Contacts of the helix formed by residues 199 - 213 (chain E) in PDB entry 1LVO
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 199 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108E GLY* 4.5 13.5 - - - -
197E VAL 3.8 1.6 + - - -
198E MET* 1.3 70.4 - - - +
200E SER* 1.3 62.2 + - - +
201E ASP* 3.6 6.2 + - - +
202E ASN* 3.1 42.3 + - - -
203E VAL* 3.0 25.4 + - - +
239E THR* 3.5 11.8 + - - -
285E ASP* 3.0 16.5 + - - +
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Residues in contact with SER 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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198E MET 3.3 1.8 + - - -
199E SER* 1.3 71.4 - - - +
201E ASP* 1.4 63.9 + - - +
203E VAL* 3.0 5.9 + - - +
204E VAL* 2.9 27.4 + - - +
229E TYR* 2.8 36.8 + - - -
238E PHE* 3.3 14.3 - - - +
239E THR* 2.4 36.8 + - - -
240E GLU 4.3 3.1 - - - -
241E LEU* 4.0 11.4 - - - -
265E ILE* 5.0 0.4 - - - -
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Residues in contact with ASP 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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199E SER* 3.3 6.4 + - - +
200E SER* 1.4 76.7 - - - +
202E ASN* 1.3 66.3 + - - +
205E ALA* 3.1 19.8 + - - +
239E THR* 4.4 1.6 + - - -
240E GLU 4.1 2.5 - - - +
241E LEU* 3.3 12.1 - - - +
242E SER* 2.5 50.8 + - - -
246E ALA* 5.5 0.5 - - - +
247E PHE* 3.4 23.2 - - - -
289E PRO* 3.7 17.6 - - + +
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Residues in contact with ASN 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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108E GLY* 3.0 24.3 + - - +
128E ASN* 3.5 10.9 + - - +
199E SER* 3.1 23.3 + - - +
201E ASP* 1.3 77.2 - - - +
203E VAL* 1.3 60.0 + - - +
205E ALA* 3.3 1.5 + - - -
206E PHE* 3.0 27.5 + - - +
284E CYS 3.8 2.2 - - - +
285E ASP 2.9 30.4 + - - +
287E PHE 2.9 26.7 + - - +
288E THR* 3.2 18.2 - - - +
289E PRO* 3.5 6.8 - - - +
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Residues in contact with VAL 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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198E MET* 3.8 18.6 - - + -
199E SER 3.0 14.3 + - - +
200E SER* 3.0 9.6 + - - +
202E ASN* 1.3 74.5 - - - +
204E VAL* 1.3 66.3 + - - +
206E PHE* 3.2 4.0 + - + +
207E LEU* 3.0 24.2 + - + +
238E PHE* 4.1 8.3 - - + -
265E ILE* 3.5 31.0 - - + -
283E LEU* 3.9 27.1 - - + -
284E CYS 3.7 12.3 - - - +
285E ASP* 3.5 18.8 - - + -
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Residues in contact with VAL 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 SER 2.9 19.1 + - - +
203E VAL* 1.3 74.6 - - - +
205E ALA* 1.3 62.0 + - - +
207E LEU* 3.4 8.3 + - - +
208E TYR* 3.1 39.7 + - + -
241E LEU* 3.8 8.7 - - + -
247E PHE* 3.5 35.2 - - + -
258E VAL* 4.5 7.4 - - + -
261E LEU* 4.3 10.5 - - + -
262E LEU* 3.7 22.0 - - + -
265E ILE* 3.6 21.1 - - + -
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Residues in contact with ALA 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 ASP 3.1 11.8 + - - +
202E ASN 3.5 8.3 - - - +
204E VAL* 1.3 77.6 - - - +
206E PHE* 1.3 56.2 + - - +
208E TYR* 3.3 5.9 + - - +
209E ALA 3.0 23.6 + - - -
247E PHE* 3.8 8.2 - - + -
250E LEU* 4.8 2.0 - - + -
287E PHE 4.0 0.2 - - - +
288E THR 3.9 2.2 - - - +
289E PRO* 3.6 29.8 - - + -
292E VAL* 3.5 35.7 - - + +
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Residues in contact with PHE 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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3E LEU* 4.2 14.1 - - + -
202E ASN 3.0 13.8 + - - +
203E VAL* 3.2 8.9 + - - +
205E ALA* 1.3 77.7 - - - +
207E LEU* 1.3 72.4 + - + +
209E ALA* 3.2 8.9 + - - +
210E ALA* 3.0 26.2 + - - +
