Contacts of the helix formed by residues 258 - 272 (chain F) in PDB entry 1M54
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 GLY 258 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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255F VAL* 3.2 28.3 - - - +
257F THR* 1.3 78.4 - - - +
259F GLY* 1.3 62.5 + - - +
260F THR 3.6 1.3 - - - -
261F ILE* 4.3 2.2 - - - -
262F THR* 2.4 33.2 + - - -
314F VAL 3.7 6.9 - - - +
315F LEU* 3.5 17.8 - - - +
1610F PLP 3.3 1.0 + - - -
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Residues in contact with GLY 259 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228F ASN* 3.0 25.1 - - - -
229F PRO* 3.6 14.6 - - - +
232F HIS* 3.4 12.1 - - - -
257F THR* 3.0 13.1 + - - +
258F GLY* 1.3 80.4 - - - +
260F THR* 1.3 59.4 + - - +
263F GLY* 3.4 14.4 + - - -
1610F PLP 3.4 6.0 + - - -
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Residues in contact with THR 260 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118F VAL* 3.9 17.5 - - + -
232F HIS* 3.0 39.3 - - + +
236F THR* 5.8 1.1 - - + -
253F ALA* 4.4 5.0 - - - +
254F SER 4.9 1.2 + - - -
258F GLY 3.6 0.2 - - - -
259F GLY* 1.3 71.6 - - - +
261F ILE* 1.3 73.2 + - - +
263F GLY 3.6 0.2 + - - -
264F ILE* 3.0 34.0 + - - +
373F ILE* 4.0 25.5 - - + +
1610F PLP 2.8 34.5 + - - +
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Residues in contact with ILE 261 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251F LEU* 5.8 0.7 - - - -
253F ALA* 4.1 17.5 - - + +
255F VAL* 3.6 38.1 - - + -
258F GLY* 4.0 6.3 - - - +
260F THR* 1.3 82.1 + - - +
262F THR* 1.3 57.5 + - - +
264F ILE* 4.7 3.1 - - - -
265F ALA* 2.8 40.8 + - - +
277F ILE* 3.3 21.0 - - + +
278F ILE 3.5 24.0 - - - +
279F GLY* 3.7 8.7 - - - -
315F LEU* 4.4 5.6 - - + -
320F VAL* 3.5 32.3 - - + -
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Residues in contact with THR 262 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229F PRO* 4.9 5.8 - - + -
258F GLY 2.4 25.6 + - - -
259F GLY 4.2 0.7 - - - -
260F THR 3.3 0.4 - - - -
261F ILE* 1.3 77.2 - - - +
263F GLY* 1.3 61.4 + - - +
266F ARG* 2.8 63.0 + - + +
315F LEU* 3.2 26.4 - - - +
316F ASP* 3.4 24.3 + - + +
319F VAL* 4.2 7.9 - - - -
1620F HEM 4.9 5.6 - - + -
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Residues in contact with GLY 263 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229F PRO 3.4 26.6 + - - -
232F HIS 4.1 0.7 - - - -
233F TYR* 3.0 39.4 - - - -
259F GLY 3.4 9.8 + - - -
260F THR 4.0 0.2 - - - -
262F THR* 1.3 78.7 - - - +
264F ILE* 1.3 64.6 + - - +
266F ARG* 4.8 0.7 - - - -
267F LYS* 3.2 4.2 + - - +
1620F HEM 4.4 4.7 - - - -
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Residues in contact with ILE 264 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232F HIS* 3.7 15.0 - - + +
236F THR* 3.7 22.0 - - + -
237F ALA* 4.1 14.1 - - + -
240F ILE* 4.0 9.6 - - + -
251F LEU* 3.2 18.6 - - + -
260F THR* 3.0 21.0 + - - +
261F ILE* 4.1 2.2 - - - +
263F GLY* 1.3 72.4 - - - +
265F ALA* 1.3 69.2 + - - +
267F LYS* 2.7 16.8 + - - +
268F LEU* 2.7 41.1 + - + -
277F ILE* 4.8 0.7 - - + -
373F ILE* 3.5 31.0 - - + -
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Residues in contact with ALA 265 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261F ILE 2.8 25.2 + - - +
262F THR 3.5 2.0 - - - +
