Contacts of the helix formed by residues 232 - 245 (chain A) in PDB entry 1LV2
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 232 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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185A LYS* 5.2 1.1 - - - -
230A GLN 3.4 4.2 + - - +
231A ILE* 1.3 75.4 - - - +
233A ASP* 1.3 64.6 + - - +
234A ASN* 2.9 21.2 + - - +
235A GLU* 2.9 33.8 + - - +
236A TYR* 3.0 23.8 + - - +
272A TYR* 2.7 26.2 + - - -
276A ARG* 5.2 5.4 + - - -
283A ARG* 5.1 1.1 + - - +
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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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110A GLU* 6.0 0.3 - - - -
114A ARG* 5.3 7.8 + - - -
185A LYS* 2.7 31.1 + - - +
232A ASP* 1.3 76.1 - - - +
234A ASN* 1.3 61.5 + - - +
236A TYR* 3.5 8.5 + - - +
237A ALA* 3.0 29.8 + - - +
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Residues in contact with ASN 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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103A ILE* 3.5 29.7 - - + +
107A ALA* 5.0 7.6 - - - +
232A ASP* 2.9 9.3 + - - +
233A ASP* 1.3 77.3 - - - +
235A GLU* 1.3 65.3 + - - +
237A ALA* 3.3 6.8 + - - +
238A CYS* 3.1 28.4 + - - -
272A TYR* 2.9 42.6 + - + -
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Residues in contact with GLU 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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231A ILE* 3.4 17.2 - - + +
232A ASP* 2.9 32.0 + - - +
234A ASN* 1.3 73.9 - - - +
236A TYR* 1.3 62.6 + - - +
238A CYS* 3.1 5.7 + - - +
239A LEU* 3.0 24.7 + - - +
269A LEU* 3.8 17.9 - - + +
272A TYR* 3.7 19.9 - - + -
273A ILE* 4.1 9.2 - - + +
276A ARG* 4.9 4.3 + - - -
283A ARG* 2.6 50.2 + - - -
287A LEU* 4.1 15.7 - - + +
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Residues in contact with TYR 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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110A GLU* 4.3 11.4 - - - -
178A HIS* 5.1 0.5 + - - -
181A LEU* 3.6 25.4 - - + +
182A GLY* 3.4 25.1 + - - -
185A LYS* 3.2 50.0 - - + +
226A PHE* 4.0 15.9 - + - -
231A ILE* 3.6 16.7 - - + +
232A ASP 3.0 16.9 + - - +
233A ASP* 3.8 5.8 - - - +
235A GLU* 1.3 77.4 - - - +
237A ALA* 1.3 66.1 + - - +
239A LEU* 3.2 3.6 + - + +
240A LYS* 2.9 58.1 + - + +
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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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106A LEU* 3.9 27.3 - - + +
107A ALA* 5.9 1.1 - - - -
110A GLU* 4.4 21.5 - - + +
152A TRP* 5.2 1.6 - - - -
233A ASP 3.0 18.9 + - - +
234A ASN* 3.3 7.4 + - - +
236A TYR* 1.3 80.2 - - - +
238A CYS* 1.3 57.1 + - - +
240A LYS* 3.3 9.5 - - - +
241A ALA* 3.0 28.6 + - - +
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Residues in contact with CYS 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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102A SER* 6.0 0.9 - - - -
103A ILE* 4.1 19.1 - - - -
106A LEU* 4.1 15.5 - - - -
234A ASN 3.1 15.4 + - - -
235A GLU 3.1 9.7 + - - +
237A ALA* 1.3 75.1 - - - +
239A LEU* 1.3 59.8 + - - +
241A ALA* 3.1 1.4 + - - -
242A ILE* 2.8 35.6 + - + +
265A VAL* 3.7 16.7 - - + +
268A GLY* 4.8 0.4 - - - -
269A LEU* 3.8 45.3 - - + -
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Residues in contact with LEU 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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181A LEU* 4.6 20.9 - - + -
