Contacts of the helix formed by residues 207 - 217 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14C SER 5.7 0.6 - - - +
59C GLN* 4.9 13.9 - - + +
203C THR 3.7 0.4 + - - -
204C ALA 2.6 12.8 + - - +
206C ARG* 1.3 89.4 + - - +
208C ILE* 1.3 62.1 + - + +
209C VAL 3.4 1.1 - - - -
210C ARG* 3.1 54.7 + - - +
211C ASP* 3.4 13.0 - - - +
288E ASP* 3.9 6.7 - - - +
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Residues in contact with ILE 208 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200C PHE* 3.7 23.8 - - + -
204C ALA* 3.5 7.2 + - + +
205C GLU* 3.1 35.2 + - + +
207C GLU* 1.3 78.5 - - + +
209C VAL* 1.3 63.8 + - - +
210C ARG 3.3 0.2 - - - -
211C ASP* 3.6 13.8 + - - +
212C ILE* 3.2 29.3 + - + +
240C TYR* 4.8 13.2 - - + +
242C LEU* 4.2 12.1 - - + -
243C PRO* 4.3 28.7 - - + -
248C ILE* 5.1 1.3 - - + -
291E LYS* 5.0 4.3 - - - -
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Residues in contact with VAL 209 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186C THR* 3.4 24.0 - - + +
189C LEU* 3.2 16.7 - - + +
190C MET* 3.8 37.9 - - + -
193C LEU* 4.6 3.1 - - + -
200C PHE* 4.0 33.4 - - + -
205C GLU 4.6 0.4 - - - +
206C ARG 2.9 24.2 - - - +
208C ILE* 1.3 77.9 - - - +
210C ARG* 1.4 64.8 + - - +
212C ILE* 3.0 9.4 + - + -
213C LYS* 2.9 21.3 + - - +
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Residues in contact with ARG 210 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C SER 5.1 2.2 - - - -
15C GLY* 3.9 34.6 + - - -
16C MET* 4.8 10.1 - - - +
186C THR* 4.0 21.8 - - + +
207C GLU* 3.1 45.4 + - - +
209C VAL* 1.4 79.4 - - - +
211C ASP* 1.3 80.4 + - - +
213C LYS* 3.5 5.9 - - - +
214C GLU* 3.0 70.9 + - - +
215C LYS* 4.7 3.2 - - - +
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Residues in contact with ASP 211 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207C GLU* 3.4 16.8 - - - +
208C ILE* 3.6 13.8 + - - +
209C VAL 3.2 0.4 - - - -
210C ARG* 1.3 94.4 + - - +
212C ILE* 1.3 59.9 + - - +
214C GLU* 4.3 2.2 - - - +
215C LYS* 2.6 63.9 + - + +
240C TYR* 3.3 24.7 - - + +
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Residues in contact with ILE 212 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189C LEU* 4.1 13.2 - - + -
193C LEU* 3.9 18.6 - - + -
200C PHE* 4.4 5.2 - - + -
208C ILE* 3.2 21.3 + - + +
209C VAL* 3.0 14.4 + - - +
211C ASP* 1.3 74.1 - - - +
213C LYS* 1.3 57.0 + - - +
215C LYS 2.8 0.7 + - - -
216C LEU* 2.7 62.1 + - + +
217C CYS* 3.7 1.8 + - - -
240C TYR* 3.8 25.4 - - + -
248C ILE* 3.9 22.4 - - + -
250C ILE* 3.8 18.4 - - + -
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Residues in contact with LYS 213 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157C ASP* 5.9 0.4 + - - -
182C GLY* 3.2 20.5 + - - -
185C LEU* 3.6 5.2 - - + +
186C THR* 2.6 44.0 + - - +
189C LEU* 3.6 10.9 - - + +
209C VAL 2.9 16.1 + - - +
210C ARG* 3.5 7.7 - - - +
212C ILE* 1.3 76.0 - - - +
214C GLU* 1.3 88.6 + - - +
217C CYS* 3.2 30.9 + - - +
257C CYS* 4.0 17.0 - - - -
306C TYR* 3.8 27.3 - - - +
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Residues in contact with GLU 214 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C GLY* 5.1 2.6 - - - -
210C ARG* 3.0 69.1 + - - +
211C ASP* 4.3 3.1 - - - +
213C LYS* 1.3 100.6 + - - +
215C LYS* 1.3 66.3 + - + +
217C CYS 4.8 3.1 + - - +
306C TYR* 5.4 5.5 - - - -
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Residues in contact with LYS 215 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210C ARG* 4.7 4.9 - - - +
211C ASP* 2.6 65.1 + - + +
212C ILE* 2.8 3.1 + - - +
214C GLU* 1.3 81.2 + - + +
216C LEU* 1.3 70.5 + - + +
217C CYS 3.9 0.7 - - - -
218C TYR* 5.7 1.9 - - - -
240C TYR* 4.5 15.2 + - + -
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Residues in contact with LEU 216 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212C ILE* 2.7 43.7 + - + +
215C LYS* 1.3 86.5 - - + +
217C CYS* 1.4 65.9 + - - +
218C TYR* 3.1 10.5 - - - -
238C LYS* 3.9 31.0 - - + +
239C SER 5.2 5.4 - - - +
240C TYR* 4.3 14.1 - - + -
250C ILE* 3.7 20.9 - - + -
254C ARG* 2.8 44.5 + - + +
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Residues in contact with CYS 217 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189C LEU* 4.5 6.7 - - - -
212C ILE* 4.6 2.0 - - - -
213C LYS* 3.2 33.4 + - - +
214C GLU 5.1 2.4 - - - +
215C LYS 5.1 1.4 - - - -
216C LEU* 1.4 78.4 - - - +
218C TYR* 1.3 70.4 - - - +
250C ILE* 6.3 0.2 - - - -
254C ARG* 3.0 26.7 - - - +
257C CYS* 3.7 22.7 - - - -
258C PRO* 3.8 3.4 - - + -
306C TYR* 3.8 22.7 - - + -
307C PRO* 3.8 14.0 - - - +
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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