Contacts of the helix formed by residues 258 - 272 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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255C VAL* 3.2 26.5 - - - -
256C GLY 2.8 4.4 - - - -
257C THR* 1.3 79.3 - - - +
259C GLY* 1.3 64.0 + - - +
261C ILE* 2.9 6.0 - - - +
262C THR* 2.8 28.8 + - - -
314C VAL 4.9 0.9 - - - -
315C LEU* 3.8 12.1 - - - -
1310C PLP 3.0 7.7 + - - -
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Residues in contact with GLY 259 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228C ASN* 3.5 26.2 - - - +
229C PRO* 4.5 11.1 - - - +
232C HIS* 3.6 5.8 - - - -
257C THR* 3.2 9.1 + - - -
258C GLY* 1.3 77.2 - - - +
260C THR* 1.3 65.2 + - - +
262C THR* 4.6 2.2 - - - -
263C GLY* 2.7 23.9 + - - -
314C VAL* 4.9 0.8 - - - +
1310C PLP 3.4 4.2 + - - -
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Residues in contact with THR 260 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118C VAL* 3.9 20.2 - - + -
232C HIS* 2.9 42.3 - - + +
236C THR* 5.7 0.7 - - + -
253C ALA* 4.8 0.3 - - - +
254C SER* 3.9 11.4 + - - -
259C GLY* 1.3 69.2 - - - -
261C ILE* 1.3 59.4 + - - +
264C ILE* 2.9 38.3 + - - +
373C ILE* 4.0 24.1 - - + +
375C PRO* 5.9 1.5 - - + +
1310C PLP 2.6 34.2 + - + +
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Residues in contact with ILE 261 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251C LEU* 5.3 2.7 - - + -
253C ALA* 3.7 22.4 - - + -
254C SER 4.8 0.2 - - - +
255C VAL* 3.8 23.8 - - + -
258C GLY* 2.9 28.3 - - - +
259C GLY 2.8 3.6 + - - -
260C THR* 1.3 76.6 + - - +
262C THR* 1.3 62.0 + - - +
263C GLY 3.2 1.3 - - - -
264C ILE* 4.8 2.7 - - - -
265C ALA* 2.7 36.3 + - + +
277C ILE* 3.9 16.6 - - + -
278C ILE 3.2 27.6 - - - +
279C GLY* 3.8 11.4 - - - -
315C LEU* 4.2 8.1 - - + -
320C VAL* 3.7 23.8 - - + -
373C ILE* 5.4 0.2 - - - -
1310C PLP 4.8 1.3 - - - +
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Residues in contact with THR 262 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229C PRO* 4.6 1.1 - - + -
258C GLY 2.8 23.7 + - - -
259C GLY* 3.7 2.5 - - - -
261C ILE* 1.3 74.5 - - - +
263C GLY* 1.3 63.8 + - - +
265C ALA* 4.0 0.5 - - - +
266C ARG* 3.1 33.2 + - - +
314C VAL 3.4 18.6 - - - +
315C LEU* 3.2 15.0 - - - +
316C ASP* 3.2 39.2 + - + +
319C VAL* 4.6 9.2 - - - -
1320C HEM 3.9 17.9 - - + -
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Residues in contact with GLY 263 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229C PRO* 3.4 25.1 - - - +
232C HIS* 4.2 0.9 - - - -
233C TYR* 3.3 37.0 - - - -
259C GLY 2.7 13.2 + - - -
260C THR 4.1 0.7 - - - -
262C THR* 1.3 81.0 - - - +
264C ILE* 1.3 59.7 + - - +
267C LYS* 3.6 2.8 + - - +
1320C HEM 4.1 8.7 - - - +
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Residues in contact with ILE 264 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232C HIS* 3.6 17.5 - - + +
236C THR* 3.6 24.0 - - + -
237C ALA* 4.1 11.2 - - - +
240C ILE* 3.8 15.5 - - + -
251C LEU* 3.5 27.4 - - + -
260C THR* 2.9 27.2 + - - +
261C ILE* 4.3 2.2 - - - +
263C GLY* 1.3 74.3 - - - +
265C ALA* 1.3 57.4 + - - +
267C LYS* 4.2 0.3 - - - +
268C LEU* 2.9 40.1 + - + +
373C ILE* 3.3 30.1 - - + -
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Residues in contact with ALA 265 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261C ILE 2.7 24.1 + - - +
