2.9 31.9 + - - +
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Residues in contact with LEU 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181A MET* 5.7 1.3 - - - -
190A PHE* 4.5 5.4 - - + -
193A LEU* 4.1 23.7 - - + +
202A ILE* 4.2 21.3 - - + -
204A PHE* 3.8 50.9 - - + -
219A GLN 3.0 13.2 + - - +
220A LEU* 3.2 20.8 + - + +
222A GLN* 1.3 75.4 - - - +
224A VAL* 1.3 58.2 + - - +
226A PHE* 3.3 4.1 - - + +
227A ALA* 3.0 29.1 + - - +
234A ILE* 3.9 24.9 - - + -
236A TYR* 5.0 0.2 - - + -
252A ILE* 4.4 6.7 - - + -
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Residues in contact with VAL 224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220A LEU 2.8 23.2 + - - +
221A THR 3.8 2.7 - - - +
223A LEU* 1.3 69.7 - - - +
225A GLU* 1.3 55.8 + - + +
227A ALA* 3.5 1.7 + - - +
228A LYS* 2.8 44.0 + - - +
234A ILE* 4.2 11.4 - - + -
252A ILE* 4.0 17.7 - - + -
255A ILE* 3.4 31.0 - - + -
256A PRO 4.3 3.4 - - - +
257A GLY* 3.8 29.4 - - - +
258A ALA* 4.3 9.4 - - + -
261A VAL* 3.9 5.7 - - + +
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Residues in contact with GLU 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218A GLU* 5.4 1.2 - - - +
221A THR* 3.1 36.3 + - - +
222A GLN* 3.3 15.6 + - - +
224A VAL* 1.3 75.8 - - + +
226A PHE* 1.3 51.9 + - - +
228A LYS* 3.1 7.8 + - + +
229A LYS* 2.7 37.0 + - - +
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Residues in contact with PHE 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181A MET* 5.9 1.3 - - - -
193A LEU* 3.2 47.8 - - + -
196A VAL* 3.4 39.9 - - + -
197A GLY 4.7 3.1 - - - -
198A ARG* 5.6 0.2 - - - -
199A THR 6.1 0.7 - - - -
202A ILE* 4.0 25.6 - - + -
222A GLN 2.9 17.6 + - - +
223A LEU* 3.3 7.4 - - + +
225A GLU* 1.3 72.0 - - - +
227A ALA* 1.3 61.4 + - - +
229A LYS* 3.3 13.3 + - + +
230A ASN* 2.9 59.1 + - - +
232A SER* 5.6 0.2 - - - -
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Residues in contact with ALA 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202A ILE* 4.1 9.4 - - + -
223A LEU 3.0 16.3 + - - +
224A VAL 3.8 2.9 - - - +
226A PHE* 1.3 76.9 - - - +
228A LYS* 1.3 57.7 + - - +
231A GLY* 2.8 26.7 + - - -
232A SER* 3.0 31.8 + - - +
234A ILE* 3.7 30.5 - - + -
261A VAL* 4.0 6.7 - - + -
20B TYR* 4.0 0.2 + - - -
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Residues in contact with LYS 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224A VAL* 2.8 28.2 + - - +
225A GLU* 3.1 7.2 + - + +
227A ALA* 1.3 72.7 - - - +
229A LYS* 1.3 63.0 + - - +
231A GLY 3.4 1.6 + - - -
257A GLY* 3.3 33.0 + - - -
260A GLU* 2.4 41.5 + - - +
261A VAL* 3.7 9.3 - - + +
20B TYR* 2.8 44.2 + - + -
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Residues in contact with LYS 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225A GLU 2.7 19.6 + - - +
226A PHE* 3.8 12.3 - - + +
228A LYS* 1.3 76.3 - - - +
230A ASN* 1.3 72.4 + - - +
231A GLY 3.3 0.6 + - - -
23B LYS* 3.8 13.0 + - - -
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Residues in contact with ASN 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196A VAL 4.8 0.6 + - - -
198A ARG* 3.0 59.5 + - + +
226A PHE* 2.9 52.1 + - + +
229A LYS* 1.3 89.0 - - - +
231A GLY* 1.3 64.0 + - - +
232A SER* 3.7 11.9 + - - +
23B LYS* 3.8 12.4 + - - +
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Residues in contact with GLY 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198A ARG* 3.0 13.7 + - - -
227A ALA 2.8 10.5 + - - -
228A LYS 3.4 1.2 + - - -
229A LYS 3.3 4.6 + - - -
230A ASN* 1.3 76.8 - - - +
232A SER* 1.3 56.1 - - - -
20B TYR* 3.5 18.2 - - - -
22B THR* 4.2 2.0 - - - -
23B LYS* 2.8 40.2 + - - +
24B VAL* 3.6 5.4 - - - +
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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