Contacts of the helix formed by residues 236 - 247 (chain D) in PDB entry 5LS6
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 THR 236 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126D THR* 5.8 7.0 - - + +
156D LYS* 4.2 15.5 - - - +
228D SER* 4.0 2.9 - - - -
235D GLY* 1.3 79.1 + - - -
237D ALA* 1.3 65.0 + - - +
238D GLU* 3.7 13.2 + - - +
239D GLU* 3.1 28.8 + - - +
240D LEU* 3.3 17.7 + - - +
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Residues in contact with ALA 237 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224D PHE* 3.1 45.0 - - + +
225D GLU* 3.6 19.3 - - + +
228D SER* 3.8 8.2 + - - +
236D THR* 1.3 73.1 - - - +
238D GLU* 1.3 59.6 + - - +
240D LEU* 3.2 6.3 + - - +
241D LYS* 3.0 24.0 + - - +
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Residues in contact with GLU 238 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236D THR* 3.4 8.4 + - - +
237D ALA* 1.3 77.5 - - - +
239D GLU* 1.3 60.8 + - + +
241D LYS* 3.2 22.5 + - - +
242D GLU* 3.1 36.2 + - - +
245D LYS* 5.6 4.2 + - - -
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Residues in contact with GLU 239 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126D THR* 4.2 17.5 + - - +
234D LYS 4.9 2.9 - - - +
235D GLY 3.7 7.3 - - - +
236D THR* 3.1 43.3 + - - +
237D ALA 3.3 0.6 - - - -
238D GLU* 1.3 79.1 - - + +
240D LEU* 1.3 57.4 + - - +
242D GLU* 3.6 6.9 + - - +
243D LYS* 3.0 33.9 + - + +
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Residues in contact with LEU 240 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171D PHE* 4.3 18.7 - - + -
224D PHE* 3.4 20.8 - - + +
227D ILE* 3.7 21.5 - - + +
228D SER* 3.5 36.8 - - - -
231D PHE* 5.9 0.4 - - + -
234D LYS* 3.1 42.4 - - + +
236D THR 3.3 3.6 + - - +
237D ALA 3.2 8.5 + - - +
239D GLU* 1.3 75.6 - - - +
241D LYS* 1.3 59.1 + - - +
242D GLU 3.3 0.2 - - - -
243D LYS* 3.8 20.1 - - + +
244D TYR* 3.0 23.6 + - - +
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Residues in contact with LYS 241 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216D ARG* 4.2 18.8 - - - +
221D ASP* 3.6 25.5 + - - +
224D PHE* 3.5 34.0 - - + -
237D ALA 3.0 13.3 + - - +
238D GLU* 3.2 26.0 + - - +
240D LEU* 1.3 75.0 - - - +
242D GLU* 1.3 58.0 + - - +
244D TYR* 3.4 4.6 + - + +
245D LYS* 3.2 52.3 + - - +
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Residues in contact with GLU 242 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238D GLU* 3.1 24.4 + - - +
239D GLU* 3.8 7.6 - - - +
241D LYS* 1.3 74.3 - - - +
243D LYS* 1.3 64.7 + - - +
245D LYS* 3.3 22.9 + - + +
246D GLU* 3.0 46.0 + - - +
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Residues in contact with LYS 243 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168D ASP* 5.3 9.0 + - - -
171D PHE* 4.8 15.0 - - + -
234D LYS* 5.3 8.3 - - + +
239D GLU* 3.0 22.6 + - + +
240D LEU* 3.8 24.2 - - + +
241D LYS 3.4 0.2 - - - -
242D GLU* 1.3 76.1 + - - +
244D TYR* 1.3 63.0 + - - +
246D GLU* 3.1 13.6 + - - +
247D LEU* 3.0 27.7 + - + +
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Residues in contact with TYR 244 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171D PHE* 4.7 10.9 - + + -
172D VAL* 4.5 11.7 - - + -
175D VAL* 3.4 34.5 - - + +
176D ASN 5.7 0.2 - - - -
216D ARG* 4.1 46.9 - - + +
224D PHE* 3.8 25.1 - + + -
240D LEU 3.0 18.1 + - - +
241D LYS* 3.5 7.0 - - + +
242D GLU 3.3 0.2 - - - -
243D LYS* 1.3 77.3 - - - +
245D LYS* 1.3 53.7 + - - +
247D LEU* 3.3 5.5 + - + +
248D THR* 2.8 61.0 + - + +
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Residues in contact with LYS 245 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216D ARG* 3.6 41.9 - - - +
238D GLU* 5.6 3.8 + - - -
241D LYS* 3.2 40.5 + - - +
242D GLU* 3.5 24.5 - - - +
243D LYS 3.3 0.4 - - - -
244D TYR* 1.3 73.1 - - + +
246D GLU* 1.3 66.1 + - - +
248D THR* 3.2 25.4 + - - +
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Residues in contact with GLU 246 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242D GLU* 3.0 39.4 + - - +
243D LYS* 3.1 15.4 + - - +
245D LYS* 1.3 77.0 - - - +
247D LEU* 1.3 58.6 + - + +
248D THR 3.3 3.2 + - - -
249D GLN* 4.2 16.5 + - - +
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Residues in contact with LEU 247 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168D ASP* 3.8 43.7 - - + +
171D PHE* 4.7 11.2 - - + -
172D VAL* 3.2 35.5 - - + +
243D LYS* 3.0 18.0 + - - +
244D TYR* 3.3 4.9 + - + +
245D LYS 3.2 0.4 - - - -
246D GLU* 1.3 75.8 - - + +
248D THR* 1.3 64.8 + - - +
249D GLN* 4.0 4.6 + - - -
348E SER* 5.6 3.6 - - - -
349E ASN* 5.7 1.6 - - - +
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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