Contacts of the helix formed by residues 237 - 245 (chain A) in PDB entry 1LCY
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 SER 237 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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235A THR* 3.2 13.8 + - - -
236A LEU* 1.3 73.8 - - - +
238A PRO* 1.3 77.2 - - - +
239A SER* 3.1 20.6 + - - -
240A ILE* 3.2 22.7 + - - +
241A LEU* 2.9 23.8 + - - +
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Residues in contact with PRO 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 LEU 4.7 0.4 - - - +
237A SER* 1.3 86.8 - - - +
239A SER* 1.3 64.7 + - - +
241A LEU* 3.1 18.3 - - + +
242A ALA* 2.9 26.2 + - - +
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Residues in contact with SER 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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163A GLN* 5.6 4.2 + - - -
237A SER* 3.1 13.2 + - - -
238A PRO* 1.3 82.5 - - - +
240A ILE* 1.3 74.4 + - - +
242A ALA* 3.4 5.4 - - - +
243A GLU* 3.1 32.0 + - - +
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Residues in contact with ILE 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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161A TYR* 5.9 1.3 - - + -
163A GLN* 5.7 2.9 - - - +
192A VAL* 4.6 7.2 - - + -
198A PHE* 3.6 35.7 - - + -
234A LEU* 4.1 18.4 - - + -
235A THR 3.6 15.9 - - - +
236A LEU* 4.1 19.5 - - + -
237A SER* 3.2 24.1 + - - +
239A SER* 1.3 86.0 + - - +
241A LEU* 1.3 58.0 + - - +
243A GLU* 3.5 13.9 - - - +
244A LEU* 2.8 41.6 + - + +
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Residues in contact with LEU 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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236A LEU* 3.7 34.1 - - + +
237A SER 2.9 30.7 + - - +
238A PRO* 3.1 15.7 - - + +
240A ILE* 1.3 73.4 - - - +
242A ALA* 1.3 84.1 + - + +
244A LEU* 3.9 5.1 - - - +
245A GLN* 2.8 46.4 + - - +
251A PHE* 4.7 10.4 - - + -
254A VAL 4.9 6.7 - - - +
255A GLN 3.8 28.3 - - - +
256A HIS 4.6 0.4 - - - +
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Residues in contact with ALA 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 PRO 2.9 21.1 + - - +
239A SER* 3.4 6.5 - - - +
241A LEU* 1.3 84.2 - - + +
243A GLU* 1.3 60.2 + - + +
245A GLN* 3.1 26.6 - - - +
246A LEU* 3.2 9.7 + - - +
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Residues in contact with GLU 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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163A GLN* 4.1 12.1 + - - +
192A VAL* 5.9 2.6 - - + +
196A ILE* 3.5 28.3 - - + +
198A PHE* 5.8 0.5 - - - -
239A SER* 3.2 20.0 - - - +
240A ILE* 3.5 15.6 + - - +
242A ALA* 1.3 76.9 - - - +
244A LEU* 1.3 65.0 + - - +
245A GLN 3.3 0.2 - - - -
246A LEU* 2.9 31.5 - - + +
247A ARG* 2.9 29.0 + - - +
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Residues in contact with LEU 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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192A VAL* 4.1 17.0 - - + +
193A THR* 3.0 32.3 - - + +
234A LEU* 5.4 2.7 - - + -
236A LEU* 4.0 14.1 - - + -
240A ILE* 2.8 28.6 + - + +
241A LEU* 3.9 4.0 - - - +
243A GLU* 1.3 80.0 - - + +
245A GLN* 1.3 60.6 + - - +
246A LEU 3.3 1.0 + - - -
247A ARG* 3.3 20.8 + - - +
251A PHE* 3.4 43.1 - - + +
259A LEU* 4.8 7.4 - - + -
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Residues in contact with GLN 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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241A LEU* 2.8 38.0 + - - +
242A ALA* 3.1 18.5 - - - +
244A LEU* 1.3 72.9 - - - +
246A LEU* 1.3 60.3 + - - +
247A ARG* 3.0 7.6 + - - -
248A GLU 4.0 13.4 + - - +
249A PRO* 4.7 5.1 - - + +
251A PHE* 4.0 29.0 - - + +
252A PRO 3.9 16.2 + - - -
253A ASP* 4.7 5.3 - - - +
254A VAL 4.4 12.6 + - - +
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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