Contacts of the helix formed by residues 236 - 248 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126A THR* 6.0 4.9 - - + +
156A LYS* 4.0 17.5 - - - +
228A SER* 4.1 2.7 - - - -
235A GLY* 1.3 76.7 + - - -
237A ALA* 1.3 65.3 + - - +
238A GLU* 3.6 20.0 - - - +
239A GLU* 2.8 37.9 + - - +
240A LEU* 3.3 8.8 + - - +
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Residues in contact with ALA 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224A PHE* 3.4 40.4 - - + +
225A GLU* 3.8 18.2 - - + +
228A SER* 3.9 8.0 + - - +
236A THR* 1.3 74.3 - - - +
238A GLU* 1.3 63.1 + - - +
240A LEU* 3.3 4.9 + - - +
241A LYS* 3.1 23.4 + - - +
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Residues in contact with GLU 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236A THR* 3.6 12.3 + - - +
237A ALA* 1.3 78.0 - - - +
239A GLU* 1.3 64.6 + - + +
241A LYS* 3.3 19.0 + - - +
242A GLU* 3.2 22.6 + - + +
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Residues in contact with GLU 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A THR* 4.0 20.1 + - - +
234A LYS 4.3 7.2 - - - +
235A GLY 3.4 7.3 - - - +
236A THR* 2.8 45.3 + - - +
238A GLU* 1.3 81.0 - - + +
240A LEU* 1.3 58.6 + - - +
242A GLU* 3.6 6.2 + - - +
243A LYS* 3.0 36.1 + - + +
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Residues in contact with LEU 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171A PHE* 4.1 16.1 - - + -
224A PHE* 3.8 17.0 - - + +
227A ILE* 3.9 17.5 - - + +
228A SER* 3.3 46.2 - - - +
234A LYS* 3.1 40.4 - - + +
235A GLY* 4.1 2.9 - - - +
236A THR 3.3 4.4 + - - +
237A ALA 3.7 5.4 - - - +
238A GLU 3.3 0.4 - - - -
239A GLU* 1.3 76.2 - - - +
241A LYS* 1.3 60.4 + - - +
243A LYS* 3.3 16.1 + - + +
244A TYR* 2.8 30.0 + - - +
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Residues in contact with LYS 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216A ARG* 5.1 14.8 - - - +
220A SER 5.3 0.7 - - - +
221A ASP* 5.1 19.0 + - + +
224A PHE* 3.7 37.6 - - + -
237A ALA 3.1 13.0 + - - +
238A GLU* 3.3 21.5 + - - +
240A LEU* 1.3 78.3 - - - +
242A GLU* 1.3 57.3 + - - +
244A TYR* 3.6 4.3 + - - +
245A LYS* 3.1 51.7 + - - +
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Residues in contact with GLU 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238A GLU* 3.2 15.9 + - + +
239A GLU* 4.0 6.7 - - - +
241A LYS* 1.3 74.3 - - - +
243A LYS* 1.3 62.7 + - - +
245A LYS* 3.3 19.9 + - + +
246A GLU* 3.1 50.2 + - - +
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Residues in contact with LYS 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A ASP* 4.6 15.5 + - - -
171A PHE* 4.7 13.0 - - + -
234A LYS* 4.8 17.7 - - - +
239A GLU* 3.0 25.7 + - + +
240A LEU* 3.3 24.4 + - + +
242A GLU* 1.3 78.6 - - - +
244A TYR* 1.3 62.2 + - - +
246A GLU* 3.5 7.2 + - - +
247A LEU* 3.2 27.9 + - + +
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Residues in contact with TYR 244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171A PHE* 4.3 10.7 - + + -
172A VAL* 4.0 22.4 - - + -
175A VAL* 4.1 27.8 - - + +
176A ASN* 5.8 3.3 + - + +
216A ARG* 4.1 46.1 - - + +
224A PHE* 3.6 27.4 - + + -
240A LEU 2.8 17.2 + - - +
241A LYS 3.7 4.7 - - - +
242A GLU 3.3 0.2 - - - -
243A LYS* 1.3 75.9 - - - +
245A LYS* 1.3 56.4 + - - +
247A LEU* 3.4 4.1 + - - +
248A THR* 3.0 62.4 + - + +
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Residues in contact with LYS 245 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216A ARG* 3.5 42.2 - - - +
241A LYS* 3.1 41.0 + - - +
242A GLU* 3.5 22.6 - - + +
243A LYS 3.3 0.6 - - - -
244A TYR* 1.3 73.6 - - - +
246A GLU* 1.3 63.8 + - - +
248A THR* 3.5 21.3 - - - +
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Residues in contact with GLU 246 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242A GLU* 3.1 39.2 + - - +
243A LYS* 3.8 9.9 - - - +
244A TYR 3.5 0.2 - - - -
245A LYS* 1.3 77.1 - - - +
247A LEU* 1.3 63.5 + - + +
248A THR 4.6 0.2 - - - -
249A GLN* 4.2 16.5 + - - +
602C GLU* 5.3 4.3 - - - +
604C SER* 6.4 1.8 - - - -
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Residues in contact with LEU 247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A ASP* 3.8 40.8 - - + +
171A PHE* 4.2 14.8 - - + -
172A VAL* 3.4 32.3 - - + -
243A LYS* 3.2 18.8 + - + +
244A TYR* 3.8 5.6 - - - +
245A LYS 3.3 0.4 - - - -
246A GLU* 1.3 81.1 - - + +
248A THR* 1.3 58.3 + - + +
249A GLN* 3.4 14.3 + - - +
348B SER* 5.6 7.0 - - - -
349B ASN* 5.8 2.2 - - - +
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Residues in contact with THR 248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A VAL* 4.1 14.1 - - + -
216A ARG* 5.7 3.5 + - - -
244A TYR* 3.0 52.5 + - + +
245A LYS* 3.5 16.7 + - - +
246A GLU 3.5 0.4 - - - -
247A LEU* 1.3 73.4 - - - +
249A GLN* 1.3 62.4 + - - +
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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