Contacts of the helix formed by residues 187 - 204 (chain A) in PDB entry 3TKR
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 187 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A PHE* 4.7 2.9 - - - -
186A ARG* 1.3 78.2 - - - +
188A VAL* 1.3 63.0 + - - +
189A ASP* 3.4 9.9 + - - +
190A GLU* 3.0 22.2 + - - +
191A THR* 2.8 27.9 + - - -
190I GLU* 3.6 27.1 + - - -
193I ARG* 3.7 14.6 + - - +
211I GLY* 4.4 7.9 - - - +
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Residues in contact with VAL 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A ALA* 3.7 40.4 - - + +
94A PHE* 3.8 24.2 - - + +
97A ARG* 3.7 38.1 - - + +
101A PHE* 3.9 26.5 - - + -
186A ARG 4.3 1.0 + - - -
187A SER* 1.3 69.4 + - - +
189A ASP* 1.3 64.3 + - - +
191A THR* 3.3 1.2 + - - -
192A LEU* 2.9 23.5 + - + +
210I ALA* 5.5 2.4 - - + +
211I GLY* 5.4 2.0 - - - +
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Residues in contact with ASP 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A ARG* 2.9 32.5 + - - +
187A SER* 3.4 7.5 + - - +
188A VAL* 1.3 78.7 - - - +
190A GLU* 1.3 62.7 + - - +
192A LEU* 3.4 6.2 + - - +
193A ARG* 3.0 23.8 + - - +
213I LYS* 4.8 11.8 + - - -
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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
----------------------------------------------------------
187A SER* 3.0 16.6 + - - +
189A ASP* 1.3 79.4 - - - +
191A THR* 1.3 62.8 + - - +
193A ARG* 2.8 48.3 + - - +
194A LEU* 3.0 41.3 + - + +
186I ARG* 5.3 0.7 - - - -
187I SER* 3.6 14.7 + - - -
190I GLU* 3.9 36.7 - - + +
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Residues in contact with THR 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A VAL* 3.8 34.5 - - + -
94A PHE* 3.5 27.0 - - + -
101A PHE* 4.1 2.5 - - + -
165A LEU* 3.7 18.3 - - + +
167A ILE* 4.5 3.6 - - + -
186A ARG* 5.6 0.2 - - - +
187A SER 2.8 23.5 + - - -
188A VAL 3.6 4.3 - - - -
189A ASP 3.3 0.2 - - - -
190A GLU* 1.3 77.2 - - - +
192A LEU* 1.3 57.6 + - - +
194A LEU* 3.3 11.0 + - - +
195A VAL* 3.0 27.9 + - - +
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Residues in contact with LEU 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A ARG* 4.3 8.5 - - - +
100A GLU* 3.7 41.7 - - + +
101A PHE* 4.2 23.5 - - + -
104A ILE* 3.6 31.6 - - + -
188A VAL* 2.9 17.2 + - + +
189A ASP* 3.7 5.2 - - - +
191A THR* 1.3 72.5 - - - +
193A ARG* 1.3 61.0 + - - +
195A VAL* 3.3 2.0 + - + +
196A GLN* 2.9 55.2 + - - +
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Residues in contact with ARG 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A ASP 3.0 14.0 + - - +
190A GLU* 2.8 46.0 + - - +
192A LEU* 1.3 75.3 - - - +
194A LEU* 1.3 70.6 + - - +
196A GLN* 3.4 14.0 + - - +
197A ALA* 2.9 28.3 + - - +
208A CYS* 6.1 0.2 - - - +
209A PRO 4.7 0.4 + - - -
211A GLY* 3.6 5.6 - - - -
212A TRP* 2.9 54.3 + - + +
213A LYS* 4.0 23.3 - - + -
184I VAL* 5.1 4.4 - - - +
185I GLY 3.1 26.7 + - - -
186I ARG* 3.6 12.5 - - - +
187I SER* 3.6 9.4 - - - -
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Residues in contact with LEU 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A LEU* 6.1 0.7 - - + -
167A ILE* 3.6 17.7 - - + -
176A GLN* 3.9 30.1 - - + +
178A THR* 4.8 3.6 - - - +
190A GLU* 3.0 43.1 + - + +
191A THR* 3.7 3.4 - - - +
193A ARG* 1.3 93.2 - - - +
195A VAL* 1.3 66.1 + - - +
197A ALA* 3.2 4.0 + - - +
198A PHE* 2.9 35.5 + - + -
178I THR* 6.1 1.3 - - + -
180I ASN* 3.7 28.7 - - - +
184I VAL* 3.9 11.2 - - + -
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Residues in contact with VAL 195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A TYR* 4.3 8.2 - - + -
75A VAL* 3.8 27.6 - - + -
101A PHE* 4.5 4.0 - - + -
104A ILE* 3.9 16.4 - - + -
106A THR* 3.4 29.2 - - + +
167A ILE* 4.1 20.4 - - + -
191A THR* 3.0 22.0 + - + +
192A LEU* 3.7 5.8 - - - +
194A LEU* 1.3 75.5 - - - +
