Contacts of the helix formed by residues 185 - 201 (chain A) in PDB entry 3TR6
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 SER 185 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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174A ARG* 4.5 5.4 + - - -
177A GLN* 4.2 5.0 + - - -
183A ASN* 2.8 27.5 + - - -
184A GLN* 1.3 79.4 - - - +
186A GLU* 1.3 66.6 + - - +
187A ASN* 4.5 2.4 + - - -
188A ASN* 3.0 25.3 + - - +
189A GLN* 3.1 8.7 + - - +
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Residues in contact with GLU 186 (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 ALA* 6.5 0.4 - - + -
184A GLN 3.5 2.9 + - - -
185A SER* 1.3 73.1 - - - +
187A ASN* 1.3 71.8 + - + +
189A GLN* 3.4 7.0 + - - +
190A LEU* 3.2 37.4 + - + +
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Residues in contact with ASN 187 (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 LYS* 3.7 26.3 - - - +
148A ALA* 4.0 24.3 + - - +
174A ARG* 3.5 25.5 - - - +
185A SER* 3.3 2.7 + - - +
186A GLU* 1.3 82.7 - - - +
188A ASN* 1.3 64.5 + - - +
190A LEU* 3.3 11.4 + - - +
191A ILE* 3.2 28.3 + - - +
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Residues in contact with ASN 188 (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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174A ARG* 3.5 20.8 + - - +
177A GLN* 3.3 44.3 + - - +
178A VAL* 3.5 4.5 + - - +
180A ASP 3.9 1.4 + - - -
183A ASN* 3.5 20.8 - - - +
184A GLN 4.3 3.6 - - - +
185A SER* 3.0 27.7 + - - +
187A ASN* 1.3 78.7 - - - +
189A GLN* 1.3 58.8 + - - +
191A ILE* 3.4 2.1 + - - +
192A ARG* 3.0 47.2 + - - +
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Residues in contact with GLN 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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181A GLU* 4.0 4.0 - - - +
184A GLN* 3.3 50.3 + - - +
185A SER 3.1 13.2 + - - +
186A GLU* 3.8 10.8 - - - +
187A ASN 3.3 0.2 - - - -
188A ASN* 1.3 74.2 + - - +
190A LEU* 1.3 60.6 + - + +
192A ARG* 3.9 24.8 + - - +
193A LEU* 3.0 30.4 + - - +
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Residues in contact with LEU 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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147A LYS 4.7 2.0 - - - +
148A ALA* 3.7 38.8 - - + +
186A GLU* 3.2 33.9 + - + +
187A ASN* 3.6 17.9 - - - +
188A ASN 3.3 0.2 - - - -
189A GLN* 1.3 78.9 - - + +
191A ILE* 1.3 63.6 + - + +
193A LEU* 3.5 16.1 + - + +
194A PHE* 2.9 28.1 + - - +
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Residues in contact with ILE 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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147A LYS* 4.4 15.3 - - + +
150A THR* 4.0 30.3 - - + +
171A ASN 4.3 6.1 - - - +
172A VAL* 3.6 36.8 - - + +
174A ARG* 3.9 25.6 - - + +
178A VAL* 4.1 5.6 - - + -
187A ASN 3.2 16.4 + - - +
188A ASN 3.4 1.3 + - - +
190A LEU* 1.3 79.2 - - + +
192A ARG* 1.3 61.9 + - - +
194A PHE* 3.6 7.8 - - + +
195A ASN* 2.9 36.3 + - - +
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Residues in contact with ARG 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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178A VAL* 2.8 47.8 + - + +
179A ALA* 4.4 5.1 + - - +
181A GLU* 3.5 48.5 + - - +
188A ASN* 3.0 35.1 + - - +
189A GLN* 3.9 22.0 + - - +
191A ILE* 1.3 75.5 - - - +
193A LEU* 1.3 62.8 + - - +
195A ASN* 4.0 3.9 - - - +
196A GLN* 3.4 28.9 + - - +
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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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189A GLN 3.0 19.1 + - - +
190A LEU* 3.6 17.3 - - + +
