Contacts of the helix formed by residues 203 - 209 (chain D) in PDB entry 1GZ0
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 203 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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165C GLN* 5.6 6.0 + - + -
168C ASN* 3.5 27.1 + - - +
169C ILE 6.0 2.0 - - - -
170C TRP* 3.7 28.3 - - + +
211C ASP* 3.6 11.9 - - - +
101D ASP* 3.3 22.4 + - - +
127D PRO* 3.1 37.4 - - - +
129D ASP* 3.3 22.6 + - - -
130D ARG* 3.9 18.3 - - - +
157D LEU* 3.5 18.4 - - - +
201D GLY 3.9 0.2 + - - -
202D MSE 1.3 79.0 - - - +
204D ARG* 1.3 65.9 + - - +
205D LEU* 3.2 9.4 - - + +
206D THR* 3.7 11.4 + - - +
207D ARG* 3.0 21.4 + - - +
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Residues in contact with ARG 204 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162C ARG* 3.7 25.7 - - - +
165C GLN* 3.1 25.5 + - - +
208C GLU 3.3 26.0 + - - +
209C HIS* 3.6 28.5 + - - +
210C CYS 4.3 9.2 - - - +
211C ASP* 2.8 20.4 + - - +
202D MSE 3.9 0.2 + - - -
203D ARG* 1.3 72.3 - - - +
205D LEU* 1.3 70.7 + - - +
207D ARG* 3.6 29.4 + - - +
208D GLU* 2.8 58.9 + - - +
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Residues in contact with LEU 205 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162C ARG* 4.6 3.1 - - + +
165C GLN* 3.9 17.9 + - + +
166C GLU* 3.6 52.9 - - + +
211C ASP* 4.4 1.0 + - - -
158D ALA* 3.9 18.6 - - + -
203D ARG* 3.2 7.5 - - + +
204D ARG* 1.3 90.2 - - - +
206D THR* 1.3 64.4 + - - +
208D GLU* 3.3 19.6 + - - +
209D HIS* 2.9 59.2 + - + -
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Residues in contact with THR 206 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101D ASP* 2.5 29.2 + - - +
157D LEU* 3.6 16.9 - - + +
158D ALA* 5.5 3.1 + - - +
161D MSE 3.8 25.7 - - + +
194D VAL* 3.9 13.7 - - + -
202D MSE 3.9 17.9 - - + -
203D ARG* 3.3 18.5 + - - +
205D LEU* 1.3 76.8 - - - +
207D ARG* 1.3 63.3 + - - +
209D HIS* 3.2 15.7 + - - +
210D CYS* 3.5 10.7 + - - -
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Residues in contact with ARG 207 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210C CYS 5.2 4.0 + - - -
211C ASP 5.4 5.1 + - - -
175D ALA* 4.5 5.3 - - - +
177D GLU* 3.0 30.9 + - - +
202D MSE 3.7 41.1 + - + +
203D ARG 3.0 7.6 + - - +
204D ARG* 3.8 28.8 + - - +
206D THR* 1.3 78.2 - - - +
208D GLU* 1.3 64.6 + - - +
210D CYS* 3.0 21.3 + - - +
213D LEU* 3.6 35.2 - - + +
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Residues in contact with GLU 208 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205A LEU* 5.3 9.8 - - + +
162C ARG* 6.0 0.3 - - - -
204D ARG* 2.8 51.2 + - - +
205D LEU* 3.3 25.4 - - - +
207D ARG* 1.3 78.7 - - - +
209D HIS* 1.3 70.2 + - + +
210D CYS 3.2 7.2 + - - +
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Residues in contact with HIS 209 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166C GLU* 5.8 0.2 - - - -
158D ALA* 3.6 15.4 - - + +
161D MSE 4.1 23.6 - - + +
162D ARG* 2.7 54.0 + - + -
165D GLN* 2.8 38.8 + - - +
171D ILE* 4.1 2.1 - - - +
205D LEU* 2.9 41.0 + - + +
206D THR 3.2 10.0 + - - +
208D GLU* 1.3 85.7 - - + +
210D CYS* 1.3 59.3 + - - +
211D ASP 3.7 0.2 + - - -
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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