Contacts of the helix formed by residues 214 - 228 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51B THR 4.3 3.6 - - - -
52B GLU* 5.3 1.6 - - - +
210B GLN* 3.0 23.6 - - + +
211B PHE* 2.7 21.7 + - + +
213B SER* 1.3 81.9 - - - +
215B SER* 1.3 60.2 + - - +
216B THR* 3.5 7.4 + - - -
217B GLY 3.3 8.5 + - - -
218B GLN* 2.9 28.9 + - - +
477B HIS* 4.0 28.3 - - + +
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Residues in contact with SER 215 (chain B).
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* 4.9 0.7 + - - -
233A PRO* 3.0 26.7 - - - +
51B THR* 3.3 36.7 + - - -
52B GLU* 3.6 28.0 + - - +
214B THR* 1.3 73.5 - - - +
216B THR* 1.3 65.7 + - - +
218B GLN 3.1 0.5 + - - -
219B LEU* 2.7 30.2 + - - +
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Residues in contact with THR 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215A SER* 4.7 6.1 + - - -
216A THR* 4.1 15.8 + - - -
211B PHE* 3.7 23.8 - - + -
214B THR* 3.4 5.8 + - - -
215B SER* 1.3 80.5 + - - +
217B GLY* 1.3 58.3 + - - +
219B LEU* 3.2 9.2 + - + +
220B TYR* 2.9 28.2 + - - +
227B MET* 4.2 17.0 - - + +
233B PRO* 4.2 21.0 - - + +
234B GLN* 4.6 1.8 - - - +
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Residues in contact with GLY 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104B GLN* 5.6 0.3 + - - -
106B THR* 4.5 1.3 + - - -
211B PHE* 3.2 41.3 + - - -
212B THR* 4.2 5.3 - - - -
214B THR* 3.3 8.9 + - - -
216B THR* 1.3 76.8 - - - +
218B GLN* 1.3 64.5 + - - +
220B TYR* 3.4 5.4 + - - +
221B GLU* 3.2 23.7 + - - +
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Residues in contact with GLN 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B THR* 3.5 24.4 - - + +
54B MET* 3.2 41.0 - - + +
73B LEU* 6.1 0.6 - - - +
104B GLN* 4.6 1.4 + - - -
212B THR 3.1 18.6 - - - +
213B SER 5.0 0.2 - - - -
214B THR 2.9 19.8 + - - +
215B SER 3.9 0.4 - - - +
217B GLY* 1.3 74.6 - - - +
219B LEU* 1.3 64.4 + - - +
221B GLU* 3.2 36.8 + - - +
222B MET* 3.6 10.7 + - - +
368B MET* 4.1 9.5 - - - +
392B TYR* 4.9 5.7 + - - -
479B GLY* 4.1 20.6 - - - -
480B PHE* 3.6 10.3 + - - +
900B GOL 4.9 2.3 + - - -
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Residues in contact with LEU 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219A LEU* 6.2 3.8 - - + -
46B TYR* 3.7 31.6 - - + +
51B THR* 3.7 12.0 - - + +
215B SER 2.7 20.6 + - - +
216B THR* 3.2 11.2 + - + +
218B GLN* 1.3 73.2 - - - +
220B TYR* 1.3 57.6 + - - +
222B MET* 2.9 10.5 + - - +
223B PHE* 2.8 49.7 + - + -
227B MET* 4.0 23.3 - - + -
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Residues in contact with TYR 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B ALA* 3.5 25.8 + - + -
106B THR* 3.5 25.8 - - - +
109B TRP* 3.9 6.2 - - - +
211B PHE* 4.6 4.9 - + + -
216B THR 2.9 13.6 + - - +
217B GLY* 3.4 13.7 - - - +
219B LEU* 1.3 76.7 - - - +
221B GLU* 1.3 62.3 + - - +
224B SER* 2.9 56.5 + - - -
227B MET* 3.6 25.0 - - + -
228B LYS* 3.2 30.4 - - - +
234B GLN* 3.7 13.2 - - + -
238B PHE* 3.1 34.9 - + - -
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Residues in contact with GLU 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73B LEU* 5.3 3.1 - - + -
76B ARG* 2.9 47.7 + - - +
103B GLU* 4.1 1.6 - - - +
104B GLN* 3.2 29.6 + - - +
105B ALA* 3.0 36.2 + - - +
