Contacts of the helix formed by residues 211 - 218 (chain M) in PDB entry 5X6E
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 LEU 211 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148M LEU* 4.9 7.9 - - + -
151M THR* 3.6 34.5 - - + -
152M TYR* 3.9 31.4 - - + +
162M ILE* 5.4 6.1 - - + -
208M VAL* 4.2 6.7 - - + -
209M GLN 4.2 0.2 - - - -
210M ASN* 1.3 70.9 + - - +
212M ASP* 1.3 65.6 + - - +
213M TYR 3.2 2.7 - - - -
214M LEU* 3.0 30.0 + - + +
215M LYS* 2.9 39.7 + - + +
236M LEU* 4.7 13.5 - - + +
237M ASN* 4.7 9.6 - - - +
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Residues in contact with ASP 212 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210M ASN* 3.4 10.8 + - - +
211M LEU* 1.3 78.2 + - - +
213M TYR* 1.3 57.3 + - - +
214M LEU 3.3 0.2 - - - -
215M LYS* 3.4 27.4 - - + +
216M ARG* 2.8 46.8 + - + +
237M ASN* 5.6 1.0 - - - +
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Residues in contact with TYR 213 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140M LEU* 6.1 0.5 - - - +
144M CYS* 4.8 6.5 - - - -
192M LYS* 5.2 2.9 + - - -
193M LEU* 4.3 19.3 - - + -
195M GLN* 4.7 3.9 + - - -
196M GLU* 3.2 31.6 + - + -
197M LYS* 4.9 13.0 - - + -
198M VAL* 4.4 26.7 - - + -
210M ASN* 3.6 16.5 + - - +
211M LEU 3.2 0.8 - - - -
212M ASP* 1.3 79.7 - - - +
214M LEU* 1.3 64.2 + - + +
216M ARG* 3.4 25.6 + - - +
217M TYR* 3.6 53.3 + + - -
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Residues in contact with LEU 214 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144M CYS* 3.7 44.1 - - + +
147M LEU* 4.3 20.2 - - + -
148M LEU* 3.5 15.3 - - + +
151M THR* 4.2 10.1 - - - +
193M LEU* 5.1 4.3 - - + -
198M VAL* 4.1 22.7 - - + -
199M ILE* 5.5 2.7 - - + -
208M VAL* 4.1 17.5 - - + -
211M LEU* 3.0 31.4 + - + +
213M TYR* 1.3 77.6 - - + +
215M LYS* 1.3 59.8 + - - +
217M TYR* 3.2 2.1 + - - +
218M ALA* 2.9 27.7 + - - +
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Residues in contact with LYS 215 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148M LEU* 3.7 11.2 - - + -
152M TYR* 4.5 2.2 - - - +
211M LEU* 2.9 34.6 + - + +
212M ASP* 3.2 34.7 + - + +
214M LEU* 1.3 77.2 - - - +
216M ARG* 1.3 59.5 + - + +
218M ALA 3.2 1.6 - - - -
219M PRO* 3.2 31.2 - - - +
222M ASP* 2.5 46.2 + - - +
233M TRP* 6.2 1.5 - - - -
237M ASN* 4.9 11.9 - - - +
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Residues in contact with ARG 216 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137M ASN* 5.5 0.7 + - - -
197M LYS* 4.4 15.9 - - - +
212M ASP* 2.8 30.3 + - + +
213M TYR* 3.4 40.8 - - - +
215M LYS* 1.3 75.2 - - + +
217M TYR* 1.3 63.3 + - + +
219M PRO* 4.1 11.6 - - - +
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Residues in contact with TYR 217 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133M ASP* 4.2 10.6 - - - +
136M ILE* 4.8 1.7 - - - +
137M ASN* 3.3 48.8 + - + +
140M LEU* 5.0 17.4 - - + +
141M GLY* 4.2 20.2 - - - +
144M CYS* 4.0 20.4 - - + -
213M TYR* 3.6 55.1 + + - +
214M LEU 3.2 5.2 + - - +
216M ARG* 1.3 84.8 - - + +
218M ALA* 1.3 57.6 + - - +
219M PRO* 3.5 7.3 - - - +
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Residues in contact with ALA 218 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133M ASP* 3.3 16.6 - - + +
141M GLY 5.0 0.7 - - - +
145M GLY* 3.7 31.9 - - - +
148M LEU* 3.3 22.3 - - + +
214M LEU 2.9 12.6 + - - +
215M LYS 3.2 4.2 - - - +
217M TYR* 1.3 78.4 - - - +
219M PRO* 1.3 64.8 - - - +
221M LEU* 3.9 8.3 - - + -
222M ASP* 3.6 8.5 + - - +
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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