Contacts of the helix formed by residues 285 - 300 (chain C) in PDB entry 2XMR
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 GLN 285 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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274C MET* 3.2 24.0 - - + +
275C ALA 3.4 15.0 + - - +
276C ASP* 3.5 15.1 + - - +
277C SER* 3.1 25.3 - - - -
281C PRO 2.8 13.4 + - - +
284C THR* 1.3 96.4 - - - +
286C PRO* 1.4 65.5 - - - +
287C GLY 3.2 2.6 + - - +
288C LYS* 3.5 15.1 + - + +
289C LEU* 3.0 22.7 + - - +
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Residues in contact with PRO 286 (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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67C PRO* 4.5 6.3 - - + +
68C LEU* 3.8 23.9 - - + +
71C PHE* 4.1 31.9 - - + -
281C PRO 4.0 0.4 - - - -
282C GLN 4.4 7.2 - - - +
283C LEU 3.7 14.4 - - - +
284C THR 3.3 8.3 - - - +
285C GLN* 1.4 89.3 - - - +
287C GLY* 1.3 51.9 + - - +
289C LEU* 4.4 0.7 - - + -
290C THR* 2.7 41.8 + - - -
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Residues in contact with GLY 287 (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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71C PHE* 3.6 25.5 - - - -
73C ASP* 5.7 0.9 - - - +
285C GLN 3.2 1.2 - - - -
286C PRO* 1.3 84.1 - - - +
288C LYS* 1.3 56.6 + - - +
290C THR* 3.7 2.3 - - - -
291C GLU* 3.1 28.0 + - - +
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Residues in contact with LYS 288 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272C LEU* 5.4 10.5 - - + -
274C MET* 3.4 32.4 - - + +
275C ALA* 4.5 22.4 + - - +
285C GLN* 3.5 16.6 + - + +
287C GLY* 1.3 72.4 - - - +
289C LEU* 1.3 60.3 + - - +
291C GLU* 3.3 12.3 + - + +
292C ALA* 2.9 28.4 + - - +
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Residues in contact with LEU 289 (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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68C LEU* 3.8 21.5 - - + -
74C MET* 5.0 1.1 - - + -
153C VAL* 5.3 2.5 - - + -
155C ILE* 4.3 12.1 - - + -
244C MET* 5.0 5.4 - - + -
246C VAL* 4.0 36.3 - - + -
272C LEU* 4.4 4.7 - - + -
274C MET* 4.0 13.9 - - + +
281C PRO* 4.8 0.9 - - + +
282C GLN* 3.5 37.9 - - + +
285C GLN 3.0 18.6 + - - +
286C PRO 3.9 3.4 - - - +
288C LYS* 1.3 77.6 - - - +
290C THR* 1.3 56.8 + - - +
292C ALA* 3.3 6.4 + - + +
293C PHE* 2.9 27.6 + - + +
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Residues in contact with THR 290 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C LEU* 3.7 4.0 - - - +
71C PHE* 3.6 9.9 - - - -
73C ASP* 3.6 13.2 - - + -
74C MET* 3.4 61.0 - - + +
77C ILE* 3.7 12.9 - - + +
286C PRO 2.7 27.8 + - - -
287C GLY 3.7 4.7 - - - -
289C LEU* 1.3 68.7 - - - +
291C GLU* 1.3 67.0 + - - +
293C PHE* 3.2 2.9 + - - +
294C LYS* 3.0 22.3 + - - +
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Residues in contact with GLU 291 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C ILE* 5.7 0.2 - - - -
287C GLY 3.1 15.6 + - - +
288C LYS* 3.3 14.8 + - + +
290C THR* 1.3 77.1 - - - +
292C ALA* 1.3 62.8 + - - +
294C LYS* 3.3 24.5 + - - +
295C TYR* 2.7 50.1 + - + +
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Residues in contact with ALA 292 (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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244C MET* 3.9 17.5 - - + +
272C LEU* 3.6 34.3 - - + -
288C LYS* 2.9 14.6 + - + +
289C LEU* 3.5 8.3 - - - +
290C THR 3.3 0.2 - - - -
291C GLU* 1.3 77.1 - - - +
293C PHE* 1.3 57.1 + - - +
295C TYR* 3.2 12.0 + - - +
296C PHE* 2.8 27.7 + - - +
