Contacts of the helix formed by residues 230 - 239 (chain A) in PDB entry 1L4E
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 ASP 230 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145A ARG* 2.9 35.6 + - - -
227A ASN* 2.9 28.2 + - - +
228A PRO 3.2 0.2 - - - -
229A ARG* 1.3 79.1 - - - +
231A GLY* 1.3 62.3 + - - +
232A ILE* 3.2 13.2 + - - +
233A ASP* 3.0 25.7 + - + +
234A VAL* 3.1 11.2 + - - +
276A GLN* 4.5 0.7 - - - -
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Residues in contact with GLY 231 (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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190A PHE* 4.0 21.2 - - - -
229A ARG 3.9 0.4 + - - -
230A ASP* 1.3 73.0 + - - +
232A ILE* 1.3 56.6 + - - +
234A VAL* 3.4 2.6 + - - +
235A LEU* 3.1 32.3 + - - +
273A ALA 4.4 1.8 - - - -
276A GLN* 3.7 16.1 - - - +
277A ILE* 3.9 22.7 - - - +
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Residues in contact with ILE 232 (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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4A LEU* 4.2 9.6 - - + -
8A LEU* 5.7 2.7 - - + -
145A ARG* 3.8 37.7 - - + +
148A ALA* 4.3 12.8 - - + -
149A GLU* 4.0 27.4 - - + +
152A LEU* 4.2 17.0 - - + -
230A ASP* 3.1 9.4 + - - +
231A GLY* 1.3 73.6 - - - +
233A ASP* 1.3 66.8 + - - +
235A LEU* 3.3 6.0 + - + +
236A SER* 2.9 23.9 + - - -
277A ILE* 3.6 30.2 - - + +
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Residues in contact with ASP 233 (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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145A ARG* 3.8 10.6 + - - +
226A PRO* 3.3 3.6 - - - +
227A ASN* 2.7 33.4 + - - +
230A ASP* 3.0 32.9 + - + +
232A ILE* 1.3 77.1 - - - +
234A VAL* 1.3 62.8 + - - +
236A SER* 3.2 8.5 + - - -
237A LYS* 3.0 60.9 + - - +
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Residues in contact with VAL 234 (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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186A MET* 3.6 28.9 - - + -
189A VAL* 4.1 14.6 - - + -
190A PHE* 3.7 30.5 - - + -
226A PRO* 4.0 9.6 - - + -
227A ASN 3.3 29.4 - - - +
228A PRO* 4.0 3.6 - - + -
230A ASP 3.1 7.0 + - - +
231A GLY 3.7 6.1 - - - +
233A ASP* 1.3 77.7 - - - +
235A LEU* 1.3 62.1 + - - +
238A VAL* 3.0 33.9 + - + +
239A GLY* 3.5 1.2 + - - -
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Residues in contact with LEU 235 (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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143A MET* 3.9 5.7 - - - +
148A ALA* 5.3 2.7 - - + -
152A LEU* 4.9 7.6 - - + -
186A MET* 3.7 27.4 - - + -
231A GLY 3.1 20.9 + - - +
232A ILE* 3.7 6.7 - - - +
234A VAL* 1.3 77.2 - - - +
236A SER* 1.3 57.6 + - - +
239A GLY* 2.9 31.9 + - - +
240A GLY 3.9 1.7 + - - -
243A LEU* 4.0 16.8 - - + -
244A VAL* 4.1 23.1 - - + +
247A THR* 3.9 31.0 - - + +
273A ALA* 3.9 17.5 - - + -
277A ILE* 4.2 9.9 - - + -
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Residues in contact with SER 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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142A ALA* 3.1 5.4 + - - +
143A MET* 3.0 60.5 + - - +
144A SER 3.9 9.2 - - - -
145A ARG* 4.1 12.8 + - - +
148A ALA* 3.9 9.2 - - - +
232A ILE 2.9 18.5 + - - -
233A ASP* 3.2 10.4 + - - -
235A LEU* 1.3 78.0 - - - +
237A LYS* 1.3 64.3 + - - +
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Residues in contact with LYS 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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137A ILE* 3.5 6.6 - - - +
141A PRO* 3.5 16.1 - - + +
142A ALA 3.2 17.8 + - - -
224A ASN* 3.4 41.8 + - + +
225A GLN* 3.4 16.2 + - - +
226A PRO* 3.7 11.4 - - + -
233A ASP* 3.0 50.6 + - - +
234A VAL 4.1 0.7 - - - +
236A SER* 1.3 82.8 + - - +
238A VAL* 1.3 64.2 + - - +
239A GLY 3.6 0.7 - - - -
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Residues in contact with VAL 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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137A ILE* 3.9 10.2 - - + +
182A PRO* 3.1 28.1 - - - +
185A ALA* 3.9 20.6 - - + +
186A MET* 4.1 8.5 - - + +
189A VAL* 4.8 1.6 - - + -
220A ALA* 3.8 33.7 - - + +
221A ILE* 4.4 3.1 - - + +
224A ASN* 4.0 11.4 - - + +
226A PRO* 4.3 17.3 - - + -
234A VAL* 3.0 29.0 + - + +
237A LYS* 1.3 79.1 - - - +
239A GLY* 1.3 61.6 + - - +
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Residues in contact with GLY 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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70A HIS* 4.7 0.2 + - - -
134A CYS* 4.4 2.9 - - - -
137A ILE* 3.9 4.7 - - - +
142A ALA* 3.4 14.6 - - - +
182A PRO* 3.6 16.5 - - - +
186A MET* 3.9 21.5 - - - -
234A VAL 3.5 1.8 + - - -
235A LEU* 2.9 20.5 + - - -
237A LYS 3.6 1.4 - - - -
238A VAL* 1.3 82.8 - - - +
240A GLY* 1.3 58.0 + - - -
243A LEU* 4.5 1.3 - - - -
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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