Contacts of the helix formed by residues 187 - 203 (chain A) in PDB entry 1OOA
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 THR 187 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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183A ASP* 5.9 2.2 - - - +
185A GLN 4.5 5.6 - - - +
186A LEU* 1.3 78.3 - - - +
188A ASP* 1.3 65.5 + - - +
189A ARG* 3.4 7.4 + - - +
190A GLU* 2.6 49.6 + - - +
191A LYS* 3.3 20.1 + - - +
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Residues in contact with ASP 188 (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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187A THR* 1.3 73.7 - - - +
189A ARG* 1.3 65.5 + - - +
191A LYS* 3.3 24.6 + - - +
192A GLU* 3.3 24.6 + - - +
195A ARG* 5.1 1.0 + - - -
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Residues in contact with ARG 189 (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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187A THR* 3.4 6.5 + - - +
188A ASP* 1.3 78.7 - - - +
190A GLU* 1.3 64.5 + - + +
192A GLU* 3.2 38.0 - - - +
193A ILE* 3.1 41.1 + - - +
196A GLN* 4.0 16.5 - - - +
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Residues in contact with GLU 190 (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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159A CYS* 6.3 0.4 - - - -
173A LEU* 4.6 10.2 - - + +
175A TYR* 2.5 43.7 + - - +
176A LEU* 3.8 15.8 - - + +
183A ASP* 4.5 4.7 - - - +
185A GLN 4.3 0.7 - - - +
186A LEU* 3.1 22.2 - - + +
187A THR* 2.6 55.8 + - - +
189A ARG* 1.3 74.9 - - + +
191A LYS* 1.3 66.1 + - - +
192A GLU 3.0 1.6 - - - -
193A ILE* 3.0 12.0 + - + +
194A ILE* 3.0 27.5 + - + +
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Residues in contact with LYS 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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156A THR* 6.4 0.9 - - + -
186A LEU* 3.3 37.7 + - + +
187A THR 3.3 10.4 + - - +
188A ASP* 3.3 27.1 + - - +
190A GLU* 1.3 77.5 - - - +
192A GLU* 1.3 56.2 + - - +
194A ILE* 3.5 12.2 + - + +
195A ARG* 3.0 56.8 + - - +
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Residues in contact with GLU 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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188A ASP 3.3 16.0 + - - +
189A ARG* 3.2 30.7 + - - +
190A GLU 3.0 0.2 - - - -
191A LYS* 1.3 75.6 - - - +
193A ILE* 1.3 65.6 + - - +
195A ARG* 2.7 40.7 + - - +
196A GLN* 2.9 34.6 + - - +
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Residues in contact with ILE 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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169A VAL* 5.5 0.2 - - + -
170A HIS* 3.6 38.1 - - + -
172A ASP* 3.6 18.8 - - - +
173A LEU* 3.8 29.4 - - + -
175A TYR* 5.0 4.3 - - + +
189A ARG* 3.2 42.6 - - - +
190A GLU* 3.0 9.6 + - - +
192A GLU* 1.3 77.1 - - - +
194A ILE* 1.3 56.4 + - - +
196A GLN* 3.2 9.6 + - - +
197A ALA* 2.9 28.1 + - - +
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Residues in contact with ILE 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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152A GLU* 3.8 23.1 - - + +
155A MET* 3.7 22.2 - - + +
156A THR* 3.7 24.5 - - - +
159A CYS* 3.8 20.6 - - - -
169A VAL* 4.4 9.2 - - + -
173A LEU* 4.5 2.7 - - + -
186A LEU* 3.5 31.9 - - + -
190A GLU 3.0 14.4 + - - +
191A LYS* 3.6 10.5 - - - +
193A ILE* 1.3 75.9 - - - +
195A ARG* 1.3 53.7 + - - +
197A ALA* 3.1 7.2 + - - +
198A ALA* 2.6 34.3 + - - +
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Residues in contact with ARG 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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148A PHE* 4.5 4.1 - - + -
