Contacts of the helix formed by residues 214 - 228 (chain D) in PDB entry 1Z10
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 214 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51D THR 4.3 2.2 - - - -
52D GLU* 5.1 0.7 - - - -
210D GLN* 3.3 19.7 - - + +
211D PHE* 2.7 27.1 + - + +
213D SER* 1.3 82.3 - - - +
215D SER* 1.3 64.8 + - - +
216D THR* 3.6 6.4 + - - -
217D GLY 3.1 11.1 + - - -
218D GLN* 3.0 22.9 + - - +
477D HIS* 4.0 29.6 - - + +
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Residues in contact with SER 215 (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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51D THR* 2.7 36.8 + - - -
52D GLU* 3.7 28.7 + - - +
214D THR* 1.3 75.8 - - - +
216D THR* 1.3 58.6 + - - +
218D GLN 3.2 1.2 + - - -
219D LEU* 2.8 29.9 + - - +
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Residues in contact with THR 216 (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 PHE* 3.9 13.7 - - + -
214D THR* 3.2 6.9 + - - -
215D SER* 1.3 78.9 + - - +
217D GLY* 1.3 58.1 + - - +
219D LEU* 3.2 11.2 + - + +
220D TYR* 2.9 27.7 + - - +
227D MET* 4.0 12.0 - - + +
233D PRO* 4.2 18.6 - - + +
234D GLN* 3.8 26.5 - - - +
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Residues in contact with GLY 217 (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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104D GLN* 5.4 0.3 + - - -
106D THR* 4.6 1.9 + - - -
211D PHE* 3.3 38.3 + - - -
212D THR* 4.3 7.0 - - - +
214D THR* 3.1 12.6 + - - -
216D THR* 1.3 77.8 - - - +
218D GLN* 1.3 61.8 + - - +
220D TYR* 3.3 15.1 - - - +
221D GLU* 3.4 15.1 + - - +
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Residues in contact with GLN 218 (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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51D THR* 3.4 23.8 - - - +
54D MET* 3.2 36.6 - - + +
73D LEU* 6.2 0.4 - - - +
104D GLN* 4.7 1.4 + - - -
212D THR 3.1 19.0 - - - +
214D THR 3.0 15.0 + - - +
217D GLY* 1.3 73.7 - - - +
219D LEU* 1.3 67.5 + - - +
220D TYR 3.1 1.6 - - - -
221D GLU* 3.2 34.8 + - - +
222D MET* 3.5 11.4 + - - +
368D MET* 3.6 18.1 - - - +
392D TYR* 5.1 3.0 + - - -
478D VAL 5.0 0.2 - - - +
479D GLY* 3.9 20.6 - - - -
480D PHE* 3.4 12.1 + - - +
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Residues in contact with LEU 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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46D TYR* 3.7 33.7 - - + +
51D THR* 3.9 17.0 - - + +
215D SER* 2.8 18.3 + - - +
216D THR* 3.6 10.3 - - + +
218D GLN* 1.3 77.0 - - - +
220D TYR* 1.3 58.6 + - - +
222D MET* 2.9 9.0 + - - +
223D PHE* 2.9 48.1 + - + +
227D MET* 4.0 17.7 - - + -
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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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105D ALA* 3.5 33.1 + - + -
106D THR* 3.4 26.2 - - - -
109D TRP* 4.1 5.7 - - - +
211D PHE* 4.5 5.4 - + + -
216D THR 2.9 14.2 + - - +
217D GLY* 3.3 13.9 - - - +
219D LEU* 1.3 77.6 - - - +
221D GLU* 1.3 58.1 + - - +
224D SER* 2.8 44.8 + - - -
227D MET* 3.7 25.8 - - + -
228D LYS* 3.2 44.9 - - - +
234D GLN* 3.7 12.1 - - + -
238D PHE* 3.3 25.7 - + - -
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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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73D LEU* 4.8 4.7 - - + +
76D ARG* 3.0 46.6 + - - +
103D GLU* 4.3 0.5 - - - +
104D GLN* 3.2 26.0 + - - +
105D ALA* 2.7 40.6 + - - +
106D THR* 3.2 16.1 + - - -
217D GLY 3.4 11.9 + - - +
218D GLN* 3.2 30.5 + - - +
