Contacts of the helix formed by residues 203 - 209 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101A ASP* 2.7 36.9 + - - +
102A GLY* 6.4 0.7 - - - -
127A PRO* 4.2 17.2 - - - +
129A ASP 4.6 3.8 + - - -
130A ARG* 5.6 2.0 + - - +
156A ASN* 5.6 2.6 - - - +
157A LEU* 3.6 30.1 - - - +
200A GLU* 5.6 5.8 - - - +
201A GLY 5.1 2.2 - - - +
202A MSE 1.3 74.6 - - - +
204A ARG* 1.3 67.0 + - - +
205A LEU* 4.5 7.9 - - + +
206A THR* 2.9 20.4 + - - +
207A ARG* 3.1 9.4 + - - +
170D TRP* 3.7 37.8 - - - -
211D ASP* 5.1 7.8 + - - +
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Residues in contact with ARG 204 (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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202A MSE 3.6 0.6 + - - -
203A ARG* 1.3 73.0 - - - +
205A LEU* 1.3 75.8 + - - +
207A ARG* 3.1 38.9 + - - +
208A GLU* 2.7 73.0 + - - +
179D ASP* 4.6 18.5 + - - +
213D LEU* 6.3 1.6 - - - +
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Residues in contact with LEU 205 (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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156A ASN* 5.1 7.4 - - - +
158A ALA* 4.2 18.8 - - + -
203A ARG* 3.1 6.8 + - + +
204A ARG* 1.3 89.7 - - - +
206A THR* 1.3 61.1 + - - +
208A GLU* 3.2 19.1 + - - +
209A HIS* 2.8 51.9 + - + -
208D GLU* 5.3 10.1 - - + +
210D CYS 5.6 5.4 - - - +
211D ASP* 6.4 1.1 - - - -
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Residues in contact with THR 206 (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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101A ASP* 3.3 16.9 + - - +
157A LEU* 3.2 25.3 - - + +
158A ALA* 5.7 1.3 + - - +
161A MSE 3.3 33.2 - - + +
194A VAL* 3.9 16.6 - - + -
202A MSE 3.6 25.4 - - + -
203A ARG* 2.9 19.1 + - - -
205A LEU* 1.3 78.4 - - - +
207A ARG* 1.3 62.6 + - - +
209A HIS* 3.2 9.8 + - - -
210A CYS* 3.6 2.1 - - - -
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Residues in contact with ARG 207 (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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175A ALA* 4.8 1.3 - - - -
177A GLU* 2.8 33.4 + - - -
202A MSE 3.4 42.9 + - + -
203A ARG 3.1 8.4 + - - +
204A ARG* 3.1 48.7 - - - +
206A THR* 1.3 77.7 - - - +
208A GLU* 1.3 67.3 + - + +
209A HIS 3.3 0.2 - - - -
210A CYS* 3.5 17.8 - - - +
213A LEU* 3.7 26.3 - - + +
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Residues in contact with GLU 208 (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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204A ARG* 2.7 63.7 + - + +
205A LEU* 3.6 14.1 - - - +
206A THR 3.1 0.6 - - - -
207A ARG* 1.3 80.8 + - + +
209A HIS* 1.3 63.8 + - + +
210A CYS 3.1 9.9 + - - +
204B ARG* 3.3 17.7 + - - +
207B ARG* 5.1 3.3 + - - -
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Residues in contact with HIS 209 (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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158A ALA* 3.7 36.6 - - + +
161A MSE 3.7 32.1 - - + +
162A ARG* 3.8 31.1 + - + -
165A GLN* 3.0 24.9 + - - +
171A ILE* 4.0 1.0 - - - +
205A LEU* 2.8 46.5 + - + +
206A THR 3.2 1.0 + - - -
208A GLU* 1.3 82.6 - - + +
210A CYS* 1.3 56.7 + - - -
204B ARG* 3.3 20.8 - - - +
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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