Contacts of the helix formed by residues 214 - 228 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51C THR 4.4 2.0 - - - -
210C GLN* 3.4 11.0 + - - +
211C PHE* 3.1 28.5 + - + +
213C SER* 1.3 79.1 - - - +
215C SER* 1.3 64.6 + - - +
216C THR* 3.4 14.8 - - - +
217C GLY 3.0 15.1 + - - +
218C GLN* 2.9 22.5 + - - +
233C PRO* 5.7 1.3 - - + -
477C HIS* 4.0 22.5 + - - -
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Residues in contact with SER 215 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C ASN* 5.4 0.2 + - - -
51C THR* 2.8 34.3 + - - -
52C GLU* 3.7 29.9 + - - +
213C SER 4.3 0.2 + - - -
214C THR* 1.3 71.5 - - - +
216C THR* 1.3 58.8 + - - +
218C GLN 3.2 0.5 + - - -
219C LEU* 2.8 30.2 + - - +
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Residues in contact with THR 216 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211C PHE* 4.0 10.8 - - + -
214C THR* 3.2 11.3 - - - +
215C SER* 1.3 79.5 + - - +
217C GLY* 1.3 57.9 + - - +
219C LEU* 3.6 10.1 - - + +
220C TYR* 2.8 28.8 + - - +
227C MET* 3.8 11.9 - - + -
233C PRO* 4.3 19.0 - - + +
234C GLN* 3.7 25.8 - - - +
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Residues in contact with GLY 217 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104C GLN* 5.4 0.3 + - - -
106C THR* 4.5 1.9 + - - -
211C PHE* 3.3 40.6 - - - -
212C THR* 4.4 5.0 - - - -
214C THR* 3.0 12.6 + - - +
216C THR* 1.3 78.9 - - - +
218C GLN* 1.3 62.9 + - - +
220C TYR* 3.3 15.2 - - - +
221C GLU* 3.4 14.7 + - - +
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Residues in contact with GLN 218 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51C THR* 3.5 26.2 - - - +
54C MET* 3.3 35.6 - - + +
73C LEU* 6.1 0.8 - - - +
104C GLN* 4.5 1.7 + - - -
212C THR 3.1 19.0 - - - +
214C THR 2.9 13.6 + - - +
215C SER 3.9 0.4 - - - +
217C GLY* 1.3 73.6 - - - +
219C LEU* 1.3 67.6 + - - +
220C TYR 3.1 1.3 - - - -
221C GLU* 3.2 36.3 + - - +
222C MET* 3.6 10.0 + - - +
368C MET* 3.6 17.2 - - - +
392C TYR* 5.1 3.2 + - - -
478C VAL 4.9 0.7 - - - +
479C GLY* 3.9 22.2 - - - -
480C PHE* 3.5 10.9 + - - +
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Residues in contact with LEU 219 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C TYR* 3.4 41.3 - - + +
51C THR* 3.9 16.3 - - + +
215C SER* 2.8 18.2 + - - +
216C THR* 3.6 9.6 - - + +
218C GLN* 1.3 77.1 - - - +
220C TYR* 1.3 63.2 + - - +
222C MET* 2.9 9.2 + - - +
223C PHE* 2.9 39.0 + - + +
227C MET* 3.9 22.0 - - + -
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Residues in contact with TYR 220 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105C ALA* 3.6 25.6 + - + -
106C THR* 3.4 26.5 - - - -
109C TRP* 4.1 4.2 - - - +
211C PHE* 4.5 4.5 - + + -
216C THR 2.8 13.6 + - - +
217C GLY* 3.3 13.5 - - - +
218C GLN 3.1 0.2 - - - -
219C LEU* 1.3 78.5 - - - +
221C GLU* 1.3 59.7 + - - +
224C SER* 2.9 56.7 + - - -
227C MET* 3.6 25.3 - - + -
228C LYS* 3.3 32.2 - - - +
234C GLN* 4.1 13.7 - - + -
238C PHE* 3.2 34.1 - + - -
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Residues in contact with GLU 221 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73C LEU* 4.5 5.5 - - + +
76C ARG* 2.9 48.2 + - - +
103C GLU* 5.1 0.3 - - - +
104C GLN* 3.1 31.7 + - - +
