Contacts of the helix formed by residues 212 - 217 (chain C) in PDB entry 1Z1G
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 ARG 212 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211C GLN* 1.3 75.7 + - - +
213C VAL* 1.3 54.9 + - - +
215C ASP* 2.6 31.0 + - - +
216C LEU* 2.7 33.1 + - - +
233C GLN* 2.7 39.1 + - - +
235C LYS* 4.2 31.4 - - + +
236C THR* 4.4 8.9 + - - +
308C HIS* 4.2 19.4 - - + +
311C ARG* 3.3 25.2 - - - +
331C LEU 4.6 1.6 + - - -
332C GLY 4.9 3.0 + - - -
333C HIS* 6.3 1.0 - - - +
342C PHE* 4.8 0.4 - - - -
11K T 4.6 0.4 + - - -
12K A 2.0 56.9 + - - -
21L A 4.9 0.9 - - - +
22L G 3.7 19.3 - - - +
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Residues in contact with VAL 213 (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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211C GLN 3.4 3.9 + - - +
212C ARG* 1.3 70.5 - - - +
214C GLY* 1.3 65.7 + - - +
216C LEU* 2.8 23.3 + - + +
217C CYS* 3.0 15.5 + - - +
282C SER* 3.8 31.4 - - - +
285C VAL* 4.7 13.0 - - + -
286C SER 5.2 1.1 - - - +
307C PHE* 3.2 41.5 - - + -
308C HIS* 4.5 10.2 + - - +
22L G 4.2 10.3 + - - +
23L C 3.8 17.5 - - - +
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Residues in contact with GLY 214 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213C VAL* 1.3 82.4 - - - +
215C ASP* 1.3 63.8 + - - +
217C CYS* 3.8 8.8 + - - +
218C GLU* 3.9 11.3 + - - +
234C SER* 5.5 4.6 - - - -
282C SER* 4.4 12.1 - - - -
21L A 4.9 0.4 - - - -
22L G 2.9 26.1 + - - -
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Residues in contact with ASP 215 (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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211C GLN* 4.5 3.3 - - + +
212C ARG* 2.6 41.4 + - - +
214C GLY* 1.3 74.1 - - - +
216C LEU* 1.3 60.8 + - - +
217C CYS 3.2 0.4 - - - -
218C GLU* 2.9 26.7 + - - +
219C MSE 3.4 14.4 + - - +
231C VAL* 4.2 20.6 - - + +
232C GLU 4.3 2.1 - - - +
233C GLN* 3.9 14.7 + - - +
234C SER* 2.7 43.0 + - - -
235C LYS 4.3 1.0 + - - -
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Residues in contact with LEU 216 (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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202C ALA* 4.0 21.1 - - + +
205C LEU* 3.6 39.5 - - + +
206C ALA* 4.0 14.8 - - + +
209C THR* 4.7 8.1 - - - +
211C GLN* 5.1 4.3 - - + +
212C ARG 2.7 12.6 + - - +
213C VAL* 2.8 14.6 + - + +
215C ASP* 1.3 76.9 - - - +
217C CYS* 1.3 63.2 + - - +
218C GLU 3.0 4.2 + - - -
219C MSE 3.4 31.5 + - + +
270C THR* 5.3 0.3 - - - +
271C ILE* 5.7 0.3 - - - +
272C ILE* 3.9 32.8 + - + +
285C VAL* 5.1 3.6 - - + -
307C PHE* 4.7 9.9 - - + -
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Residues in contact with CYS 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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213C VAL* 3.0 15.3 + - - +
214C GLY 4.2 6.3 - - - +
215C ASP 3.2 0.4 - - - -
216C LEU* 1.3 83.7 - - - +
218C GLU* 1.3 58.5 + - - +
219C MSE 3.6 0.4 - - - -
270C THR* 3.6 19.9 - - - +
272C ILE* 5.2 10.8 - - - -
279C PRO* 4.8 4.0 - - - +
280C LEU* 3.9 28.7 + - - +
282C SER* 4.3 17.7 - - - +
285C VAL* 3.8 30.5 - - - -
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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