196A GLN* 1.3 64.3 + - - +
198A PHE* 3.9 2.0 - - - +
199A GLN* 3.0 32.7 + - - +
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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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104A ILE* 4.2 20.3 - - + +
192A LEU* 2.9 45.1 + - - +
193A ARG* 3.5 13.7 - - - +
195A VAL* 1.3 78.0 - - - +
197A ALA* 1.3 56.6 + - - +
199A GLN* 3.4 8.1 + - - +
200A TYR* 2.8 29.8 + - - +
212A TRP* 3.9 12.4 - - + -
214A PRO* 3.4 33.6 - - + +
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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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193A ARG* 2.9 20.5 + - - +
194A LEU* 3.2 2.2 + - - +
196A GLN* 1.3 78.1 - - - +
198A PHE* 1.3 56.3 + - - +
200A TYR* 3.2 1.6 + - - +
201A THR* 2.8 34.1 + - - +
208A CYS* 4.0 7.6 - - + -
212A TRP* 3.5 24.8 - - + -
184I VAL* 3.6 31.4 - - + -
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Residues in contact with PHE 198 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A TYR* 3.3 24.9 - - + +
167A ILE* 4.8 5.6 - - + -
175A ARG* 3.3 50.3 - - + -
176A GLN* 3.8 27.1 - - + -
194A LEU* 2.9 34.4 + - + +
195A VAL 4.1 0.2 - - - +
197A ALA* 1.3 75.9 - - - +
199A GLN* 1.3 57.7 + - - +
201A THR* 3.2 4.8 + - - -
202A ASP* 2.9 34.3 + - - +
180I ASN* 4.7 2.2 - - - -
181I ASP* 3.7 30.7 - - + -
183I PRO* 4.4 2.0 - - + -
184I VAL* 3.5 34.8 - - + -
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Residues in contact with GLN 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A TYR* 3.7 33.9 - - + +
104A ILE* 2.8 44.7 + - - +
105A ASN* 4.4 6.7 + - - +
106A THR* 3.4 11.7 + - - -
195A VAL* 3.0 24.1 + - - +
196A GLN* 3.7 7.2 - - - +
198A PHE* 1.3 75.6 - - - +
200A TYR* 1.3 64.3 + - - +
202A ASP* 3.4 5.9 + - - +
203A LYS* 3.2 24.3 + - - +
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Residues in contact with TYR 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 2.8 18.5 + - - +
197A ALA* 3.2 4.9 + - - +
199A GLN* 1.3 78.0 - - - +
201A THR* 1.3 63.1 + - + +
203A LYS* 3.2 2.6 + - - -
204A HIS* 3.0 61.2 + + + +
206A GLU* 2.6 38.8 + - + -
208A CYS* 4.2 12.8 - - - -
212A TRP* 3.9 24.7 - + + -
218A THR* 3.8 18.4 + - + +
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Residues in contact with THR 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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175A ARG* 4.8 0.2 + - - -
197A ALA 2.8 22.4 + - - +
198A PHE* 3.2 14.6 + - - -
200A TYR* 1.3 75.0 - - + +
202A ASP* 1.3 63.2 + - - +
204A HIS 3.0 19.0 - - - +
206A GLU 3.4 24.4 - - - +
207A VAL* 3.9 0.9 - - - -
208A CYS* 3.5 23.3 - - - -
183I PRO* 3.6 39.2 - - + +
184I VAL* 3.9 2.7 - - + +
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Residues in contact with ASP 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A TYR* 2.6 32.4 + - - -
169A ASP* 4.3 2.5 - - - +
170A ASP* 4.2 6.3 - - - +
175A ARG* 2.8 28.4 + - - -
198A PHE 2.9 18.3 + - - +
199A GLN* 3.6 6.3 - - - +
201A THR* 1.3 79.8 - - - +
203A LYS* 1.3 61.7 + - + +
204A HIS 4.6 0.7 - - - +
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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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199A GLN 3.2 12.7 + - - +
200A TYR* 3.2 6.2 + - - +
202A ASP* 1.3 81.3 - - + +
204A HIS* 1.3 88.1 + - + +
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Residues in contact with HIS 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 TYR* 3.0 61.4 + + + +
201A THR 3.0 19.1 - - - +
202A ASP 4.5 0.6 - - - -
203A LYS* 1.3 109.4 + - + +
205A GLY* 1.3 58.7 + - - +
206A GLU* 2.9 32.4 + - + +
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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
------------------------------------------------------------
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