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Residues in contact with PHE 293 (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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51C ILE* 4.0 31.9 - - + -
69C PHE* 6.0 1.6 - + - -
74C MET* 3.9 27.4 - - + -
77C ILE* 4.1 8.1 - - + -
78C ILE* 4.4 4.9 - - + -
127C ILE* 4.3 10.8 - - + -
129C VAL* 4.2 11.0 - - + -
153C VAL* 3.8 32.1 - - + -
244C MET* 4.1 4.4 - - + +
289C LEU* 2.9 15.1 + - + +
290C THR 3.2 8.5 + - - +
292C ALA* 1.3 72.7 - - - +
294C LYS* 1.3 66.2 + - - +
296C PHE* 3.1 15.0 + + - +
297C LEU* 2.9 56.9 + - + +
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Residues in contact with LYS 294 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C ILE* 3.7 27.8 - - + +
290C THR 3.0 7.5 + - - +
291C GLU* 3.4 15.7 - - - +
293C PHE* 1.3 76.1 - - - +
295C TYR* 1.3 87.0 + - + +
297C LEU* 3.4 7.0 + - - +
298C GLN* 3.1 35.2 + - - +
304C ALA* 3.6 36.2 + - - +
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Residues in contact with TYR 295 (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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291C GLU* 2.7 53.4 + - + +
292C ALA* 3.2 9.9 + - - +
294C LYS* 1.3 96.6 + - + +
296C PHE* 1.3 59.4 + - - +
298C GLN* 3.3 26.7 + - - +
299C GLY* 3.0 24.9 + - - -
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Residues in contact with PHE 296 (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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127C ILE* 4.4 4.9 - - + -
151C GLY* 4.1 4.5 - - - -
152C LEU 3.4 23.6 - - - -
153C VAL* 3.8 25.1 - - + -
242C PRO* 3.4 28.7 - - + -
243C VAL 3.8 6.7 - - - -
244C MET* 3.7 40.6 - - + -
270C SER* 4.9 4.0 - - - -
292C ALA 2.8 14.3 + - - +
293C PHE* 3.1 16.8 + + - +
295C TYR* 1.3 76.8 - - - +
297C LEU* 1.3 59.3 + - + +
299C GLY* 3.1 4.7 + - - -
300C MET* 3.0 44.3 + - - +
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Residues in contact with LEU 297 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C ILE* 3.4 32.8 - - + -
81C PHE* 4.0 25.8 - - + -
127C ILE* 3.7 29.8 - - + -
293C PHE* 2.9 40.8 + - + +
294C LYS 3.5 6.3 - - - +
296C PHE* 1.3 74.3 - - + +
298C GLN* 1.3 62.5 + - - +
300C MET* 3.1 18.4 + - - +
301C GLY 3.3 0.5 + - - -
302C TYR* 3.0 30.1 + - + +
304C ALA* 3.9 17.3 - - + -
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Residues in contact with GLN 298 (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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294C LYS* 3.1 24.3 + - - +
295C TYR* 3.5 28.8 - - - +
296C PHE 3.3 0.2 - - - -
297C LEU* 1.3 75.7 - - - +
299C GLY* 1.3 57.0 + - - +
301C GLY* 3.0 19.1 + - - -
302C TYR 3.3 17.0 + - - +
303C MET* 5.0 1.8 - - - -
304C ALA* 3.1 28.1 - - - +
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Residues in contact with GLY 299 (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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242C PRO* 4.8 8.4 - - - +
295C TYR 3.0 14.6 + - - -
296C PHE* 3.1 5.3 + - - -
298C GLN* 1.3 76.1 - - - +
300C MET* 1.3 61.3 + - - +
301C GLY 3.5 0.5 + - - -
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Residues in contact with MET 300 (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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127C ILE* 3.7 23.6 - - + -
150C GLU* 3.5 46.5 - - + +
151C GLY* 3.9 5.4 - - - -
242C PRO* 3.9 22.9 - - + -
296C PHE* 3.0 38.6 + - + +
297C LEU* 3.1 14.3 + - - +
299C GLY* 1.3 77.5 - - - +
301C GLY* 1.3 56.9 + - - +
302C TYR* 3.6 31.7 - - + -
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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