Contacts of the helix formed by residues 190 - 206 (chain A) in PDB entry 3GJ0
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 ASP 190 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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188A VAL* 3.4 8.0 + - - +
189A MET* 1.3 74.2 - - - +
191A PRO* 1.3 72.4 - - - +
192A ALA* 3.3 13.5 + - - +
193A LEU* 3.0 38.8 + - + +
194A ALA* 2.9 26.7 + - - +
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Residues in contact with PRO 191 (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 VAL* 5.3 6.1 - - + -
189A MET 3.2 8.7 - - - +
190A ASP* 1.3 92.6 - - - +
192A ALA* 1.3 56.7 + - - +
194A ALA* 3.4 7.5 + - + +
195A ALA* 3.0 29.1 + - - +
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Residues in contact with ALA 192 (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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190A ASP* 3.3 12.8 + - - +
191A PRO* 1.3 80.6 - - - +
193A LEU* 1.3 58.4 + - - +
195A ALA* 3.3 7.7 + - - +
196A GLN* 3.0 27.6 + - - +
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Residues in contact with LEU 193 (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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124A VAL 4.1 10.3 - - - +
125A ASP 5.3 6.3 - - - +
127A LYS* 5.3 20.6 - - + -
189A MET* 4.2 6.5 - - + -
190A ASP* 3.0 29.7 + - + +
192A ALA* 1.3 73.4 - - - +
194A ALA* 1.3 65.3 + - - +
196A GLN* 3.2 22.6 + - - +
197A TYR* 2.9 66.5 + - + +
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Residues in contact with ALA 194 (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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155A TYR* 3.7 31.8 + - + -
189A MET* 3.9 17.1 - - + +
190A ASP 2.9 13.7 + - - +
191A PRO* 3.6 11.9 - - + +
193A LEU* 1.3 77.3 - - - +
195A ALA* 1.3 61.9 + - - +
197A TYR* 3.3 3.6 + - - +
198A GLU* 2.9 33.4 + - - +
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Residues in contact with ALA 195 (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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191A PRO 3.0 17.3 + - - +
192A ALA* 3.6 6.7 - - - +
194A ALA* 1.3 75.6 - - - +
196A GLN* 1.3 62.2 + - - +
198A GLU* 3.3 14.1 + - - +
199A HIS* 3.1 23.7 + - - +
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Residues in contact with GLN 196 (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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132A LYS* 5.6 5.1 - - - +
192A ALA 3.0 14.5 + - - +
193A LEU* 3.6 24.5 - - - +
195A ALA* 1.3 76.7 - - - +
197A TYR* 1.3 70.8 + - - +
199A HIS* 3.3 6.8 + - + +
200A ASP* 2.9 54.9 + - - +
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Residues in contact with TYR 197 (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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124A VAL* 3.6 22.9 + - + -
126A ILE 4.6 0.9 + - - -
127A LYS 4.4 8.0 + - - -
129A ARG* 3.4 53.3 - - - +
132A LYS* 4.7 10.4 + - - -
133A ALA* 5.0 0.5 - - - +
148A ASP* 3.5 14.4 - - - +
155A TYR* 5.0 4.0 - + - +
189A MET* 4.0 14.1 - - + -
193A LEU* 2.9 53.5 + - + +
194A ALA* 3.7 4.5 - - - +
196A GLN* 1.3 91.3 - - - +
198A GLU* 1.3 62.0 + - - +
200A ASP* 3.3 10.9 + - + +
201A LEU* 3.0 29.5 + - - +
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Residues in contact with GLU 198 (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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155A TYR* 2.6 35.5 + - - +
156A ASN* 4.7 7.0 - - - +
194A ALA* 2.9 24.4 + - - +
195A ALA* 3.7 12.2 - - - +
196A GLN 3.2 0.4 - - - -
197A TYR* 1.3 77.0 - - - +
199A HIS* 1.3 63.7 + - - +
201A LEU* 3.3 13.8 + - + +
202A GLU* 3.1 30.7 + - - +
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Residues in contact with HIS 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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195A ALA 3.1 13.6 + - - +
196A GLN* 3.6 9.9 - - + +
198A GLU* 1.3 77.2 - - - +
200A ASP* 1.3 71.8 + - - +
202A GLU* 3.0 23.0 + - - +
203A VAL* 3.0 46.2 + - + +
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Residues in contact with ASP 200 (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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132A LYS* 5.8 3.6 - - - -
133A ALA* 3.6 18.0 - - + +
196A GLN* 2.9 48.4 + - - +
197A TYR* 3.6 14.0 - - + +
198A GLU 3.3 0.2 - - - -
199A HIS* 1.3 86.9 - - - +
201A LEU* 1.3 56.0 + - - +
203A VAL* 3.5 6.9 + - - +
204A ALA* 3.0 27.9 + - - +
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Residues in contact with LEU 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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133A ALA* 3.7 25.4 - - + +
136A ILE* 5.1 3.1 - - + +
139A HIS* 6.2 2.2 - - + +
146A TYR* 3.7 34.1 - - + +
147A TYR* 5.4 1.1 - - - -
148A ASP* 3.8 32.1 - - + +
197A TYR 3.0 19.6 + - - +
198A GLU* 3.6 13.2 - - + +
199A HIS 3.2 0.2 - - - -
200A ASP* 1.3 72.8 - - - +
202A GLU* 1.3 60.6 + - + +
204A ALA* 3.3 4.1 + - + +
205A GLN* 2.9 31.5 + - - +
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Residues in contact with GLU 202 (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 GLU* 3.1 22.7 + - - +
199A HIS* 3.0 24.9 + - + +
201A LEU* 1.3 75.4 - - - +
203A VAL* 1.3 65.5 + - + +
205A GLN* 3.3 7.0 + - - +
206A THR* 3.2 28.3 + - - +
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Residues in contact with VAL 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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199A HIS* 3.0 49.6 + - + +
200A ASP* 3.9 5.8 - - - +
202A GLU* 1.3 75.8 - - + +
204A ALA* 1.3 64.6 + - - +
206A THR* 3.0 20.0 + - - +
207A THR 3.2 17.2 + - - +
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Residues in contact with ALA 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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133A ALA* 3.8 26.2 - - + +
134A LYS* 4.6 6.7 - - - +
140A ARG* 4.0 22.7 + - - +
200A ASP 3.0 18.1 + - - +
201A LEU* 3.6 7.9 - - + +
202A GLU 3.3 0.2 - - - -
203A VAL* 1.3 79.3 - - - +
205A GLN* 1.3 58.5 + - - +
207A THR* 2.8 23.6 + - - +
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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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139A HIS* 3.5 16.5 + - - -
140A ARG* 3.3 44.4 + - - +
201A LEU 2.9 18.3 + - - +
202A GLU* 3.6 7.9 - - - +
203A VAL 3.2 0.2 - - - -
204A ALA* 1.3 77.7 - - - +
206A THR* 1.3 61.5 + - + +
207A THR* 3.0 5.1 + - - -
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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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202A GLU* 3.2 13.0 + - + +
203A VAL* 3.0 17.0 + - - +
205A GLN* 1.3 77.2 - - + +
207A THR* 1.3 69.9 + - - +
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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