Contacts of the helix formed by residues 205 - 215 (chain A) in PDB entry 5GRH
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 LEU 205 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171A VAL* 3.6 26.5 - - + -
172A HIS 2.8 14.5 + - - +
173A LYS* 3.7 25.6 - - + -
203A MET 3.8 0.2 + - - -
204A TYR* 1.3 71.6 - - - +
206A ASP* 1.3 58.9 + - - +
208A VAL* 3.2 3.1 + - - +
209A CYS* 3.0 40.0 + - - -
224A MET* 6.1 0.7 - - + -
228A TYR* 4.1 27.6 - - + -
232A LEU* 4.2 22.0 - - + -
237B TYR 4.2 5.8 - - - +
240B ILE* 3.9 31.4 - - + -
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Residues in contact with ASP 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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173A LYS* 3.8 25.6 + - - -
175A ASN* 5.0 0.5 - - - +
204A TYR* 3.6 18.8 - - - +
205A LEU* 1.3 70.9 + - - +
207A THR* 1.3 56.4 + - - +
209A CYS* 3.2 4.9 + - - +
210A LEU* 2.8 34.5 + - - +
238B GLY 4.0 12.7 + - - +
239B ASN* 4.2 9.4 + - - +
240B ILE* 5.5 0.4 - - - +
243B ASN* 3.0 38.7 + - + +
272B ARG* 6.1 1.0 - - - +
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Residues in contact with THR 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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203A MET* 3.5 18.6 - - + -
204A TYR* 3.2 27.3 + - - +
206A ASP* 1.3 77.1 + - - +
208A VAL* 1.3 60.0 + - - +
210A LEU* 3.5 13.7 - - + +
211A ASN* 2.9 40.9 + - - +
243B ASN* 4.7 0.6 - - - +
273B ASN* 5.1 12.1 + - - +
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Residues in contact with VAL 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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169A THR* 5.5 0.4 - - + -
171A VAL* 4.0 21.1 - - + -
203A MET* 3.4 34.3 - - + -
204A TYR 3.0 18.5 + - - +
205A LEU* 3.4 8.5 - - - +
207A THR* 1.3 77.4 - - - +
209A CYS* 1.3 52.6 + - - +
211A ASN* 3.4 0.7 + - - -
212A MET* 2.7 50.8 + - + +
219A PHE* 3.9 17.4 - - + -
222A LEU* 4.5 3.6 - - + -
232A LEU* 4.3 21.5 - - + -
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Residues in contact with CYS 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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205A LEU* 3.0 23.3 + - - -
206A ASP* 3.5 9.6 - - - +
208A VAL* 1.3 74.5 - - - +
210A LEU* 1.3 65.0 + - - +
212A MET* 3.6 5.5 - - - +
213A VAL* 3.1 31.7 + - - +
232A LEU* 4.0 22.4 - - - -
235A LEU* 4.1 6.5 - - - -
240B ILE* 4.1 37.7 - - - +
243B ASN* 4.6 1.8 - - + -
244B VAL* 3.9 17.7 - - + -
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Residues in contact with LEU 210 (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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206A ASP 2.8 20.0 + - - +
207A THR* 3.5 14.8 - - + +
208A VAL 3.3 0.2 - - - -
209A CYS* 1.3 75.3 - - - +
211A ASN* 1.3 71.5 + - - +
213A VAL* 3.8 3.8 + - - +
214A GLN* 3.5 24.5 + - - +
243B ASN* 3.6 29.7 - - - +
246B ALA* 4.2 7.6 - - + -
247B GLY* 3.5 29.5 - - - +
252B PRO* 4.1 37.2 - - + -
271B THR* 5.2 3.6 - - - +
273B ASN* 5.7 4.9 - - - +
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Residues in contact with ASN 211 (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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203A MET* 3.5 18.6 - - - +
207A THR* 2.9 29.5 + - - +
210A LEU* 1.3 86.1 - - - +
212A MET* 1.3 57.9 + - - +
214A GLN* 3.1 14.7 + - - +
215A ASP 2.7 37.2 + - - +
218A GLN* 3.4 26.6 + - - +
219A PHE* 3.8 11.4 - - + -
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Residues in contact with MET 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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110A TYR* 4.3 0.3 - - - -
115A ILE* 3.5 30.1 - - + -
208A VAL* 2.7 31.8 + - + +
209A CYS* 3.6 8.1 - - - +
210A LEU 3.4 0.2 - - - -
211A ASN* 1.3 72.6 - - - +
213A VAL* 1.3 62.4 + - - +
216A PRO* 3.3 38.4 - - - +
219A PHE* 3.5 28.4 - - + -
222A LEU* 3.9 21.8 - - + -
232A LEU* 4.8 3.4 - - + -
235A LEU* 4.1 20.0 - - + -
236A CYS* 3.9 12.1 - - - -
239A LEU* 3.8 19.3 - - + +
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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
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110A TYR* 2.9 38.8 + - - +
209A CYS 3.1 17.3 - - - +
210A LEU 3.9 5.8 - - - +
212A MET* 1.3 77.3 - - - +
214A GLN* 1.3 57.4 + - - +
235A LEU* 4.7 10.5 - - + -
239A LEU* 5.1 2.7 - - - -
118B ARG* 4.0 2.6 + - - -
119B HIS* 5.4 0.2 - - + -
222B VAL* 4.9 3.6 - - + -
244B VAL* 3.8 35.0 - - + +
247B GLY 3.7 3.8 - - - +
248B LEU* 3.2 47.3 - - + +
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Residues in contact with GLN 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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210A LEU* 3.5 19.8 + - - +
211A ASN* 3.1 19.4 + - - +
213A VAL* 1.3 80.8 - - - +
215A ASP* 1.3 58.2 + - + +
216A PRO* 4.2 0.4 - - - -
218A GLN* 5.9 0.7 - - - +
118B ARG* 2.7 31.5 + - - +
247B GLY* 3.5 18.9 + - - +
250B GLY* 3.0 29.7 + - - -
251B GLY* 3.5 15.0 - - - +
252B PRO* 4.7 3.7 - - - +
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Residues in contact with ASP 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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112A ASP* 3.3 14.2 - - - +
211A ASN 2.7 14.8 + - - +
214A GLN* 1.3 79.2 - - + +
216A PRO* 1.3 62.0 - - - +
217A SER* 2.9 26.1 + - - -
218A GLN* 2.9 43.1 + - - +
219A PHE* 4.3 0.2 - - - -
118B ARG* 4.1 4.2 + - - +
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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