Contacts of the helix formed by residues 211 - 221 (chain A) in PDB entry 1ZGA
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 GLY 211 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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205A ASP* 5.4 0.2 - - - -
208A GLY 2.9 12.9 + - - -
209A GLY 3.3 1.6 + - - -
210A THR* 1.3 79.4 - - - +
212A GLY* 1.3 58.7 + - - +
213A VAL 3.2 2.7 - - - -
214A THR* 3.2 4.1 + - - +
215A LYS* 2.8 32.2 + - - +
228A VAL* 3.9 23.5 - - - +
244A LEU* 5.9 0.9 - - - -
246A PHE* 4.3 3.4 - - - -
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Residues in contact with GLY 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208A GLY 4.1 2.8 + - - -
210A THR* 3.6 7.2 + - - +
211A GLY* 1.3 76.8 - - - +
213A VAL* 1.3 61.5 + - - +
215A LYS* 3.3 8.6 + - - +
216A LEU* 3.2 28.1 + - - +
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Residues in contact with VAL 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A PHE* 3.7 25.8 - - + -
205A ASP* 3.6 18.4 - - - +
208A GLY* 4.9 5.5 + - - +
211A GLY 3.2 0.2 - - - -
212A GLY* 1.3 71.5 - - - +
214A THR* 1.3 67.2 + - - +
216A LEU* 3.1 13.3 + - + +
217A ILE* 2.9 35.1 + - + +
262A LEU* 4.2 5.8 - - + -
264A LYS* 3.9 18.2 - - + +
3994A SAH 3.0 32.1 - - - +
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Residues in contact with THR 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205A ASP* 3.1 26.2 + - - +
211A GLY* 3.2 7.9 + - - +
213A VAL* 1.3 79.7 - - - +
215A LYS* 1.3 59.1 + - - +
217A ILE* 3.1 12.4 + - - +
218A HIS* 2.8 48.2 + - + +
226A CYS* 3.5 23.9 - - + +
228A VAL* 3.3 18.9 - - + +
244A LEU* 3.6 16.8 - - + -
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Residues in contact with LYS 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211A GLY 2.8 17.0 + - - +
212A GLY* 3.4 9.4 - - - +
214A THR* 1.3 78.9 - - - +
216A LEU* 1.3 63.8 + - + +
218A HIS* 3.2 10.6 + - + +
219A GLU* 3.0 39.2 + - + +
244A LEU* 6.6 0.4 - - - -
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Residues in contact with LEU 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183A SER* 3.7 26.0 - - - +
184A ARG* 4.5 7.6 - - - -
186A PHE* 4.3 14.4 - - + -
187A LYS* 4.3 20.4 - - + +
190A LEU* 3.9 10.8 - - + -
212A GLY 3.2 16.5 + - - +
213A VAL* 3.1 14.2 + - + +
215A LYS* 1.3 82.2 - - + +
217A ILE* 1.3 64.8 + - - +
219A GLU* 3.0 32.7 + - - +
220A ILE* 3.0 20.1 - - - +
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Residues in contact with ILE 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186A PHE* 4.4 3.1 - - + -
190A LEU* 3.8 21.1 - - + -
197A PHE* 4.9 6.1 - - + -
203A LEU* 4.5 17.0 - - + -
213A VAL* 2.9 23.1 + - + +
214A THR* 3.1 17.0 + - - +
216A LEU* 1.3 77.2 - - - +
218A HIS* 1.3 56.7 + - - +
220A ILE 3.2 2.3 + - - -
221A PHE* 2.8 37.7 + - + +
224A LEU* 3.9 28.3 - - + -
226A CYS* 4.0 8.3 - - - -
262A LEU* 3.6 31.0 - - + -
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Residues in contact with HIS 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214A THR* 2.8 32.2 + - + +
215A LYS* 3.6 9.0 - - - +
216A LEU 3.2 0.2 - - - -
217A ILE* 1.3 71.0 - - - +
219A GLU* 1.3 63.5 + - - +
220A ILE 3.1 2.2 - - - -
221A PHE 3.6 12.7 + - - -
222A PRO* 3.3 32.3 + - + +
224A LEU 2.8 29.5 + - - -
226A CYS* 3.4 21.3 - - - +
241A ASN* 5.8 0.9 - - - -
243A ASN* 3.0 27.1 + - + -
244A LEU* 3.9 16.9 - - + +
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Residues in contact with GLU 219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187A LYS* 3.4 31.9 + - - +
215A LYS* 3.0 35.4 + - + +
216A LEU* 3.0 28.2 + - - +
218A HIS* 1.3 78.8 - - - +
220A ILE* 1.3 66.2 + - + +
222A PRO* 4.7 2.7 - - - +
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Residues in contact with ILE 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187A LYS* 3.8 28.5 - - + -
190A LEU* 4.1 15.5 - - + +
191A GLN* 4.2 18.4 - - + -
194A LYS* 3.3 30.8 + - + +
216A LEU 3.0 19.1 - - - +
217A ILE 3.2 2.1 + - - +
219A GLU* 1.3 89.4 - - + +
221A PHE* 1.3 93.9 + - + +
222A PRO* 3.3 11.4 - - - +
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Residues in contact with PHE 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190A LEU* 4.5 11.4 - - + -
194A LYS* 3.7 37.5 - - + -
197A PHE* 3.6 48.9 - + + -
198A GLU* 4.6 8.5 - - + -
217A ILE* 2.8 29.5 + - + +
218A HIS* 3.6 11.1 + - - -
220A ILE* 1.3 100.6 - - + +
222A PRO* 1.3 64.4 - - - +
223A HIS 3.2 3.6 - - - -
224A LEU* 3.1 30.9 + - + +
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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