Contacts of the helix formed by residues 212 - 217 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211B GLN* 1.3 73.1 - - - +
213B VAL* 1.3 67.4 + - - +
215B ASP* 2.7 32.8 + - - +
216B LEU* 2.7 21.9 + - - +
233B GLN* 2.3 40.6 + - - +
235B LYS* 3.8 30.7 - - - +
236B THR* 3.7 16.6 + - - +
308B HIS* 5.8 3.0 - - + +
311B ARG* 3.0 38.3 - - - +
331B LEU 4.3 2.6 + - - -
332B GLY 5.6 2.4 + - - -
333B HIS* 5.1 3.8 + - - -
12J A 3.0 38.4 + - - -
21K A 5.8 0.2 - - - -
22K C 3.7 18.4 - - - +
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Residues in contact with VAL 213 (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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211B GLN 3.3 1.0 + - - -
212B ARG* 1.3 70.0 - - - +
214B GLY* 1.3 59.7 + - - +
216B LEU* 2.7 35.9 + - + +
217B CYS* 2.9 15.2 + - - +
282B SER* 3.9 30.3 - - - +
285B VAL* 4.6 12.3 - - + -
286B SER* 5.3 1.1 - - - +
307B PHE* 3.9 33.4 - - + -
308B HIS* 4.6 8.1 - - - +
311B ARG* 6.4 0.2 - - - -
22K C 4.2 23.1 - - - +
23K T 4.2 14.4 - - - +
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Residues in contact with GLY 214 (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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212B ARG 3.1 1.6 - - - -
213B VAL* 1.3 81.8 - - - +
215B ASP* 1.3 60.6 + - - +
217B CYS* 3.9 7.1 + - - +
218B GLU* 3.3 20.6 - - - +
234B SER* 4.5 5.1 + - - -
282B SER* 4.5 12.8 + - - -
21K A 5.1 0.2 - - - -
22K C 3.3 26.8 + - - -
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Residues in contact with ASP 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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211B GLN* 4.1 3.3 - - - +
212B ARG* 2.7 48.7 + - - +
214B GLY* 1.3 72.9 - - - -
216B LEU* 1.3 59.3 + - - +
217B CYS 3.1 2.5 - - - -
218B GLU* 2.7 34.8 + - + +
219B MSE 3.3 13.0 + - + +
231B VAL* 4.1 20.2 - - + +
232B GLU 4.7 7.2 - - - +
233B GLN* 3.5 12.7 + - - +
234B SER* 3.7 26.7 + - - +
235B LYS* 4.8 0.3 + - - +
22K C 4.8 0.5 + - - -
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Residues in contact with LEU 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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202B ALA 5.4 0.7 - - - +
205B LEU* 4.5 9.6 - - + -
206B ALA* 4.0 25.8 - - + +
209B THR* 3.9 16.2 - - - +
211B GLN* 3.1 40.4 - - + +
212B ARG 2.7 14.3 + - - +
213B VAL* 3.1 26.7 - - + +
215B ASP* 1.3 77.9 - - - +
217B CYS* 1.3 56.3 + - - +
218B GLU 3.0 5.0 + - - -
219B MSE 3.3 35.9 + - - +
272B ILE* 4.1 20.1 + - + +
307B PHE* 4.2 7.2 - - + -
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Residues in contact with CYS 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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213B VAL* 2.9 13.9 + - - +
214B GLY 4.0 7.2 - - - +
215B ASP 3.1 0.2 - - - -
216B LEU* 1.3 76.4 - - - +
218B GLU* 1.3 64.9 + - - +
219B MSE 3.6 0.7 - - - -
270B THR* 4.4 17.9 + - - +
272B ILE* 5.1 12.4 - - - +
279B PRO* 4.9 4.2 - - - +
280B LEU* 3.6 32.9 + - - +
281B SER 4.0 0.2 - - - -
282B SER* 3.7 22.0 - - - +
285B VAL* 3.7 30.1 - - - -
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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