192A ARG* 1.3 77.8 - - - +
194A PHE* 1.3 61.6 + - - +
196A GLN* 3.6 6.2 + - + +
197A LYS* 3.2 22.2 + - + +
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Residues in contact with PHE 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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150A THR* 3.8 26.0 - - - +
151A ASP* 4.0 22.7 - - + +
154A TYR* 3.8 39.3 - + + -
169A VAL* 4.2 29.4 - - + -
172A VAL* 4.5 6.5 - - + -
190A LEU 2.9 19.1 + - - +
191A ILE* 3.6 10.8 - - + +
192A ARG 3.2 0.4 - - - -
193A LEU* 1.3 74.8 - - - +
195A ASN* 1.3 79.0 + - - +
197A LYS* 3.1 9.1 + - + +
198A VAL* 3.0 45.8 + - + +
216A THR* 5.6 3.4 - - - -
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Residues in contact with ASN 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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172A VAL* 3.0 50.9 + - - +
173A LEU* 5.7 0.6 - - - +
178A VAL* 3.7 12.9 - - - +
191A ILE* 2.9 24.3 + - - +
192A ARG* 4.0 4.5 - - - +
193A LEU 3.5 0.4 - - - -
194A PHE* 1.3 83.6 - - - +
196A GLN* 1.3 58.4 + - + +
198A VAL* 3.6 4.2 + - - +
199A TYR* 3.0 29.1 + - - +
206A MSE 5.3 2.3 - - - +
208A LEU* 5.1 11.0 - - + +
216A THR* 4.7 2.9 + - - -
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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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192A ARG* 3.4 15.9 + - - +
193A LEU* 3.9 7.4 - - + +
194A PHE 3.2 0.6 - - - -
195A ASN* 1.3 76.3 - - + +
197A LYS* 1.3 65.7 + - - +
199A TYR* 3.4 21.7 + - - +
200A LYS* 3.1 34.9 + - + +
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Residues in contact with LYS 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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151A ASP* 2.7 32.7 + - - +
154A TYR* 4.0 13.9 - - + -
155A GLU* 3.2 24.6 + - - -
193A LEU* 3.2 15.7 + - + +
194A PHE* 3.1 12.9 + - + +
196A GLN* 1.3 76.9 - - - +
198A VAL* 1.3 64.7 + - + +
200A LYS* 3.3 5.1 + - - +
201A ASP* 2.9 30.0 + - + +
203A ARG* 3.8 17.9 - - - +
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Residues in contact with VAL 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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154A TYR* 3.8 26.5 - - + +
194A PHE* 3.0 52.2 + - + +
195A ASN* 4.0 4.9 - - - +
197A LYS* 1.3 73.9 - - + +
199A TYR* 1.3 67.1 + - - +
201A ASP* 3.1 23.3 + - - +
204A VAL* 4.3 1.9 - - + +
206A MSE 3.8 36.9 - - + +
216A THR* 4.1 14.6 - - + -
218A ALA* 4.8 4.9 - - + -
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Residues in contact with TYR 199 (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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195A ASN 3.0 20.5 + - - +
196A GLN* 3.7 22.4 - - - +
198A VAL* 1.3 77.0 - - - +
200A LYS* 1.3 83.4 + - + +
201A ASP 4.9 1.4 - - - +
206A MSE 4.4 28.8 - - + +
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Residues in contact with LYS 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 24.8 + - + +
197A LYS* 3.9 4.3 - - - +
199A TYR* 1.3 103.7 - - + +
201A ASP* 1.3 65.0 + - - +
202A GLU* 3.2 14.4 + - - +
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Residues in contact with ASP 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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154A TYR* 2.8 22.5 + - - -
158A LEU* 4.0 2.6 - - - +
197A LYS* 2.9 19.2 + - + +
198A VAL* 3.1 16.1 + - - +
199A TYR 4.9 1.4 - - - +
200A LYS* 1.3 76.8 - - - +
202A GLU* 1.3 61.6 + - - +
203A ARG* 2.9 59.1 + - - +
204A VAL* 3.5 23.8 - - + +
206A MSE 5.8 0.5 - - - +
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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