152A GLU* 3.0 30.7 - - - +
188A ASP 5.1 1.2 + - - -
191A LYS* 3.0 41.3 + - - +
192A GLU* 2.7 44.9 + - - +
194A ILE* 1.3 77.3 - - - +
196A GLN* 1.3 62.0 + - + +
198A ALA* 3.9 1.2 - - - +
199A VAL* 3.1 24.4 + - - +
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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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189A ARG* 4.0 23.6 - - - +
192A GLU* 2.9 27.8 + - - +
193A ILE* 3.7 9.0 - - - +
195A ARG* 1.3 77.2 - - + +
197A ALA* 1.3 60.6 + - - +
199A VAL* 2.8 27.0 - - + +
200A GLN* 3.1 13.7 + - - +
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Residues in contact with ALA 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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155A MET* 3.6 13.2 - - + -
169A VAL* 3.6 29.8 - - + +
170A HIS* 4.6 9.4 - - + +
193A ILE 2.9 17.3 + - - +
194A ILE 3.4 4.5 - - - +
196A GLN* 1.3 75.0 - - - +
198A ALA* 1.3 67.2 + - - +
200A GLN* 3.3 3.9 + - - -
201A GLN* 2.9 32.4 + - - +
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Residues in contact with ALA 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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148A PHE* 3.8 16.2 - - + -
151A LEU* 3.3 30.2 - - + +
152A GLU* 4.1 18.6 - - + +
155A MET* 3.6 4.2 - - - +
194A ILE 2.6 19.9 + - - +
195A ARG 3.9 2.2 - - - +
197A ALA* 1.3 72.7 - - - +
199A VAL* 1.3 51.9 + - - +
201A GLN* 3.8 0.7 - - - +
202A THR* 2.3 39.7 + - - +
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Residues in contact with VAL 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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148A PHE* 3.5 16.5 - - + -
195A ARG 3.1 13.8 + - - +
196A GLN* 2.8 31.9 - - + +
198A ALA* 1.3 79.1 - - - +
200A GLN* 1.3 70.4 + - + +
202A THR* 2.8 17.0 + - - -
203A LYS* 3.7 9.4 + - - +
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Residues in contact with GLN 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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196A GLN 3.1 15.4 + - - +
197A ALA* 3.9 4.3 - - - +
199A VAL* 1.3 86.6 - - - +
201A GLN* 1.3 60.2 + - + +
203A LYS* 2.8 68.8 - - - +
204A GLU* 4.6 0.3 + - - +
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Residues in contact with GLN 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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105A HIS* 3.4 51.5 + - + +
106A LEU 4.2 7.3 + - - +
151A LEU* 4.7 4.3 - - + +
155A MET* 3.3 25.6 - - + +
168A LEU 4.0 2.9 + - - +
169A VAL 3.0 28.5 + - - -
197A ALA* 2.9 19.0 + - - +
198A ALA* 3.8 2.9 - - - +
200A GLN* 1.3 79.0 - - + +
202A THR* 1.3 59.3 - - - +
203A LYS 3.4 0.4 + - - -
204A GLU 3.9 9.4 + - - +
205A MET* 3.9 23.3 + - + +
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Residues in contact with THR 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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147A VAL* 3.7 31.5 - - + +
148A PHE* 3.6 29.7 - - + -
151A LEU* 4.4 11.9 - - + -
198A ALA 2.3 31.4 + - - +
199A VAL* 2.8 15.4 + - - +
200A GLN 3.3 0.2 - - - -
201A GLN* 1.3 73.8 - - - +
203A LYS* 1.3 60.3 + - - +
204A GLU 3.1 7.0 + - - -
205A MET* 4.2 11.3 + - + +
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Residues in contact with LYS 203 (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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199A VAL 3.7 6.2 + - - +
200A GLN* 2.8 56.6 + - - +
202A THR* 1.3 78.4 - - - +
204A GLU* 1.3 82.3 - - + +
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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