277E ILE* 3.4 47.3 - - + -
278E LEU* 3.4 22.8 - - + +
280E TYR* 3.6 28.5 - + + -
282E SER 4.8 1.1 - - - -
283E LEU* 4.7 6.5 - - + -
284E CYS* 3.5 42.8 - - + +
287E PHE* 4.7 4.9 + + + -
292E VAL* 4.4 1.5 - - - +
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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 VAL* 3.0 20.7 + - + +
204E VAL* 3.4 1.5 + - - +
206E PHE* 1.3 86.0 - - + +
208E TYR* 1.3 60.6 + - - +
210E ALA* 3.2 6.1 + - - +
211E LEU* 2.8 31.7 + - - +
218E PHE* 3.8 14.7 - - + -
261E LEU* 3.7 34.8 - - + +
264E SER* 4.2 13.0 - - - -
265E ILE* 3.8 30.1 - - + +
268E LEU* 4.0 11.0 - - + -
277E ILE* 4.0 26.5 - - + -
283E LEU* 4.3 4.9 - - + -
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Residues in contact with TYR 208 (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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204E VAL* 3.1 37.5 + - + -
205E ALA 3.7 6.3 - - - +
207E LEU* 1.3 72.7 - - - +
209E ALA* 1.3 68.3 + - - +
211E LEU* 3.1 14.4 + - + +
212E ILE* 2.9 30.6 + - + +
247E PHE* 3.9 14.1 - + + -
250E LEU* 3.6 45.1 - - + -
251E ALA* 3.4 8.2 - - + +
254E THR* 3.3 29.6 - - + -
256E GLN 2.7 23.4 + - - -
257E SER 3.2 0.9 - - - -
258E VAL* 3.0 26.3 + - + +
261E LEU* 3.6 18.6 - - + -
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Residues in contact with ALA 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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2E GLY 6.1 0.6 - - - -
3E LEU* 3.8 32.8 - - + -
205E ALA 3.0 13.9 + - - +
206E PHE 3.2 9.2 + - - +
208E TYR* 1.3 76.4 - - - +
210E ALA* 1.3 64.6 + - - +
212E ILE* 3.1 9.6 + - - +
213E ASN* 2.9 22.2 + - - +
278E LEU* 4.1 6.1 - - + -
292E VAL* 4.0 13.4 - - + +
296E MET* 4.4 12.8 - - + +
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Residues in contact with ALA 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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206E PHE 3.0 12.0 + - - +
207E LEU 3.4 8.5 - - - +
208E TYR 3.2 0.2 - - - -
209E ALA* 1.3 78.0 - - - +
211E LEU* 1.3 60.9 + - - +
213E ASN* 3.1 10.0 + - - +
214E GLY 3.2 0.2 + - - -
215E GLU* 2.9 29.7 + - + +
218E PHE* 4.0 11.4 - - + -
277E ILE* 3.5 32.8 - - + -
278E LEU* 3.8 18.6 - - + +
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Residues in contact with LEU 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 2.8 16.1 + - - +
208E TYR* 3.1 26.4 + - + +
210E ALA* 1.3 74.1 - - - +
212E ILE* 1.3 64.7 + - - +
214E GLY* 2.9 14.6 + - - -
215E GLU 3.3 17.4 - - - +
216E ARG* 4.0 12.8 - - + +
218E PHE* 3.7 16.8 - - + -
219E VAL* 3.9 13.5 - - + -
254E THR* 3.8 14.8 - - + +
256E GLN* 3.6 36.3 - - + -
261E LEU* 4.1 13.2 - - + -
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Residues in contact with ILE 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 TYR 2.9 18.7 + - - +
209E ALA 3.1 7.2 + - - +
211E LEU* 1.3 77.6 - - - +
213E ASN* 1.3 58.6 + - - +
214E GLY* 3.0 5.0 + - - -
250E LEU* 3.8 23.1 - - + -
253E LYS* 5.3 0.4 - - + -
254E THR* 3.8 17.7 - - + -
296E MET* 3.9 29.8 - - + -
297E TYR* 3.0 39.7 - - + +
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Residues in contact with ASN 213 (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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1E SER* 4.1 9.7 - - - +
2E GLY* 3.2 35.2 - - - +
209E ALA 2.9 12.7 + - - +
210E ALA 3.1 9.1 + - - +
212E ILE* 1.3 75.5 - - - +
214E GLY* 1.3 59.8 + - - +
215E GLU* 3.7 17.6 + - - +
278E LEU* 3.9 14.4 - - + +
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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
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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