Contacts of the helix formed by residues 193 - 212 (chain A) in PDB entry 3TMP
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 PRO 193 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192A ASP* 1.3 87.7 - - - +
194A ALA* 1.3 56.4 + - - +
196A VAL* 3.9 7.2 - - + +
197A GLU* 3.0 34.7 + - - +
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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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192A ASP* 3.0 2.3 - - + +
193A PRO* 1.3 78.4 - - - +
195A THR* 1.3 69.1 + - + +
197A GLU* 3.4 8.4 + - - +
198A GLN* 3.1 23.4 + - - +
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Residues in contact with THR 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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192A ASP* 3.1 34.5 + - + +
194A ALA* 1.3 76.6 - - + +
196A VAL* 1.3 70.0 + - - +
198A GLN* 3.2 7.9 + - - +
199A GLN* 3.0 37.6 + - - +
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Residues in contact with VAL 196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A ASP 3.1 22.4 - - - +
193A PRO* 3.9 7.4 - - + +
195A THR* 1.3 84.0 + - - +
197A GLU* 1.3 65.4 + - - +
198A GLN 3.0 0.3 + - - -
199A GLN* 3.1 16.9 + - - +
200A GLU* 3.0 29.4 + - + +
331A ARG* 4.1 39.9 - - + +
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Residues in contact with GLU 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 PRO* 3.0 22.2 + - - +
194A ALA* 3.5 9.1 - - - +
195A THR 3.3 0.2 - - - -
196A VAL* 1.3 81.1 - - - +
198A GLN* 1.3 61.4 + - - +
200A GLU* 3.5 6.3 + - - +
201A HIS* 3.4 38.0 + - + +
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Residues in contact with GLN 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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194A ALA 3.1 12.7 + - - +
195A THR* 3.5 9.9 - - - +
196A VAL 3.1 0.8 - - - -
197A GLU* 1.3 73.9 - - - +
199A GLN* 1.3 65.6 + - + +
200A GLU 3.1 2.1 + - - -
201A HIS* 3.3 18.1 + - - +
202A TRP* 3.0 66.9 + - + +
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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
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195A THR* 3.0 30.7 + - - +
196A VAL* 3.2 19.6 + - - +
198A GLN* 1.3 77.3 - - + +
200A GLU* 1.3 57.1 + - - +
202A TRP* 3.3 6.0 + - + +
203A PHE* 2.8 30.2 + - - +
301A TYR* 3.5 35.3 - - + +
303A THR* 3.7 21.9 - - + +
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Residues in contact with GLU 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 VAL* 3.0 20.8 + - + +
197A GLU* 3.8 7.4 - - - +
198A GLN 3.1 0.2 - - - -
199A GLN* 1.3 76.0 - - - +
201A HIS* 1.3 61.3 + - + +
203A PHE* 4.2 10.5 - - - +
204A GLU* 3.0 66.8 + - - +
215A ILE* 4.1 6.6 - - - +
217A GLN* 4.5 4.9 + - - +
301A TYR* 5.9 0.9 - - - +
330A HIS* 2.9 42.1 + - - -
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Residues in contact with HIS 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 GLU* 3.4 25.3 + - + +
198A GLN* 3.3 24.2 + - - +
200A GLU* 1.3 79.5 - - + +
202A TRP* 1.3 60.5 + - + +
204A GLU* 3.9 12.0 - - - +
205A LYS* 2.9 30.5 + - - +
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Residues in contact with TRP 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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198A GLN* 3.0 50.8 + - + +
199A GLN* 3.6 6.7 - - + +
200A GLU 3.2 0.2 - - - -
201A HIS* 1.3 77.2 - - + +
203A PHE* 1.3 65.6 + - - +
205A LYS* 3.3 39.2 + - + +
206A ALA* 2.9 26.6 + - - +
301A TYR* 3.9 24.7 - - + +
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Residues in contact with PHE 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 2.8 20.1 + - - +
200A GLU* 3.8 13.5 - - - +
202A TRP* 1.3 72.8 - - - +
204A GLU* 1.3 63.8 + - - +
206A ALA* 3.1 3.8 + - - +
