Contacts of the helix formed by residues 192 - 212 (chain E) 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 ASP 192 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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190E ALA 4.1 1.2 + - - -
191E MET* 1.3 72.3 - - - +
193E PRO* 1.3 80.8 - - - +
194E ALA* 2.6 37.8 + - - +
195E THR* 3.1 30.7 + - - +
196E VAL* 3.2 12.1 + - - +
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Residues in contact with PRO 193 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191E MET 3.4 6.9 - - - +
192E ASP* 1.3 92.2 - - - +
194E ALA* 1.3 56.3 + - - +
196E VAL* 3.2 10.4 + - + +
197E GLU* 3.0 28.8 + - - +
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Residues in contact with ALA 194 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192E ASP* 2.6 24.2 + - - +
193E PRO* 1.3 74.3 - - - +
195E THR* 1.3 56.5 + - - +
197E GLU* 3.4 16.4 + - - +
198E GLN* 3.1 27.7 + - - +
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Residues in contact with THR 195 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191E MET* 3.3 22.9 - - + -
192E ASP* 3.1 25.6 + - - +
194E ALA* 1.3 76.5 - - - +
196E VAL* 1.3 64.1 + - - +
198E GLN* 3.4 17.2 + - - +
199E GLN* 3.1 33.9 + - + +
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Residues in contact with VAL 196 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188E ILE* 3.9 22.0 - - + +
191E MET* 3.8 26.2 - - + +
192E ASP 3.2 12.3 + - - +
193E PRO* 3.2 10.6 + - + +
195E THR* 1.3 75.0 - - - +
197E GLU* 1.3 59.0 + - - +
199E GLN* 3.1 8.6 + - + +
200E GLU* 2.9 41.6 + - + +
331E ARG* 4.2 25.6 - - + -
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Residues in contact with GLU 197 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193E PRO 3.0 12.7 + - - +
194E ALA* 3.6 17.0 - - - +
196E VAL* 1.3 78.2 - - - +
198E GLN* 1.3 56.5 + - - +
200E GLU* 3.8 7.3 - - - +
201E HIS* 2.9 34.1 + - + +
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Residues in contact with GLN 198 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194E ALA 3.1 13.4 + - - +
195E THR* 3.5 22.6 + - - +
196E VAL 3.2 0.2 - - - -
197E GLU* 1.3 77.5 - - - +
199E GLN* 1.3 62.3 + - + +
201E HIS* 3.9 4.1 - - - +
202E TRP* 3.0 28.8 + - - +
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Residues in contact with GLN 199 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191E MET* 3.3 34.0 - - - +
195E THR* 3.1 16.3 + - + +
196E VAL* 3.1 10.6 + - + +
198E GLN* 1.3 77.8 - - + +
200E GLU* 1.3 59.9 + - + +
202E TRP* 3.5 6.1 + - - +
203E PHE* 3.0 29.9 + - - +
301E TYR* 3.7 50.6 + - + +
303E THR* 5.0 7.0 - - - +
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Residues in contact with GLU 200 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196E VAL* 2.9 33.2 + - + +
197E GLU* 3.8 7.6 - - - +
199E GLN* 1.3 70.0 - - + +
201E HIS* 1.3 61.6 + - - +
203E PHE* 3.2 10.6 + - - +
204E GLU* 3.0 37.2 + - + +
215E ILE* 5.7 0.2 - - - +
301E TYR* 5.9 2.5 - - - +
330E HIS* 3.0 48.2 + - - +
331E ARG* 4.4 15.9 + - - +
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Residues in contact with HIS 201 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197E GLU* 2.9 23.5 + - + +
198E GLN* 4.0 5.6 - - - +
200E GLU* 1.3 73.3 - - - +
202E TRP* 1.3 67.6 + - - +
204E GLU* 3.4 9.4 + - + +
205E LYS* 3.1 37.2 + - + +
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Residues in contact with TRP 202 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198E GLN 3.0 17.8 + - - +
199E GLN* 3.6 6.5 - - - +
200E GLU 3.3 0.2 - - - -
201E HIS* 1.3 79.6 + - - +
203E PHE* 1.3 77.3 + + - +
205E LYS* 3.3 7.9 + - + +
206E ALA* 2.8 52.8 + - + +
210E LYS* 4.4 6.3 - - - -
301E TYR* 3.7 30.1 - + + -
305E THR 4.5 4.0 - - - -
306E SER* 3.2 46.4 - - - -
307E ALA 5.0 0.9 - - - -
