Contacts of the helix formed by residues 259 - 268 (chain S) in PDB entry 1M5N
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 ALA 259 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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223S CYS* 4.5 19.7 - - + -
255S TYR* 2.9 18.8 + - + +
257S GLY 3.3 0.2 - - - -
258S PRO* 1.3 82.5 - - + +
260S LEU* 1.3 62.8 + - + +
261S PHE 3.7 0.9 - - - -
262S ALA* 3.8 6.6 + - - +
263S ILE* 2.9 33.1 + - + +
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Residues in contact with LEU 260 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219S MET* 4.1 6.7 - - + -
223S CYS* 4.2 15.3 - - - -
241S LEU* 3.8 31.4 - - + -
252S MET* 3.3 24.5 - - + -
255S TYR* 2.9 20.0 + - + +
256S MET* 3.1 46.7 - - + +
259S ALA* 1.3 68.6 - - - +
261S PHE* 1.3 68.4 + - - +
262S ALA 3.2 1.6 - - - -
263S ILE* 2.9 6.0 + - + +
264S THR* 2.8 29.5 + - + +
282S PHE* 4.3 15.9 - - + -
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Residues in contact with PHE 261 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256S MET* 2.6 22.7 + - + +
257S GLY* 4.6 9.4 - - - +
260S LEU* 1.3 71.5 - - - +
262S ALA* 1.3 66.4 + - - +
264S THR* 4.0 6.3 - - - -
265S ILE* 3.0 50.7 + - + +
283S TRP* 4.3 16.3 - + + -
318S ALA* 3.6 29.8 - - + -
321S TYR* 3.7 40.4 - + + -
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Residues in contact with ALA 262 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257S GLY 5.1 4.0 + - - +
258S PRO 5.1 7.0 - - - +
259S ALA* 3.8 10.0 + - - +
260S LEU 3.2 0.6 - - - -
261S PHE* 1.3 82.6 - - - +
263S ILE* 1.3 61.2 + - + +
265S ILE* 4.2 4.2 - - - +
266S GLU* 3.1 27.9 + - - +
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Residues in contact with ILE 263 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223S CYS* 3.7 44.2 - - + +
226S THR* 3.2 30.1 - - + +
227S GLN* 4.3 14.4 - - + +
238S LEU* 4.4 6.3 - - + -
241S LEU* 4.6 8.7 - - + -
259S ALA* 2.9 20.2 - - + +
260S LEU* 2.9 10.5 + - - +
262S ALA* 1.3 76.3 - - + +
264S THR* 1.3 62.7 + - + +
266S GLU* 3.4 8.4 + - - +
267S ALA* 3.1 25.8 + - - +
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Residues in contact with THR 264 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238S LEU* 5.8 5.2 - - + -
241S LEU* 5.4 6.3 - - + -
260S LEU* 2.8 25.4 + - + +
261S PHE* 3.6 1.9 + - - -
263S ILE* 1.3 74.2 - - + +
265S ILE* 1.3 66.8 + - - +
266S GLU 3.1 2.2 + - - -
267S ALA* 3.5 6.4 + - - +
268S MET* 3.1 26.5 + - - +
279S GLY* 4.2 4.6 - - - -
282S PHE* 3.4 52.4 - - + -
283S TRP* 2.6 31.0 + - - -
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Residues in contact with ILE 265 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261S PHE* 3.0 45.6 + - + +
262S ALA* 4.2 4.7 - - - +
264S THR* 1.3 82.3 + - - +
266S GLU* 1.3 67.6 + - + +
268S MET* 3.8 14.0 - - - +
269S LYS* 4.0 15.4 + - - +
283S TRP* 4.2 5.4 - - + +
321S TYR* 3.6 11.4 - - + +
322S LEU* 3.6 30.5 - - + -
325S ILE* 3.3 34.7 - - + +
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Residues in contact with GLU 266 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227S GLN* 5.7 6.3 - - - +
234S ARG* 3.7 23.6 + - - +
262S ALA 3.1 19.6 + - - +
263S ILE* 3.4 9.4 - - + +
264S THR 3.1 0.8 - - - -
265S ILE* 1.3 81.4 - - - +
267S ALA* 1.3 59.4 + - - +
269S LYS* 2.7 50.5 + - - +
270S SER* 5.8 2.0 - - - -
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Residues in contact with ALA 267 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234S ARG* 4.6 6.3 - - - +
238S LEU* 4.3 15.7 - - + -
263S ILE 3.1 12.8 + - - +
264S THR* 3.9 6.7 - - - +
266S GLU* 1.3 86.6 - - + +
268S MET* 1.3 53.9 + - - +
270S SER* 2.6 40.3 + - - -
275S VAL* 3.9 25.8 - - + +
276S ALA* 4.0 3.6 - - - -
279S GLY* 4.3 6.7 - - - -
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Residues in contact with MET 268 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264S THR 3.1 18.2 - - - +
265S ILE* 3.8 13.9 - - - +
266S GLU 2.9 0.6 + - - -
267S ALA* 1.3 75.4 - - - +
269S LYS* 1.3 57.5 + - - +
270S SER 3.2 4.4 + - - +
276S ALA* 3.9 22.4 - - - +
279S GLY* 3.8 11.0 - - - +
280S ILE* 3.1 46.3 - - + +
283S TRP* 4.1 24.0 - - + -
322S LEU* 4.1 13.9 - - + -
325S ILE* 4.0 22.5 - - + +
326S LEU* 3.8 20.4 - - + -
329S THR* 4.7 7.6 + - - +
332S LYS* 5.3 2.1 + - - -
351S CYS* 5.8 0.7 - - - -
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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