Contacts of the helix formed by residues 263 - 274 (chain A) in PDB entry 3LM0
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 263 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132A GLU* 3.4 19.3 + - - -
261A SER 4.2 1.0 + - - -
262A VAL* 1.3 75.4 - - - +
264A GLN* 1.3 63.4 + - - +
265A LEU* 3.7 5.5 + - - +
266A ALA* 3.3 19.6 + - - +
267A THR* 2.9 24.9 + - - -
292A TRP* 4.0 4.0 + - - -
330A EDO 3.7 32.8 - - - -
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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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262A VAL 3.9 0.8 + - - -
263A SER* 1.3 74.1 - - - +
265A LEU* 1.3 58.6 - - + +
267A THR* 3.1 21.4 + - - +
268A ASP* 2.8 59.1 + - - +
271A GLN* 4.6 4.0 + - - -
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Residues in contact with LEU 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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263A SER* 3.2 5.2 + - - +
264A GLN* 1.3 81.1 - - + +
266A ALA* 1.3 57.9 + - - +
268A ASP* 3.3 14.4 + - - +
269A PHE* 3.0 23.6 + - - +
290A HIS* 3.5 17.7 - - + -
291A SER* 3.9 41.3 - - - +
292A TRP* 3.7 21.0 - - + +
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Residues in contact with ALA 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A GLU* 5.0 0.9 - - - +
229A LEU* 3.7 21.5 - - + +
262A VAL* 3.8 8.1 - - + -
263A SER* 3.3 20.6 + - - +
265A LEU* 1.3 76.0 - - - +
267A THR* 1.3 64.0 + - - +
269A PHE* 3.2 4.7 + - - +
270A ILE* 3.0 27.7 + - - +
292A TRP* 3.5 34.1 - - + +
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Residues in contact with THR 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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254A TYR* 4.5 3.6 - - + -
259A PHE* 3.4 40.0 - - + +
262A VAL* 3.9 3.2 + - - +
263A SER 2.9 15.6 + - - -
264A GLN* 3.3 22.1 + - - +
266A ALA* 1.3 76.7 - - - +
268A ASP* 1.3 52.2 + - - +
270A ILE* 3.2 4.0 + - - +
271A GLN* 2.8 68.1 + - + +
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Residues in contact with ASP 268 (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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264A GLN* 2.8 51.5 + - - +
265A LEU* 3.5 20.0 - - + +
267A THR* 1.3 68.0 - - - +
269A PHE* 1.3 67.4 + - - +
271A GLN* 4.2 9.0 - - - +
272A SER* 3.0 25.5 + - - -
290A HIS* 4.1 13.1 + - + +
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Residues in contact with PHE 269 (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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139A ILE* 3.7 25.8 - - + -
143A LEU* 4.1 7.9 - - + -
221A ILE* 4.2 8.7 - - + -
225A ALA* 4.2 14.4 - - + -
265A LEU 3.0 12.8 + - - +
266A ALA 3.2 9.8 + - - +
268A ASP* 1.3 77.0 - - - +
270A ILE* 1.3 64.3 + - - +
272A SER* 2.6 21.8 + - - -
273A LEU* 3.3 33.3 + - + +
287A CYS* 4.2 29.8 - - + -
290A HIS* 3.7 29.3 + + + -
292A TRP* 3.5 26.9 - + + -
293A LEU* 4.2 11.4 - - + -
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Residues in contact with ILE 270 (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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222A GLY* 4.1 5.6 - - - +
225A ALA* 3.8 21.1 - - + -
226A TYR* 3.8 30.1 - - + +
229A LEU* 4.0 17.7 - - + -
254A TYR* 3.7 16.8 - - + +
259A PHE* 4.3 21.5 - - + -
266A ALA 3.0 18.4 + - - +
267A THR* 3.2 5.1 + - - +
269A PHE* 1.3 77.5 - - - +
271A GLN* 1.3 59.9 + - - +
273A LEU* 3.0 5.8 + - - +
274A LEU* 2.9 53.5 + - + +
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Residues in contact with GLN 271 (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 TYR* 3.4 57.0 - - + +
264A GLN* 4.6 2.9 + - - -
267A THR* 2.8 38.1 + - - +
268A ASP* 4.2 11.9 - - - +
270A ILE* 1.3 74.3 - - - +
272A SER* 1.3 57.4 + - - +
274A LEU* 4.0 4.6 + - - +
275A VAL* 3.2 23.9 - - - +
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Residues in contact with SER 272 (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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268A ASP 3.0 13.8 + - - -
269A PHE* 2.6 24.1 + - - -
271A GLN* 1.3 79.6 - - - +
273A LEU* 1.3 60.1 + - - +
275A VAL* 3.6 19.4 - - - +
280A LYS 4.4 1.6 - - - +
281A ARG* 3.9 0.5 - - - -
282A PRO* 3.4 33.4 - - - +
287A CYS* 5.5 0.9 - - - -
290A HIS* 4.9 7.4 - - - -
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Residues in contact with LEU 273 (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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218A MET* 3.5 53.2 - - + +
219A TRP* 3.8 6.8 - - - -
221A ILE* 4.0 5.6 - - + -
222A GLY* 3.8 17.9 - - - +
269A PHE* 3.3 47.1 - - + +
270A ILE 3.0 6.5 + - - +
272A SER* 1.3 78.8 + - - +
274A LEU* 1.3 59.1 + - - +
275A VAL 3.0 11.4 + - - -
281A ARG* 3.3 24.8 + - + -
282A PRO* 4.0 13.5 - - + -
287A CYS* 3.9 12.8 - - - -
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Residues in contact with LEU 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219A TRP* 3.5 52.9 - - + +
222A GLY* 4.0 9.4 - - - +
223A ILE* 4.0 14.6 - - + +
226A TYR* 4.7 5.2 - - + -
234A PRO* 4.7 4.3 - - + -
235A PHE* 4.4 7.9 - - + -
250A VAL* 3.4 19.3 - - + +
252A VAL* 4.3 18.8 - - + -
254A TYR* 3.9 16.2 + - - +
270A ILE* 2.9 37.4 + - + +
271A GLN* 4.0 3.5 - - - +
272A SER 3.6 0.2 - - - -
273A LEU* 1.3 73.7 - - - +
275A VAL* 1.3 64.9 + - - +
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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