Contacts of the helix formed by residues 236 - 245 (chain L) in PDB entry 5XVO
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 ALA 236 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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171L ASP* 4.1 6.7 - - - +
235L GLU* 1.3 79.5 + - - +
237L PHE* 1.3 67.9 + - - +
238L PRO* 3.4 11.7 - - + -
239L ILE* 3.2 19.7 + - + +
240L MET* 3.1 19.9 + - - +
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Residues in contact with PHE 237 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70L LYS 5.2 3.8 - - - -
72L LEU* 3.5 30.1 - - + -
171L ASP* 3.7 23.0 + - - +
174L ALA* 3.5 42.4 - - + -
175L GLY* 3.6 13.9 - - - -
178L TYR* 4.3 6.3 - + + -
236L ALA* 1.3 71.5 - - - +
238L PRO* 1.3 76.9 - - + +
240L MET* 3.0 16.0 + - + +
241L LYS* 2.9 57.9 + - + +
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Residues in contact with PRO 238 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236L ALA* 3.6 10.3 - - + -
237L PHE* 1.3 99.7 - - + +
239L ILE* 1.3 66.5 + - + +
241L LYS* 3.5 18.3 - - + +
242L ARG* 3.4 27.5 + - - +
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Residues in contact with ILE 239 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232L ASN* 4.4 0.4 - - - +
235L GLU* 3.8 36.1 - - + +
236L ALA* 3.2 23.8 + - + +
237L PHE 3.1 1.0 - - - -
238L PRO* 1.3 81.6 - - + +
240L MET* 1.3 69.8 + - - +
241L LYS 3.1 1.1 - - - -
242L ARG* 3.0 7.9 + - + +
243L LYS* 2.9 48.3 + - + +
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Residues in contact with MET 240 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171L ASP* 3.1 50.9 - - + +
172L ILE* 4.4 6.5 - - - -
175L GLY* 4.1 11.9 - - - -
228L ILE* 4.9 0.6 - - - +
229L ILE* 3.9 25.3 - - + +
232L ASN* 3.8 26.5 - - + +
233L ARG 5.3 2.2 - - - +
235L GLU 3.3 21.1 - - - +
236L ALA 3.1 7.1 + - - +
237L PHE* 3.0 32.7 + - + +
239L ILE* 1.3 76.1 - - - +
241L LYS* 1.3 63.8 + - - +
243L LYS* 3.2 8.7 + - - +
244L LEU* 3.0 28.6 + - - +
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Residues in contact with LYS 241 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43L GLU* 3.8 21.4 + - - -
70L LYS 5.2 1.1 - - - -
71L ARG* 3.8 35.7 + - - +
178L TYR* 3.5 37.5 + - + +
237L PHE* 2.9 47.6 + - + +
238L PRO* 3.5 18.6 - - - +
240L MET* 1.3 76.9 - - - +
242L ARG* 1.3 70.6 + - + +
244L LEU* 3.2 24.6 + - - +
245L PHE* 3.7 15.1 + - + -
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Residues in contact with ARG 242 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9L ASN* 3.6 12.7 - - - +
43L GLU* 3.2 37.7 + - - -
71L ARG* 5.5 2.4 - - - +
238L PRO 3.4 15.0 + - - +
239L ILE* 3.0 9.5 + - - +
241L LYS* 1.3 88.0 - - + +
243L LYS* 1.3 64.5 + - + +
245L PHE* 3.3 32.6 + - - +
246L ALA 4.3 1.2 + - - -
105N PHE* 3.1 32.7 - - - -
108N GLU* 3.0 33.1 + - - +
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Residues in contact with LYS 243 (chain L).
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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228L ILE* 3.8 12.9 - - + +
232L ASN* 3.4 42.1 + - - +
235L GLU* 6.0 0.2 - - - -
239L ILE* 2.9 31.6 + - + +
240L MET* 3.6 5.8 - - - +
242L ARG* 1.3 77.8 - - + +
244L LEU* 1.3 61.7 + - - +
246L ALA* 3.2 24.5 - - - +
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Residues in contact with LEU 244 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175L GLY* 3.4 26.2 - - - +
178L TYR* 3.7 13.9 - - + -
179L GLY* 3.6 18.4 - - - +
182L LEU* 4.4 11.5 - - + +
225L VAL* 4.0 23.6 - - + -
228L ILE* 3.9 21.8 - - + -
229L ILE* 4.0 10.5 - - + -
240L MET 3.0 18.7 + - - +
241L LYS* 3.4 10.1 - - - +
242L ARG 3.1 0.6 - - - -
243L LYS* 1.3 74.5 - - - +
245L PHE* 1.3 60.5 - - - +
246L ALA 3.0 5.6 - - - -
247L LEU* 3.1 37.8 + - + +
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Residues in contact with PHE 245 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5L THR* 5.1 8.3 - - + -
7L VAL* 4.7 5.2 - - + -
41L LEU* 3.5 33.4 - - + -
43L GLU* 4.4 3.1 - - - -
178L TYR* 3.6 17.5 - + - -
182L LEU* 4.7 10.8 - - + -
241L LYS* 3.8 19.7 - - + -
242L ARG* 3.3 43.0 + - - +
243L LYS 3.2 1.4 - - - -
244L LEU* 1.3 73.8 - - - +
246L ALA* 1.3 62.4 + - - +
247L LEU 3.0 7.1 + - - -
248L PHE* 3.1 41.7 + + + +
249L MET* 3.4 9.9 + - - +
103N ILE* 4.2 20.6 - - + +
105N PHE* 4.8 12.8 - + + -
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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