Contacts of the helix formed by residues 200 - 208 (chain A) in PDB entry 1G7U
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 VAL 200 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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198A PHE* 3.7 27.7 + - + +
199A ASP* 1.3 73.8 + - - +
201A THR* 1.3 63.9 + - - +
203A ALA* 3.8 1.1 - - - -
204A LEU* 2.9 36.8 + - + +
221A VAL* 3.8 26.7 - - + +
224A LEU* 4.3 6.5 - - + -
225A ALA* 4.3 17.7 - - + +
236A LEU* 5.3 3.4 - - + -
237A PHE 3.3 7.0 + - - +
238A ILE* 3.8 32.3 - - + -
263A PHE* 5.0 0.2 - - + -
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Residues in contact with THR 201 (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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199A ASP* 3.4 5.3 + - - -
200A VAL* 1.3 74.9 - - - +
202A HIS* 1.3 56.8 + - - +
203A ALA 2.8 3.7 + - - -
205A GLN* 2.8 36.8 + - - +
221A VAL* 5.4 3.6 - - + -
238A ILE* 3.8 11.2 - - + +
239A GLU* 3.2 39.3 + - - +
248A LYS* 4.1 9.2 - - + -
252A PRO* 4.4 2.0 - - - -
253A SER* 3.2 43.3 - - - +
254A ALA* 3.6 11.0 - - - +
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Residues in contact with HIS 202 (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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26A ASN* 3.8 19.3 + - - -
55A LYS* 6.0 0.4 + - - -
138A LYS* 4.6 11.1 - - - -
168A ARG* 3.5 12.7 + - + +
177A LEU* 3.1 18.7 - - - +
199A ASP* 3.2 24.9 + - - +
201A THR* 1.3 76.5 - - - +
203A ALA* 1.3 57.2 + - - +
205A GLN* 3.5 19.0 + - - +
237A PHE* 5.8 0.7 - + - -
239A GLU* 3.5 20.8 + - - -
252A PRO* 3.9 13.6 - - + +
300A PEP 2.9 56.1 + - - +
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Residues in contact with ALA 203 (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 2.8 24.9 - - - +
177A LEU* 3.1 19.2 - - - +
199A ASP 2.9 21.1 + - - +
200A VAL* 3.6 4.5 - - - +
201A THR 2.8 1.2 + - - -
202A HIS* 1.3 76.7 - - - +
204A LEU* 1.3 67.2 + - - +
205A GLN* 2.7 4.5 + - - -
206A CYS 3.3 2.8 + - - -
207A ARG* 2.8 36.3 - - - +
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Residues in contact with LEU 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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200A VAL* 2.9 16.1 + - + +
201A THR 4.2 0.7 - - - +
203A ALA* 1.3 77.6 - - - +
205A GLN* 1.3 64.5 + - - +
207A ARG* 2.7 27.2 + - + +
208A ASP* 2.6 45.5 - - + +
218A ARG 5.0 0.4 - - - +
219A ALA* 4.8 0.7 - - - -
220A GLN* 3.6 39.9 - - + +
221A VAL* 3.7 21.1 - - + +
224A LEU* 3.6 20.2 - - + -
253A SER* 4.0 10.8 - - - +
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Residues in contact with GLN 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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63A ARG* 5.3 6.8 + - - -
177A LEU* 5.0 0.8 - - - +
201A THR 2.8 19.2 + - - +
202A HIS* 3.5 22.7 + - - +
203A ALA 2.7 0.4 + - - -
204A LEU* 1.3 74.1 - - - +
206A CYS* 1.3 74.5 + - - +
208A ASP* 2.5 19.1 - - - +
209A PRO* 3.0 9.2 - - - +
217A ARG* 6.0 1.0 - - - -
251A GLY* 3.5 5.7 - - - +
252A PRO* 3.0 48.2 - - + +
253A SER* 4.1 11.1 - - - +
300A PEP 3.7 27.8 + - - +
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Residues in contact with CYS 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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63A ARG* 6.3 1.3 - - - -
175A ASP* 4.8 13.0 - - - +
176A ASN* 3.2 25.8 - - - +
177A LEU* 3.9 16.8 - - + +
203A ALA 3.3 2.2 + - - -
204A LEU 2.8 0.6 + - - -
205A GLN* 1.3 97.5 - - - +
207A ARG* 1.3 57.1 + - - +
209A PRO* 2.6 49.1 - - + +
300A PEP 6.2 0.7 - - - -
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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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168A ARG 3.3 8.3 + - - -
169A GLY* 3.4 2.4 - - - -
176A ASN* 3.4 16.1 + - - +
177A LEU* 3.3 21.7 - - - +
178A VAL* 3.8 8.8 + - - +
179A VAL* 2.7 57.6 - - - +
198A PHE* 3.1 18.0 - - - -
203A ALA* 2.8 39.5 - - - +
204A LEU* 2.7 24.8 + - + +
206A CYS* 1.3 74.3 - - - +
208A ASP* 1.3 62.5 + - - +
209A PRO 4.1 1.6 - - - -
210A PHE* 4.5 5.0 - - - +
224A LEU* 3.0 28.1 - - + +
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Residues in contact with ASP 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 LEU* 2.6 34.9 + - + +
205A GLN* 2.5 27.9 - - - +
207A ARG* 1.3 78.5 - - - +
209A PRO* 1.4 63.7 - - - +
210A PHE* 3.4 3.8 + - - +
213A ALA 4.3 0.7 - - - +
214A SER* 2.4 24.8 + - - -
217A ARG* 3.3 29.7 + - - +
218A ARG* 2.7 28.6 - - + +
253A SER* 4.7 2.7 + - - -
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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