105C ALA* 2.9 34.6 + - - +
106C THR* 3.2 16.6 + - - -
217C GLY 3.4 12.1 + - - +
218C GLN* 3.2 31.9 + - - +
220C TYR* 1.3 78.3 - - - +
222C MET* 1.3 60.5 + - + +
224C SER* 5.0 2.1 + - - -
392C TYR* 4.7 8.9 + - - +
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Residues in contact with MET 222 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43C ILE 3.8 3.4 - - - +
46C TYR* 3.6 45.8 - - + +
49C LEU* 4.0 17.3 - - + -
51C THR* 3.8 27.6 - - - -
54C MET* 5.4 2.2 - - + +
73C LEU* 3.7 28.5 - - + +
74C GLY 3.4 21.5 - - - +
75C PRO* 3.3 28.1 - - - +
76C ARG* 5.6 0.5 - - - +
218C GLN 3.8 8.5 - - - +
219C LEU* 2.9 7.7 + - - +
221C GLU* 1.3 81.3 - - + +
223C PHE* 1.3 72.6 + - + +
224C SER 3.7 1.7 + - - -
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Residues in contact with PHE 223 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42C PHE* 3.8 50.3 - + + -
43C ILE* 4.0 26.7 - - + -
46C TYR* 3.9 16.2 - + - -
74C GLY* 3.9 5.8 - - - -
75C PRO* 4.7 0.4 - - + -
219C LEU* 2.9 39.9 + - + +
220C TYR 3.7 0.7 - - - -
222C MET* 1.3 98.1 - - + +
224C SER* 1.3 64.6 + - - +
225C SER* 3.2 7.6 - - - -
226C VAL* 3.1 9.9 + - + -
227C MET* 3.0 33.6 + - + +
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Residues in contact with SER 224 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C GLU* 5.0 3.3 + - - -
105C ALA* 3.8 13.8 - - - +
220C TYR* 2.9 52.1 + - - -
221C GLU 5.1 2.1 + - - -
222C MET 3.7 1.2 - - - -
223C PHE* 1.3 75.9 - - - +
225C SER* 1.3 61.3 + - - +
228C LYS* 2.8 41.5 + - - +
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Residues in contact with SER 225 (chain C).
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* 4.0 6.1 - - - -
75B PRO* 5.5 0.5 - - - +
225B SER* 4.1 30.0 + - - -
42C PHE* 4.5 8.0 - - - -
75C PRO* 5.5 4.8 - - - +
223C PHE* 3.2 4.7 + - - -
224C SER* 1.3 80.0 + - - +
226C VAL* 1.3 68.4 + - - +
228C LYS* 4.6 10.0 - - - +
229C HIS* 3.4 22.5 + - - -
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Residues in contact with VAL 226 (chain C).
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* 3.8 31.7 - - + -
225B SER* 4.5 0.2 - - - +
226B VAL* 3.8 29.8 - - + -
42C PHE* 4.2 11.9 - - + -
223C PHE* 3.1 7.9 + - + +
225C SER* 1.3 87.4 + - - +
227C MET* 1.3 61.7 + - + +
228C LYS 3.2 1.6 - - - -
229C HIS* 3.0 27.4 + - - +
230C LEU* 3.7 24.0 - - + +
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Residues in contact with MET 227 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216C THR* 3.8 39.3 - - + +
219C LEU* 3.8 29.6 - - + +
220C TYR* 3.6 33.9 - - + +
223C PHE* 3.0 25.7 + - + +
226C VAL* 1.3 75.6 - - + +
228C LYS* 1.3 61.1 + - - +
229C HIS 2.9 6.8 + - - -
230C LEU* 3.1 25.2 + - + +
234C GLN* 3.0 36.4 - - - +
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Residues in contact with LYS 228 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108C ASP* 5.7 2.8 + - - -
109C TRP* 4.6 14.8 + - + +
220C TYR* 3.3 27.9 - - - +
224C SER* 2.8 32.0 + - - +
225C SER* 4.6 8.8 - - - +
227C MET* 1.3 71.5 - - - +
229C HIS* 1.3 90.3 + - + +
230C LEU 3.5 0.2 - - - -
235C GLN* 3.1 16.2 + - - +
238C PHE* 4.0 14.8 - - + -
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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