Contacts of the helix formed by residues 235 - 243 (chain A) in PDB entry 3LKB
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 GLY 235 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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234A GLY* 1.3 68.8 - - - -
236A PRO* 1.3 70.5 - - - +
237A ASP* 3.2 4.3 - - - -
238A LEU 2.9 17.8 + - - -
239A ILE* 3.3 8.0 + - - +
251A TRP* 3.4 27.0 - - - -
285A VAL* 4.8 0.9 - - - -
366A PHE* 3.3 27.0 - - - -
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Residues in contact with PRO 236 (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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235A GLY* 1.3 84.6 - - - +
237A ASP* 1.3 62.9 + - - +
239A ILE* 3.4 11.7 + - + +
240A ALA* 3.0 30.9 + - - +
251A TRP* 5.3 0.9 - - + -
257A MET* 5.6 5.4 - - - -
258A ALA* 5.2 7.4 - - + +
280A ASN 5.9 0.4 - - - +
283A GLU* 3.4 50.9 - - + +
284A SER* 5.0 0.4 - - - -
285A VAL* 4.4 7.6 - - + +
364A GLY 5.9 0.4 - - - +
366A PHE* 5.2 1.6 - - + -
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Residues in contact with ASP 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A ASP* 4.5 14.8 - - + +
26A PRO* 4.9 1.0 - - - +
208A ALA* 4.4 13.0 - - + -
234A GLY 3.4 16.0 - - - +
235A GLY 4.1 0.2 - - - -
236A PRO* 1.3 73.5 - - - +
238A LEU* 1.3 66.1 + - - +
240A ALA* 3.3 7.3 + - - +
241A LEU* 3.2 29.5 + - + +
280A ASN* 4.7 5.0 + - - +
284A SER* 2.7 34.2 + - - -
285A VAL* 3.9 14.2 + - - +
286A ASN* 4.4 7.9 + - - -
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Residues in contact with LEU 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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208A ALA* 4.0 13.5 - - + +
211A VAL* 3.9 18.2 - - + -
212A ALA* 5.0 1.3 - - - +
215A LEU* 3.6 15.7 - - + -
233A THR 2.7 32.5 - - - +
234A GLY* 3.9 6.1 + - - -
235A GLY 2.9 13.1 + - - +
237A ASP* 1.3 74.4 - - - +
239A ILE* 1.3 60.2 + - + +
241A LEU* 3.2 3.6 + - - +
242A ALA* 2.8 36.9 + - + +
246A ALA* 3.3 29.8 - - + -
249A PHE* 3.8 28.9 - - + -
366A PHE* 4.7 3.8 - - + -
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Residues in contact with ILE 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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235A GLY 3.3 11.8 + - - +
236A PRO* 3.7 11.0 - - + +
237A ASP 3.3 0.6 - - - -
238A LEU* 1.3 75.4 - - - +
240A ALA* 1.3 59.4 + - - +
243A GLY* 2.7 40.2 + - - +
246A ALA* 3.4 26.2 - - + -
247A GLU 5.5 0.2 - - - +
361A ALA* 4.0 13.0 - - + -
364A GLY* 3.6 43.1 - - - +
365A ARG* 5.1 0.4 - - - -
366A PHE* 4.0 22.2 - - + -
185B LEU* 4.7 0.2 - - - +
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Residues in contact with ALA 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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236A PRO 3.0 18.1 + - - +
237A ASP* 3.6 7.2 - - - +
238A LEU 3.2 0.2 - - - -
239A ILE* 1.3 79.4 - - - +
241A LEU* 1.3 65.3 + - + +
280A ASN* 6.1 5.6 - - + -
183B GLY* 5.0 5.4 - - - +
185B LEU* 3.5 20.1 - - - +
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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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22A ASP* 4.4 13.7 - - + +
208A ALA* 4.0 8.7 - - + -
209A GLY* 3.7 34.1 - - - +
212A ALA* 3.5 15.1 - - + +
216A LYS* 3.2 28.8 + - - +
237A ASP* 3.2 19.6 + - + +
238A LEU 4.0 0.9 - - - +
240A ALA* 1.3 80.4 - - + +
242A ALA* 1.3 59.1 + - - +
243A GLY 3.7 0.2 - - - -
185B LEU* 3.7 9.8 - - + +
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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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212A ALA* 3.9 18.8 - - + +
215A LEU* 4.0 8.3 - - + -
216A LYS* 4.2 10.5 - - - +
238A LEU* 2.8 21.3 + - + +
241A LEU* 1.3 77.1 - - - +
243A GLY* 1.3 64.8 + - - +
244A ASP 3.2 0.7 + - - -
245A ALA* 3.0 20.6 + - + +
246A ALA* 4.0 22.2 - - + +
185B LEU* 3.8 6.2 - - - +
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Residues in contact with GLY 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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239A ILE* 2.7 33.0 + - - +
242A ALA* 1.3 70.8 - - - +
244A ASP* 1.3 58.6 + - - -
246A ALA* 3.0 25.1 + - - +
247A GLU 4.3 0.3 + - - -
185B LEU* 3.6 14.9 - - - +
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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