Contacts of the helix formed by residues 198 - 208 (chain A) in PDB entry 3GBG
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 ASN 198 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192A CYS* 4.1 3.4 - - - -
197A THR* 1.3 78.0 - - - +
199A ARG* 1.3 60.6 + - - +
200A MET* 2.9 18.5 - - + +
201A ILE* 2.8 58.7 + - - +
202A LEU* 3.2 18.2 + - - +
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Residues in contact with ARG 199 (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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188A TRP* 3.3 64.1 - - + +
192A CYS* 3.6 18.9 - - - -
198A ASN* 1.3 70.6 - - - +
200A MET* 1.3 61.3 + - + +
201A ILE 3.1 2.2 - - - -
202A LEU* 4.3 4.5 - - - +
203A LYS* 2.8 39.9 + - + +
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Residues in contact with MET 200 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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198A ASN* 2.9 14.2 - - + +
199A ARG* 1.3 80.1 - - + +
201A ILE* 1.3 60.3 + - + +
203A LYS* 3.6 42.7 + - - +
204A LYS* 4.6 4.5 + - - +
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Residues in contact with ILE 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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197A THR* 4.0 20.2 - - + -
198A ASN* 2.8 36.0 - - - +
200A MET* 1.3 82.3 - - + +
202A LEU* 1.3 63.5 + - + +
203A LYS 3.5 0.2 - - - -
204A LYS* 2.9 39.5 + - - +
205A GLU* 5.5 0.2 - - - +
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Residues in contact with LEU 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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170A ALA* 4.4 21.1 - - + -
173A LYS* 6.4 0.2 - - + -
174A ILE* 4.5 7.1 - - + +
188A TRP* 3.7 23.7 - - + -
191A ILE* 3.8 27.4 - - + -
192A CYS* 4.3 6.5 - - - -
195A LEU* 4.3 18.6 - - + -
197A THR* 3.8 42.0 - - + +
198A ASN 3.2 11.6 + - - +
199A ARG 4.2 0.2 - - - +
201A ILE* 1.3 76.2 - - + +
203A LYS* 1.3 63.8 + - - +
204A LYS 2.9 5.6 + - - -
205A GLU* 3.0 24.0 + - - +
206A LEU* 4.2 1.0 + - - +
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Residues in contact with LYS 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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188A TRP* 3.8 20.3 - - + -
199A ARG* 2.8 32.7 + - + +
200A MET* 3.6 45.4 + - - +
202A LEU* 1.3 72.7 - - - +
204A LYS* 1.3 64.4 + - + +
206A LEU* 3.2 5.1 + - - +
207A GLU* 3.0 57.9 + - + +
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Residues in contact with LYS 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 MET 4.6 3.0 + - - +
201A ILE* 2.9 43.9 + - - +
202A LEU 2.9 1.7 + - - +
203A LYS* 1.3 83.4 - - + +
205A GLU* 1.3 83.6 + - - +
207A GLU* 4.1 12.6 - - - +
208A SER* 2.9 29.7 + - - -
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Residues in contact with GLU 205 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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169A ASP* 4.3 6.1 - - - +
170A ALA* 3.4 35.5 + - + +
171A MET* 3.6 31.2 + - - +
174A ILE* 4.2 6.7 - - + -
202A LEU* 3.0 15.7 + - - +
204A LYS* 1.3 97.5 - - + +
206A LEU* 1.3 66.2 + - + +
208A SER* 3.3 2.7 + - - -
209A ARG* 2.8 49.2 + - - +
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Residues in contact with LEU 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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171A MET* 5.3 1.3 - - - -
174A ILE* 4.5 7.4 - - + -
188A TRP* 3.8 37.5 - - + +
202A LEU 4.3 0.9 - - - +
203A LYS 3.2 5.5 + - - +
205A GLU* 1.3 85.5 - - + +
207A GLU* 1.3 68.5 + - + +
209A ARG* 3.0 4.3 + - - +
210A GLY 2.9 16.8 + - - -
211A VAL* 3.1 33.8 + - + +
212A LYS* 4.0 2.0 - - - +
213A PHE* 3.7 37.5 - - + +
216A LEU* 3.8 30.1 - - + -
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Residues in contact with GLU 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 LYS* 3.0 60.8 + - + +
204A LYS* 3.9 9.5 - - - +
206A LEU* 1.3 76.5 - - + +
208A SER* 1.3 55.1 + - - +
210A GLY* 2.8 24.5 + - - +
211A VAL 5.0 1.8 - - - +
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Residues in contact with SER 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 LYS* 2.9 19.7 + - - -
205A GLU* 3.3 8.8 + - - -
207A GLU* 1.3 75.6 - - - +
209A ARG* 1.3 73.2 + - - +
210A GLY 3.3 0.6 + - - -
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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