226A PHE* 4.8 2.5 - - + -
231A ILE* 4.0 22.0 - - + -
235A GLU 3.0 14.6 + - - +
236A TYR* 3.2 7.4 + - - +
238A CYS* 1.3 74.3 - - - +
240A LYS* 1.3 63.8 + - - +
242A ILE* 3.8 5.2 - - + +
243A VAL* 3.1 31.2 + - - +
269A LEU* 4.7 7.4 - - + -
287A LEU* 4.0 30.1 - - + +
288A LEU* 4.5 13.5 - - + -
290A LEU* 4.3 23.3 - - + -
291A LEU* 4.2 19.3 - - + -
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Residues in contact with LYS 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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110A GLU* 2.8 28.8 + - - +
113A SER* 5.5 1.4 + - - -
152A TRP* 3.7 31.0 - - + +
178A HIS* 3.4 45.8 - - + +
181A LEU* 3.9 19.6 - - + +
236A TYR* 2.9 47.0 + - + +
237A ALA* 3.3 7.6 - - - +
239A LEU* 1.3 78.9 - - - +
241A ALA* 1.3 60.1 + - - +
243A VAL* 3.5 3.3 + - - +
244A PHE* 3.2 21.5 + - - +
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Residues in contact with ALA 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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106A LEU* 3.9 22.0 - - + -
152A TRP* 4.4 6.5 - - + -
237A ALA 3.0 16.2 + - - +
238A CYS 3.1 3.3 + - - +
240A LYS* 1.3 74.0 - - - +
242A ILE* 1.3 59.6 + - - +
244A PHE* 4.2 6.1 - - - -
245A PHE* 2.9 49.9 + - + +
265A VAL* 3.9 17.7 - - + -
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Residues in contact with ILE 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 CYS 2.8 26.2 + - - +
239A LEU* 3.8 7.9 - - + +
241A ALA* 1.3 72.5 - - - +
243A VAL* 1.3 61.9 + - - +
245A PHE 3.8 2.1 + - - -
262A ARG* 2.8 58.0 + - + +
265A VAL* 3.8 18.6 - - + -
266A GLN* 4.4 23.1 - - + +
269A LEU* 4.0 25.8 - - + -
284A PHE* 5.6 0.2 - - + -
288A LEU* 4.3 16.6 - - + -
291A LEU* 4.3 21.5 - - + -
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Residues in contact with VAL 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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174A HIS* 3.8 32.4 + - + +
177A GLU* 3.9 28.0 - - + -
178A HIS* 5.3 3.4 - - + +
181A LEU* 4.5 7.4 - - + -
239A LEU 3.1 18.8 + - - +
240A LYS 3.7 5.2 - - - +
242A ILE* 1.3 79.7 - - - +
244A PHE* 1.3 62.0 + - - +
246A ASP* 3.8 9.0 - - - +
262A ARG* 4.7 2.5 - - - +
291A LEU* 3.6 29.8 - - + -
294A LEU* 4.3 11.7 - - + -
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Residues in contact with PHE 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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149A LEU* 4.6 11.2 - - + -
152A TRP* 3.8 26.0 - + + -
153A ALA* 3.8 24.2 - - + -
156A ILE* 5.7 0.4 - - + -
159A PHE* 3.8 31.0 - + - -
170A LEU* 3.6 47.0 - - + +
171A LEU* 4.0 18.2 - - + -
174A HIS* 4.9 8.7 + - + -
178A HIS* 4.9 6.0 - + + -
240A LYS 3.2 14.3 + - - +
241A ALA* 3.2 5.3 + - - +
243A VAL* 1.3 82.6 - - - +
245A PHE* 1.3 82.9 + + - +
246A ASP* 2.9 9.1 + - - +
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Residues in contact with PHE 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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106A LEU* 5.5 2.2 - - + -
152A TRP* 5.4 0.2 - + - -
156A ILE* 4.0 33.4 - - + -
158A ALA* 5.2 0.9 - - + -
159A PHE* 4.7 8.3 - - + -
170A LEU* 4.2 15.3 - - + -
241A ALA* 2.9 43.7 + - + +
242A ILE 3.9 1.1 - - - -
244A PHE* 1.3 96.7 - + - +
246A ASP* 1.3 58.7 - - - +
247A PRO* 3.5 3.8 - - - +
258A ILE* 3.7 14.6 - - + +
261A MET* 3.7 37.7 - - + -
262A ARG* 2.9 44.2 - - + +
265A VAL* 4.6 13.0 - - + -
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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