219D LEU 3.1 0.4 - - - -
220D TYR* 1.3 78.7 - - - +
222D MET* 1.3 62.7 + - + +
224D SER* 4.8 2.1 + - - -
392D TYR* 4.6 10.1 + - - +
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Residues in contact with MET 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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43D ILE 3.9 2.2 - - - +
46D TYR* 3.7 46.0 - - + +
49D LEU* 4.1 15.7 - - + -
51D THR* 3.9 28.0 - - - -
54D MET* 5.3 4.0 - - + +
73D LEU* 3.6 29.0 - - + +
74D GLY 3.6 19.5 - - - +
75D PRO* 3.3 29.1 - - - +
76D ARG* 5.5 1.0 - - - +
218D GLN 3.5 8.7 + - - +
219D LEU* 2.9 8.7 + - - +
221D GLU* 1.3 81.6 - - + +
223D PHE* 1.3 73.0 + - + +
224D SER 3.7 0.9 - - - -
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Residues in contact with PHE 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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42D PHE* 3.7 52.3 - + + -
43D ILE* 3.8 29.4 - - + -
46D TYR* 4.1 13.2 - + - -
74D GLY* 3.9 5.2 - - - -
75D PRO* 4.5 1.3 - - + -
219D LEU* 2.9 44.0 + - + +
220D TYR 3.7 1.1 - - - -
222D MET* 1.3 96.9 - - + +
224D SER* 1.3 63.7 + - - +
225D SER* 3.3 6.1 - - - -
226D VAL* 3.0 11.2 + - + +
227D MET* 3.0 33.0 + - + -
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Residues in contact with SER 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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103D GLU* 4.9 4.3 + - - -
105D ALA* 3.8 13.6 - - - +
220D TYR* 2.8 52.2 + - - -
221D GLU 5.0 1.9 + - - -
222D MET 3.7 2.2 + - - -
223D PHE* 1.3 76.8 - - - +
225D SER* 1.3 63.7 + - - +
228D LYS* 2.9 34.8 + - - +
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Residues in contact with SER 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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42A PHE* 4.0 5.4 - - - -
75A PRO* 5.4 0.2 - - - +
225A SER* 3.8 34.9 + - - -
42D PHE* 4.6 6.1 - - - -
75D PRO* 5.6 3.9 - - - +
223D PHE* 3.3 3.5 + - - -
224D SER* 1.3 81.1 + - - +
226D VAL* 1.3 65.0 + - - +
228D LYS* 4.3 9.6 - - - +
229D HIS* 3.2 24.1 + - - -
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Residues in contact with VAL 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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42A PHE* 4.0 30.7 - - + -
225A SER* 4.3 0.7 - - - +
226A VAL* 3.6 31.0 - - + -
42D PHE* 4.2 11.7 - - + -
223D PHE* 3.0 8.6 + - + +
224D SER 3.0 0.2 - - - -
225D SER* 1.3 88.0 - - - +
227D MET* 1.3 62.3 + - + +
228D LYS 3.2 2.2 - - - -
229D HIS* 2.9 27.2 + - - +
230D LEU* 3.6 24.2 - - + +
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Residues in contact with MET 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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216D THR* 4.0 26.7 - - + +
219D LEU* 3.8 28.5 - - + +
220D TYR* 3.7 32.5 - - + +
223D PHE* 3.0 25.0 + - + +
226D VAL* 1.3 73.3 - - + +
228D LYS* 1.3 62.5 + - - +
229D HIS 3.0 6.9 + - - -
230D LEU* 3.1 29.1 + - + +
234D GLN* 3.1 43.2 - - + +
235D GLN* 3.8 1.4 + - - -
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Residues in contact with LYS 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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109D TRP* 4.6 14.4 + - + +
220D TYR* 3.2 27.7 - - - +
224D SER* 2.9 29.1 + - - +
225D SER* 4.3 7.2 - - - +
226D VAL 3.1 0.2 + - - -
227D MET* 1.3 78.8 - - - +
229D HIS* 1.3 88.5 + - + +
230D LEU 3.4 0.2 - - - -
235D GLN* 3.1 15.7 + - - +
238D PHE* 4.0 13.4 - - + -
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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