Contacts of the helix formed by residues 255 - 267 (chain A) in PDB entry 1LJ2
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 255 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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253A GLU 3.4 2.1 + - - +
254A LEU* 1.3 77.2 - - - +
256A PRO* 1.3 76.0 - - + +
257A GLU* 3.2 12.6 - - - +
258A ILE* 3.2 13.7 + - + +
259A LYS* 3.2 9.4 + - - +
296B PHE* 3.4 18.1 - - + -
300B LYS* 4.5 7.4 + - - -
310B TYR* 2.8 32.7 + - - -
312B PHE* 3.7 26.5 - - + -
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Residues in contact with PRO 256 (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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254A LEU 3.6 2.0 - - - +
255A ASP* 1.3 87.2 - - + +
257A GLU* 1.3 70.2 + - - +
259A LYS* 3.8 8.7 - - + +
260A ALA* 2.8 31.1 + - - +
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Residues in contact with GLU 257 (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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255A ASP* 3.2 6.4 - - - +
256A PRO* 1.3 92.5 - - - +
258A ILE* 1.3 60.3 + - - +
260A ALA* 3.3 5.8 + - - +
261A ASP* 2.8 32.3 + - - +
312B PHE* 3.7 45.8 - - + +
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Residues in contact with ILE 258 (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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254A LEU* 3.7 33.7 - - + -
255A ASP* 3.2 11.0 + - + +
257A GLU* 1.3 77.1 - - - +
259A LYS* 1.3 59.0 + - - +
261A ASP* 3.3 6.2 + - - +
262A ILE* 2.9 34.3 + - + +
292B TYR* 3.8 21.1 - - + +
296B PHE* 3.9 34.3 - - + -
312B PHE* 3.3 35.7 - - + -
140D ILE* 4.3 6.7 - - + -
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Residues in contact with LYS 259 (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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249A LEU* 3.1 44.9 - - + +
250A ARG* 2.9 26.2 + - + +
252A MET* 2.5 33.7 + - - -
253A GLU* 4.8 0.2 - - - +
254A LEU* 3.3 25.1 + - + +
255A ASP 3.2 9.7 + - - +
256A PRO* 3.9 9.4 - - + +
258A ILE* 1.3 76.4 - - - +
260A ALA* 1.3 61.5 + - - +
263A GLU* 2.8 38.6 + - - +
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Residues in contact with ALA 260 (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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256A PRO 2.8 20.7 + - - +
257A GLU* 3.6 6.7 - - - +
259A LYS* 1.3 75.9 - - - +
261A ASP* 1.3 63.4 + - - +
263A GLU* 3.4 6.8 + - - +
264A GLN* 3.1 25.3 + - - +
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Residues in contact with ASP 261 (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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257A GLU 2.8 17.8 + - - +
258A ILE* 3.5 7.9 - - - +
260A ALA* 1.3 79.1 - - - +
262A ILE* 1.3 62.6 + - + +
264A GLN* 3.6 15.9 - - - +
265A GLN* 2.6 51.7 + - - +
137D ARG* 3.5 15.7 + - - -
138D LYS* 2.9 34.7 + - + +
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Residues in contact with ILE 262 (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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249A LEU* 3.6 33.7 - - + -
254A LEU* 4.6 4.7 - - + -
258A ILE* 2.9 36.0 + - + +
259A LYS 3.1 0.4 + - - -
261A ASP* 1.3 82.0 - - + +
263A GLU* 1.3 65.0 + - - +
265A GLN* 3.0 13.2 + - + +
266A ILE* 3.0 32.0 + - + +
284A VAL* 5.5 3.8 - - + -
288A LEU* 3.8 31.4 - - + -
291A ASP* 6.0 2.2 - - - +
285B ILE* 6.2 0.2 - - + -
289B ILE* 4.4 15.7 - - + -
292B TYR* 5.1 5.2 - - + -
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Residues in contact with GLU 263 (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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246A GLU* 3.3 31.6 - - + +
249A LEU* 3.8 15.4 - - + +
250A ARG* 3.2 46.4 + - - +
259A LYS* 2.8 27.2 + - - +
260A ALA* 3.9 6.8 - - - +
262A ILE* 1.3 72.6 - - - +
264A GLN* 1.3 63.3 + - - +
266A ILE* 3.0 7.3 + - - +
267A ASN* 2.9 36.5 + - - +
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Residues in contact with GLN 264 (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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260A ALA 3.1 17.0 + - - +
261A ASP* 3.6 17.9 - - - +
263A GLU* 1.3 76.5 - - - +
265A GLN* 1.3 60.8 + - + +
267A ASN* 3.2 14.6 - - - +
268A SER* 3.1 20.6 - - - -
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Residues in contact with GLN 265 (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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261A ASP* 2.6 37.6 + - - +
262A ILE* 3.0 14.7 + - + +
264A GLN* 1.3 79.9 - - + +
266A ILE* 1.3 65.1 + - - +
268A SER* 3.2 17.3 - - - -
269A ILE* 3.8 4.0 + - - +
280A ASP* 5.8 0.5 - - - +
284A VAL* 3.9 30.5 - - + +
287A ASN* 3.0 35.7 + - - +
291A ASP* 5.4 0.6 + - - -
137D ARG* 4.1 15.8 - - - +
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Residues in contact with ILE 266 (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 THR* 3.5 23.6 - - + +
245A ILE* 4.3 29.4 - - + -
246A GLU* 3.3 31.2 - - + +
249A LEU* 5.9 0.7 - - + -
262A ILE* 3.0 28.2 + - + +
263A GLU* 3.0 8.9 + - - +
265A GLN* 1.3 73.6 - - - +
267A ASN* 1.3 58.5 + - - +
268A SER 2.8 11.1 + - - -
269A ILE* 3.0 33.3 + - + +
284A VAL* 3.9 29.8 - - + -
285B ILE* 4.8 2.5 - - + -
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Residues in contact with ASN 267 (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 THR* 4.3 6.7 - - + -
246A GLU* 3.4 23.5 + - - +
263A GLU* 2.9 29.3 + - - +
264A GLN* 3.2 17.4 - - - +
266A ILE* 1.3 72.2 - - - +
268A SER* 1.3 58.0 + - - +
269A ILE 3.4 4.5 - - - +
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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