264C ILE* 1.3 72.5 - - - +
266C ARG* 1.3 56.8 + - - +
269C LYS* 2.7 39.8 + - - +
277C ILE* 3.7 33.9 - - + -
319C VAL* 3.5 29.4 - - + -
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Residues in contact with ARG 266 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52C CYS* 3.8 14.3 + - - +
54C TRP* 3.3 57.6 - - + +
233C TYR* 3.7 15.5 - - + -
262C THR* 3.1 18.5 + - + +
265C ALA* 1.3 75.2 - - - +
267C LYS* 1.3 59.1 + - - +
269C LYS* 4.3 0.4 - - - -
270C GLU* 3.1 33.1 + - - +
316C ASP* 2.7 43.8 + - - +
319C VAL* 4.0 5.6 - - + -
1320C HEM 3.3 57.6 + - - +
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Residues in contact with LYS 267 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233C TYR* 3.2 64.6 + - + -
234C ASP* 4.6 4.0 + - - +
237C ALA* 3.7 25.4 - - + -
238C ASP* 3.4 28.3 + - - +
241C LEU* 4.2 8.7 - - + -
263C GLY 3.6 1.7 + - - +
264C ILE 4.2 0.4 - - - +
265C ALA 3.2 0.4 - - - -
266C ARG* 1.3 77.2 - - - +
268C LEU* 1.3 61.2 + - - +
269C LYS 3.3 0.2 - - - -
270C GLU* 3.9 3.8 - - - +
271C LYS* 2.8 54.2 + - + +
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Residues in contact with LEU 268 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237C ALA* 4.9 4.9 - - + +
240C ILE* 4.6 5.2 - - + -
241C LEU* 3.4 34.5 - - + -
248C LEU* 3.9 18.2 - - + -
251C LEU* 3.3 33.9 - - + -
264C ILE* 2.9 34.4 + - + +
265C ALA* 3.7 4.0 - - - +
267C LYS* 1.3 78.8 - - - +
269C LYS* 1.3 50.4 + - - +
272C CYS* 2.1 53.3 + - + +
275C CYS* 4.4 3.8 - - + -
277C ILE* 3.9 20.0 - - + -
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Residues in contact with LYS 269 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C TRP* 5.2 0.7 - - + -
56C LEU* 3.2 40.9 - - + +
265C ALA 2.7 24.1 + - - +
266C ARG* 4.6 3.4 - - - +
267C LYS 3.3 0.2 - - - -
268C LEU* 1.3 69.6 - - - +
270C GLU* 1.3 52.6 + - - +
272C CYS 4.2 0.2 - - - -
273C PRO* 2.5 50.9 + - + +
275C CYS 3.5 15.9 + - - +
277C ILE* 3.7 14.4 - - + -
319C VAL* 3.3 26.2 - - + +
321C ASP* 3.0 38.8 + - - -
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Residues in contact with GLU 270 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54C TRP* 2.3 43.2 + - + -
55C GLN 4.3 3.3 - - - +
56C LEU* 4.5 9.6 - - + -
57C GLY 5.6 1.3 - - - +
58C ARG 4.7 9.0 - - - +
233C TYR* 2.7 26.1 + - - -
266C ARG 3.1 21.3 - - - +
267C LYS* 3.4 8.7 + - - +
268C LEU 3.2 0.2 - - - -
269C LYS* 1.3 77.8 - - - +
271C LYS* 1.4 70.7 + - + +
273C PRO* 3.3 12.7 - - - +
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Residues in contact with LYS 271 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60C ALA* 6.4 1.6 - - - -
238C ASP* 6.0 0.9 - - - +
241C LEU* 3.6 21.6 - - + +
246C GLY 5.3 1.9 - - - +
267C LYS* 2.8 41.1 + - + +
270C GLU* 1.4 87.3 - - + +
272C CYS* 1.3 57.6 + - - +
273C PRO* 3.4 3.7 - - - +
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Residues in contact with CYS 272 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241C LEU* 4.2 11.2 - - + -
246C GLY 4.0 13.2 - - - -
248C LEU* 3.4 37.0 - - - -
268C LEU* 2.1 38.8 + - + +
269C LYS* 4.3 0.2 - - - -
271C LYS* 1.3 72.3 - - - +
273C PRO* 1.4 69.1 - - - +
274C GLY* 2.5 8.5 + - - -
275C CYS* 2.5 35.5 + - + +
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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