207A LEU* 3.0 46.5 + - + +
215A ILE* 4.2 3.6 - - + -
299A TYR* 4.0 10.8 - - + -
300A GLN* 3.6 18.4 - - - -
301A TYR* 3.4 53.4 - + + -
308A VAL* 3.6 27.6 - - + -
328A SER* 4.0 18.8 - - - -
329A TYR 5.5 1.3 - - - -
330A HIS* 4.2 20.4 - + - -
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Residues in contact with GLU 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 GLU* 3.0 57.9 + - - +
201A HIS* 3.9 11.7 - - - +
203A PHE* 1.3 75.9 - - - +
205A LYS* 1.3 62.9 + - - +
207A LEU* 3.5 9.5 - - - +
208A ARG* 3.0 26.1 + - - +
213A PHE 4.6 1.2 - - - +
214A ILE* 6.0 0.2 - - - +
215A ILE* 4.0 22.3 - - + +
217A GLN* 4.5 10.2 + - - -
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Residues in contact with LYS 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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201A HIS 2.9 19.2 + - - +
202A TRP* 3.5 34.5 - - + +
203A PHE 3.2 0.2 - - - -
204A GLU* 1.3 77.7 - - - +
206A ALA* 1.3 58.1 + - - +
208A ARG* 3.4 4.6 + - - +
209A ASP* 2.8 59.1 + - - +
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Residues in contact with ALA 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 TRP 2.9 16.1 + - - +
203A PHE* 3.7 3.8 - - - +
205A LYS* 1.3 77.3 - - - +
207A LEU* 1.3 58.2 + - - +
209A ASP* 4.2 5.8 - - - -
210A LYS* 2.9 45.9 + - - +
301A TYR* 6.3 0.9 - - + -
306A SER* 3.6 30.5 - - - +
308A VAL* 3.9 11.7 - - + +
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Residues in contact with LEU 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 PHE* 3.0 42.0 + - + +
204A GLU* 3.5 5.2 - - - +
206A ALA* 1.3 75.2 - - - +
208A ARG* 1.3 60.4 + - - +
211A LYS* 3.0 12.2 + - + +
212A GLY 2.9 20.4 + - - -
213A PHE* 3.2 41.6 + - + +
215A ILE* 3.6 37.0 - - + +
299A TYR* 4.3 14.8 - - + -
308A VAL* 4.1 23.8 - - + +
338A VAL* 5.1 4.9 - - + -
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Residues in contact with ARG 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 GLU 3.0 16.9 + - - +
205A LYS* 3.8 5.8 - - - +
207A LEU* 1.3 73.9 - - - +
209A ASP* 1.3 68.3 + - - +
212A GLY* 2.9 29.8 + - - -
213A PHE 3.3 10.6 + - - +
214A ILE* 3.0 35.6 - - + +
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Residues in contact with ASP 209 (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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205A LYS* 2.8 51.3 + - - +
206A ALA* 3.9 6.5 - - - +
208A ARG* 1.3 86.5 - - - +
210A LYS* 1.3 66.5 + - + +
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Residues in contact with LYS 210 (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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206A ALA* 2.9 25.2 + - - +
209A ASP* 1.3 87.5 - - + +
211A LYS* 1.3 68.8 + - + +
212A GLY 3.8 0.2 - - - -
306A SER* 3.4 42.5 + - - +
307A ALA* 5.0 5.2 - - - +
308A VAL* 4.5 13.7 - - + +
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Residues in contact with LYS 211 (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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207A LEU* 3.0 11.5 + - + +
210A LYS* 1.3 85.9 - - - +
212A GLY* 1.3 63.4 + - - +
213A PHE* 3.2 48.3 + - + -
299A TYR* 5.0 5.3 + - + +
308A VAL* 3.8 34.1 - - + +
309A GLU* 3.1 40.4 + - - +
310A PRO* 5.0 3.6 - - - +
340A ASN* 4.7 2.1 - - - +
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Residues in contact with GLY 212 (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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207A LEU 2.9 0.4 + - - -
208A ARG* 2.9 28.1 + - - -
210A LYS 3.8 0.2 - - - -
211A LYS* 1.3 78.6 - - - +
213A PHE* 1.3 61.9 + - - +
214A ILE* 4.7 0.7 - - - +
340A ASN* 4.1 1.2 - - - +
341A PRO* 2.9 28.6 - - - +
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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