Contacts of the helix formed by residues 212 - 220 (chain A) in PDB entry 3ZYQ
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 CYS 212 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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182A CYS* 3.3 8.7 - - - +
185A CYS* 4.1 1.6 - - - -
189A PHE* 3.6 36.6 - - + -
193A CYS 3.8 10.8 - - - +
194A SER* 4.4 1.7 - - - +
196A LYS* 4.8 0.2 - - - -
211A VAL* 1.3 77.7 - - - +
213A GLU* 1.3 60.6 + - - +
214A PRO* 3.6 13.7 - - + -
215A CYS* 3.4 16.3 + - - -
216A TYR* 3.0 26.0 + - - +
1223A ZN 2.4 35.9 - - - -
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Residues in contact with GLU 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A ARG* 3.0 32.5 + - - +
192A LYS 4.2 13.9 - - - +
193A CYS 4.0 10.3 + - - +
195A SER* 4.5 6.3 + - - +
196A LYS* 3.1 35.7 + - + +
212A CYS* 1.3 72.7 - - - +
214A PRO* 1.4 73.1 - - + +
216A TYR* 3.2 8.9 + - - +
217A GLU* 3.0 30.3 + - + +
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Residues in contact with PRO 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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168A ARG* 4.9 9.9 - - - +
189A PHE* 6.1 1.1 - - + -
212A CYS* 3.6 16.2 - - + -
213A GLU* 1.4 93.2 - - + +
215A CYS* 1.3 61.1 + - - +
217A GLU* 3.3 6.2 + - + +
218A GLN* 3.0 38.2 + - - +
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Residues in contact with CYS 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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182A CYS* 3.9 2.5 - - - -
184A ALA* 3.7 25.1 - - + -
185A CYS* 3.7 15.5 - - - -
211A VAL* 4.3 2.5 - - + -
212A CYS* 3.4 7.8 + - - +
213A GLU 3.3 0.4 - - - -
214A PRO* 1.3 75.5 - - - +
216A TYR* 1.3 66.4 + - - +
218A GLN* 3.2 16.2 + - - +
219A LEU* 2.9 30.9 + - + +
1223A ZN 2.3 36.1 - - - -
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Residues in contact with TYR 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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196A LYS* 3.8 40.6 - - + -
197A TYR 3.5 28.3 - - - -
198A SER* 4.2 3.8 - - - -
211A VAL* 3.8 7.5 - - + +
212A CYS 3.0 14.9 + - - +
213A GLU 3.2 8.3 + - - +
215A CYS* 1.3 76.8 - - - +
217A GLU* 1.3 85.9 + - + +
219A LEU* 4.6 1.1 - - - -
220A ASN* 3.0 61.3 + - + +
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Residues in contact with GLU 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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196A LYS* 5.2 6.3 + - - +
213A GLU* 3.0 23.3 + - + +
214A PRO* 3.9 5.8 - - + +
216A TYR* 1.3 94.3 - - + +
218A GLN* 1.3 63.9 + - - +
219A LEU 3.3 0.2 + - - -
220A ASN* 3.3 8.3 + - - +
221A ARG* 3.3 24.6 + - - +
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Residues in contact with GLN 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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122A GLU* 5.4 3.5 - - - +
202A LYS* 6.0 1.8 - - - +
214A PRO* 3.0 35.0 + - - +
215A CYS* 3.2 16.2 + - - +
217A GLU* 1.3 75.7 - - + +
219A LEU* 1.3 64.7 + - + +
221A ARG* 3.2 47.6 + - - +
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Residues in contact with LEU 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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184A ALA* 4.2 15.3 - - + -
198A SER* 3.7 20.0 - - - +
199A THR 3.9 11.0 - - - +
200A ILE* 4.0 32.1 - - + -
201A PRO* 5.2 4.9 - - + -
202A LYS* 4.8 14.6 - - + +
211A VAL* 4.4 3.4 - - + -
215A CYS* 2.9 24.3 + - + +
218A GLN* 1.3 81.5 - - + +
220A ASN* 1.3 74.2 + - - +
221A ARG 3.6 1.0 + - - -
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Residues in contact with ASN 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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198A SER* 2.9 29.2 + - - -
199A THR* 5.6 0.9 + - - -
216A TYR* 3.0 58.9 + - + +
217A GLU* 3.3 6.6 + - - +
219A LEU* 1.3 83.3 - - - +
221A ARG* 1.3 63.3 + - - +
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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