264F ILE* 1.3 74.6 - - - +
266F ARG* 1.3 55.6 + - - +
268F LEU* 2.9 1.6 + - - +
269F LYS* 2.5 39.4 + - + +
277F ILE* 3.4 25.1 - - + +
319F VAL* 2.8 36.3 - - + +
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Residues in contact with ARG 266 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52F CYS* 3.9 11.7 + - - +
54F TRP* 2.8 70.0 + - + +
233F TYR* 4.2 6.7 - - + -
262F THR* 2.8 37.0 + - - +
263F GLY 4.0 2.9 - - - +
265F ALA* 1.3 74.0 - - - +
267F LYS* 1.3 65.8 + - - +
269F LYS* 3.4 2.2 + - - +
270F GLU* 3.0 25.2 + - - +
316F ASP* 3.3 25.8 + - - +
319F VAL* 3.6 12.3 - - + +
1620F HEM 3.1 49.9 + - - +
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Residues in contact with LYS 267 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60F ALA* 6.3 1.2 - - - +
233F TYR* 3.1 63.3 + - + +
234F ASP* 4.9 2.2 + - - +
237F ALA* 3.4 24.0 - - + +
238F ASP* 3.6 20.0 + - - +
241F LEU* 4.6 8.1 - - + -
263F GLY 3.2 11.8 + - - +
264F ILE 2.7 13.1 + - - +
266F ARG* 1.3 73.4 - - - +
268F LEU* 1.3 56.1 + - + +
270F GLU* 2.7 36.5 + - - +
271F LYS* 2.9 31.3 + - + +
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Residues in contact with LEU 268 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237F ALA* 5.7 2.0 - - + +
240F ILE* 5.5 1.6 - - + -
241F LEU* 3.3 19.5 - - + -
248F LEU* 3.2 31.4 - - + -
251F LEU* 3.5 16.6 - - + -
264F ILE* 2.7 42.2 + - + +
265F ALA* 3.3 8.5 - - - +
267F LYS* 1.3 71.6 - - + +
269F LYS* 1.3 61.9 + - - +
270F GLU 2.9 4.9 - - - -
271F LYS* 4.4 1.3 - - - +
272F CYS* 2.8 49.3 + - + +
275F CYS* 4.3 9.2 - - + -
277F ILE* 3.8 16.2 - - + -
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Residues in contact with LYS 269 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54F TRP* 4.9 1.3 - - + -
56F LEU* 3.0 34.4 - - + +
265F ALA* 2.5 31.6 + - - +
266F ARG* 3.8 6.3 - - - +
267F LYS 3.3 0.2 - - - -
268F LEU* 1.3 72.8 - - - +
270F GLU* 1.3 59.4 + - - +
273F PRO* 3.4 31.2 + - + +
275F CYS 4.6 8.8 + - - -
276F ARG* 5.6 0.2 - - - +
277F ILE* 4.6 8.7 - - + -
318F THR 5.3 1.3 - - - +
319F VAL* 4.5 26.7 - - + +
321F ASP* 2.6 42.5 + - - -
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Residues in contact with GLU 270 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54F TRP* 3.3 19.2 + - + -
56F LEU* 3.7 25.1 - - + -
58F ARG 4.6 10.9 - - - +
60F ALA* 5.1 9.2 + - - +
233F TYR* 2.5 33.7 + - - -
266F ARG 3.0 20.0 - - - +
267F LYS* 2.7 13.5 + - - +
269F LYS* 1.3 80.0 - - - +
271F LYS* 1.3 79.3 + - + +
273F PRO* 4.0 5.0 - - - +
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Residues in contact with LYS 271 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60F ALA* 6.0 4.4 - - - +
238F ASP* 5.9 0.2 - - - +
241F LEU* 3.6 29.6 - - + -
267F LYS* 2.9 37.1 + - + +
270F GLU* 1.3 90.8 + - - +
272F CYS* 1.3 59.6 + - - +
273F PRO* 3.4 7.1 - - - +
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Residues in contact with CYS 272 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241F LEU* 4.3 7.4 - - + -
246F GLY* 4.2 14.8 - - - +
247F LYS* 5.2 0.2 - - - -
248F LEU* 3.8 29.2 - - - -
268F LEU* 2.8 27.6 + - + +
271F LYS* 1.3 80.7 - - - +
273F PRO* 1.3 65.0 - - - +
274F GLY* 2.7 10.3 + - - +
275F CYS* 2.9 34.6 + - - +
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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