Contacts of the helix formed by residues 207 - 217 (chain J) in PDB entry 3LUE
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 GLU 207 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14J SER 5.7 0.6 - - - +
59J GLN* 4.9 16.2 - - + +
203J THR 3.7 2.8 + - - +
204J ALA* 2.6 14.7 + - - +
206J ARG* 1.3 90.6 + - - +
208J ILE* 1.3 62.0 + - + +
209J VAL 3.4 1.8 - - - -
210J ARG* 3.1 54.5 + - - +
211J ASP* 3.4 13.3 - - - +
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Residues in contact with ILE 208 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200J PHE* 3.7 24.7 - - + -
204J ALA* 3.5 10.2 + - + +
205J GLU* 3.1 36.3 + - + +
207J GLU* 1.3 78.7 - - + +
209J VAL* 1.3 64.1 + - - +
210J ARG 3.3 0.2 - - - -
211J ASP* 3.6 12.1 + - - +
212J ILE* 3.2 30.0 + - + +
240J TYR* 4.8 14.6 - - + +
242J LEU* 4.2 10.8 - - + -
243J PRO* 4.3 29.2 - - + -
248J ILE* 5.1 1.6 - - + -
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Residues in contact with VAL 209 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186J THR* 3.4 23.8 - - + +
189J LEU* 3.2 17.6 - - + +
190J MET* 3.8 37.2 - - + +
193J LEU* 4.6 2.9 - - + -
200J PHE* 4.0 32.8 - - + -
205J GLU 3.9 1.1 + - - +
206J ARG 2.9 24.5 - - - +
208J ILE* 1.3 77.7 - - - +
210J ARG* 1.4 63.1 + - - +
212J ILE* 3.0 10.2 + - + -
213J LYS* 2.9 21.5 + - - +
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Residues in contact with ARG 210 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14J SER 5.1 2.7 - - - -
15J GLY* 3.9 33.5 + - - -
16J MET* 4.8 10.7 - - - +
186J THR* 4.0 21.8 - - + +
207J GLU* 3.1 46.9 + - - +
208J ILE 3.3 0.4 - - - -
209J VAL* 1.4 80.9 - - - +
211J ASP* 1.3 79.6 + - - +
213J LYS* 3.5 5.3 - - - +
214J GLU* 3.0 71.1 + - - +
215J LYS* 4.7 3.4 - - - +
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Residues in contact with ASP 211 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207J GLU* 3.4 15.9 - - - +
208J ILE* 3.6 13.7 + - - +
209J VAL 3.2 1.0 - - - -
210J ARG* 1.3 93.3 + - - +
212J ILE* 1.3 59.5 + - - +
214J GLU* 4.3 2.0 - - - +
215J LYS* 2.6 64.3 + - - +
240J TYR* 3.3 25.4 - - + +
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Residues in contact with ILE 212 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189J LEU* 4.1 13.5 - - + -
193J LEU* 3.9 19.1 - - + -
200J PHE* 4.4 6.1 - - + -
208J ILE* 3.2 20.8 + - + +
209J VAL* 3.0 13.5 + - - +
211J ASP* 1.3 74.2 - - - +
213J LYS* 1.3 58.7 + - - +
215J LYS 2.8 0.3 + - - -
216J LEU* 2.7 62.0 + - + +
217J CYS* 3.7 1.6 + - - -
240J TYR* 3.8 25.4 - - + -
248J ILE* 3.9 23.1 - - + -
250J ILE* 3.8 17.7 - - + -
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Residues in contact with LYS 213 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157J ASP* 5.9 0.4 + - - -
182J GLY* 3.2 20.1 + - - -
185J LEU* 3.6 5.4 - - + +
186J THR* 2.6 45.4 + - - +
189J LEU* 3.6 11.3 - - + +
209J VAL 2.9 16.1 + - - +
210J ARG* 3.5 7.1 - - - +
212J ILE* 1.3 76.7 - - - +
214J GLU* 1.3 89.9 + - - +
217J CYS* 3.2 30.2 + - - +
257J CYS* 4.0 17.0 - - - -
303J THR* 6.0 0.2 - - - -
306J TYR* 3.8 26.8 - - - +
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Residues in contact with GLU 214 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15J GLY* 5.1 2.6 - - - -
210J ARG* 3.0 70.6 + - - +
211J ASP* 4.3 2.5 - - - +
213J LYS* 1.3 99.3 + - - +
215J LYS* 1.3 67.0 + - + +
217J CYS 4.8 2.9 + - - +
306J TYR* 5.4 5.8 - - - -
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Residues in contact with LYS 215 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210J ARG* 4.7 4.8 - - - +
211J ASP* 2.6 66.5 + - + +
212J ILE* 2.8 3.4 + - - +
214J GLU* 1.3 81.1 + - + +
216J LEU* 1.3 71.9 + - + +
217J CYS 5.1 0.4 - - - -
218J TYR* 5.7 1.6 - - - -
240J TYR* 4.5 14.4 + - + -
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Residues in contact with LEU 216 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212J ILE* 2.7 44.1 + - + +
215J LYS* 1.3 85.2 - - + +
217J CYS* 1.4 66.3 + - - +
218J TYR* 3.1 10.6 - - - -
238J LYS* 3.9 31.4 - - + +
239J SER 5.2 5.6 - - - +
240J TYR* 4.3 13.7 - - + -
250J ILE* 3.7 21.5 - - + -
254J ARG* 2.8 43.3 + - + +
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Residues in contact with CYS 217 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189J LEU* 4.5 6.7 - - - -
212J ILE* 4.6 1.6 - - - -
213J LYS* 3.2 33.0 + - - +
214J GLU 5.1 2.6 - - - +
215J LYS 3.9 1.4 - - - +
216J LEU* 1.4 78.1 + - - +
218J TYR* 1.3 69.6 - - - +
250J ILE* 6.3 0.2 - - - -
254J ARG* 3.0 27.4 - - - +
257J CYS* 3.7 23.3 - - - -
258J PRO* 3.8 4.3 - - + -
306J TYR* 3.8 22.9 - - + -
307J PRO* 3.8 13.7 - - - +
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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