308E VAL* 4.3 8.7 - - + -
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Residues in contact with PHE 203 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199E GLN 3.0 17.9 + - - +
200E GLU* 3.6 11.2 - - - +
202E TRP* 1.3 84.9 - + - +
204E GLU* 1.3 57.4 + - - +
206E ALA* 3.3 2.4 + - - +
207E LEU* 2.8 55.1 + - + +
215E ILE* 3.8 19.3 - - + -
299E TYR* 3.8 10.1 - + + -
300E GLN* 3.5 26.9 - - - -
301E TYR* 3.6 39.7 - + + -
308E VAL* 3.9 27.6 - - + -
328E SER* 4.3 10.8 - - - -
329E TYR 5.6 1.1 - - - -
330E HIS* 4.5 10.3 - + - -
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Residues in contact with GLU 204 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200E GLU* 3.0 20.2 + - + +
201E HIS* 3.8 9.3 - - + +
203E PHE* 1.3 74.9 - - + +
205E LYS* 1.3 64.9 + - - +
207E LEU* 3.2 7.5 + - - +
208E ARG* 3.1 28.9 + - - +
213E PHE 4.8 0.9 - - - +
214E ILE* 5.3 2.3 - - - +
215E ILE* 3.7 49.0 + - + +
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Residues in contact with LYS 205 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201E HIS* 3.1 30.4 + - + +
202E TRP* 3.8 8.1 - - + +
204E GLU* 1.3 78.1 - - - +
206E ALA* 1.3 57.7 + - - +
208E ARG* 3.4 23.1 + - - +
209E ASP* 3.0 55.6 + - - +
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Residues in contact with ALA 206 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202E TRP* 2.8 43.7 + - + +
203E PHE 3.6 4.0 - - - +
205E LYS* 1.3 73.9 - - - +
207E LEU* 1.3 57.4 + - - +
209E ASP* 4.5 3.6 - - - -
210E LYS* 2.9 52.0 + - - +
308E VAL* 3.7 20.5 - - + +
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Residues in contact with LEU 207 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203E PHE* 2.8 51.7 + - + +
204E GLU* 3.5 6.3 - - - +
205E LYS 3.2 0.2 - - - -
206E ALA* 1.3 74.3 - - - +
208E ARG* 1.3 67.0 + - - +
211E LYS* 3.0 23.2 + - + +
212E GLY 3.2 5.5 + - - -
213E PHE* 3.3 34.0 + - + +
215E ILE* 3.8 23.3 - - + -
299E TYR* 4.2 22.4 - - + -
308E VAL* 4.1 20.6 - - + +
338E VAL* 5.0 8.7 - - + -
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Residues in contact with ARG 208 (chain E).
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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204E GLU* 3.1 10.8 + - - +
205E LYS* 3.8 31.1 - - - +
207E LEU* 1.3 78.1 - - - +
209E ASP* 1.3 75.0 + - - +
212E GLY* 2.8 29.0 + - - -
213E PHE 3.4 11.7 + - - +
214E ILE* 3.7 33.9 - - + -
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Residues in contact with ASP 209 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205E LYS* 3.0 48.2 + - - +
206E ALA* 4.1 4.2 - - - +
208E ARG* 1.3 96.9 + - - +
210E LYS* 1.3 65.6 + - + +
212E GLY 4.7 0.2 - - - -
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Residues in contact with LYS 210 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202E TRP* 4.4 7.1 - - - -
206E ALA* 2.9 33.0 + - - +
209E ASP* 1.3 82.6 - - + +
211E LYS* 1.3 68.9 + - + +
306E SER* 3.4 29.2 + - - +
307E ALA* 4.6 3.4 - - + +
308E VAL* 3.7 27.6 - - + +
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Residues in contact with LYS 211 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207E LEU* 3.0 13.2 + - + +
210E LYS* 1.3 87.1 + - - +
212E GLY* 1.3 63.2 + - - +
213E PHE* 3.5 45.9 - - + -
299E TYR* 4.7 4.5 - - + -
308E VAL* 4.0 29.5 + - + +
309E GLU* 2.4 44.4 + - - +
310E PRO* 4.6 6.3 - - - -
340E ASN* 5.3 0.5 - - - +
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Residues in contact with GLY 212 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208E ARG* 2.8 23.9 + - - -
210E LYS 3.8 0.2 - - - -
211E LYS* 1.3 77.4 - - - +
213E PHE* 1.3 66.4 + - - +
214E ILE* 4.0 4.9 + - - +
339E VAL 4.3 2.4 - - - +
340E ASN* 4.3 11.7 - - - +
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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