106B THR* 3.3 15.1 + - - -
217B GLY 3.2 13.0 + - - +
218B GLN* 3.6 32.5 - - - +
219B LEU 3.2 1.0 - - - -
220B TYR* 1.3 74.6 - - - +
222B MET* 1.3 62.1 + - + +
224B SER* 4.9 1.9 + - - -
392B TYR* 4.6 9.0 + - - +
900B GOL 5.3 1.1 + - - +
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Residues in contact with MET 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B ILE 3.9 0.9 - - - +
46B TYR* 3.4 53.6 - - + +
49B LEU* 4.3 12.3 - - + -
51B THR* 4.9 9.0 - - - -
54B MET* 5.4 5.2 - - + +
72B HIS 4.3 0.7 - - - +
73B LEU* 3.6 29.8 - - + +
74B GLY* 3.1 22.2 - - - +
75B PRO* 3.4 27.0 - - - +
76B ARG* 5.5 0.9 - - - -
218B GLN 4.0 12.8 - - - +
219B LEU* 2.9 7.0 + - - +
221B GLU* 1.3 83.7 - - + +
223B PHE* 1.3 70.3 + - + +
224B SER* 3.6 2.1 + - - -
225B SER* 5.2 1.6 + - - -
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Residues in contact with PHE 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B PHE* 3.6 35.7 - + - -
43B ILE* 3.8 37.9 - - + -
46B TYR* 3.9 25.6 - + + -
74B GLY* 4.1 1.6 - - - -
219B LEU* 2.8 47.9 + - + +
220B TYR 3.8 0.7 - - - -
222B MET* 1.3 87.1 - - + +
224B SER* 1.3 60.7 + - - +
225B SER* 3.1 6.3 - - - +
226B VAL* 3.0 10.5 + - + +
227B MET* 2.9 38.8 + - + -
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Residues in contact with SER 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B GLU* 4.5 5.7 + - - -
105B ALA* 3.7 14.6 - - - +
220B TYR* 2.9 52.9 + - - -
221B GLU 4.9 2.3 + - - -
222B MET 3.6 1.5 - - - -
223B PHE* 1.3 77.2 - - - +
225B SER* 1.3 65.3 + - - +
228B LYS* 2.9 34.3 + - - +
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Residues in contact with SER 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B PHE* 3.4 31.7 - - - -
75B PRO* 5.2 4.8 - - - +
222B MET 5.2 1.2 + - - -
223B PHE* 4.4 1.9 + - - -
224B SER* 1.3 79.3 + - - +
226B VAL* 1.3 60.9 + - - +
228B LYS* 4.3 7.5 - - - +
229B HIS* 3.5 21.0 + - - -
42C PHE* 3.8 7.1 - - - -
75C PRO* 5.8 0.2 - - - +
225C SER* 4.1 29.5 + - - -
226C VAL* 4.5 0.5 - - - +
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Residues in contact with VAL 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B PHE* 4.1 12.6 - - + -
223B PHE* 3.0 8.7 + - + +
225B SER* 1.3 86.2 + - - +
227B MET* 1.3 67.7 + - + +
228B LYS 3.2 2.0 - - - -
229B HIS* 3.0 21.7 + - - +
230B LEU* 3.7 24.5 - - + +
42C PHE* 4.1 28.3 - - + -
226C VAL* 3.8 27.4 - - + -
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Residues in contact with MET 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216B THR* 4.2 17.0 - - + +
219B LEU* 4.0 24.0 - - + -
220B TYR* 3.6 45.5 - - + +
223B PHE* 2.9 26.7 + - + +
226B VAL* 1.3 76.8 - - + +
228B LYS* 1.3 63.7 + - - +
229B HIS 3.0 0.9 + - - -
230B LEU* 3.1 22.9 + - + +
234B GLN* 3.0 53.2 - - + +
235B GLN* 3.8 1.4 + - - -
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Residues in contact with LYS 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109B TRP* 4.5 15.5 + - + +
220B TYR* 3.2 27.9 + - - +
224B SER* 2.9 25.9 + - - +
225B SER* 4.3 6.8 - - - +
227B MET* 1.3 77.8 - - - +
229B HIS* 1.3 92.4 + - + +
235B GLN* 3.0 16.9 + - - +
238B PHE* 4.1 12.2 - - + -
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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