Contacts of the helix formed by residues 289 - 308 (chain R) in PDB entry 6CMO
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 THR 289 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36R GLN* 5.8 2.7 - - - +
40R LEU* 5.4 9.6 - - + -
182R GLY* 5.1 1.1 - - - -
183R LEU* 3.4 30.4 + - + +
285R PRO* 2.5 24.5 + - - +
286R ILE* 3.0 11.8 + - + -
288R MET* 1.3 80.3 - - - +
290R ILE* 1.3 68.8 + - + +
291R PRO* 3.5 1.4 - - - -
292R ALA* 3.7 12.1 + - - +
293R PHE* 3.2 32.4 - - + -
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Residues in contact with ILE 290 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267R PRO* 6.5 1.1 - - + -
271R VAL* 5.4 8.1 - - + -
286R ILE* 2.9 32.5 + - + +
287R PHE* 4.5 8.5 - - + +
289R THR* 1.3 75.3 - - + +
291R PRO* 1.4 80.4 - - + +
293R PHE* 3.6 21.9 + - + -
294R PHE* 2.9 36.6 + - + +
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Residues in contact with PRO 291 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267R PRO 5.7 0.4 - - - -
268R TYR* 3.6 34.0 - - + +
271R VAL* 3.8 24.0 - - + -
287R PHE 3.4 21.1 - - - +
288R MET 4.5 2.5 - - - -
289R THR 3.6 3.1 - - - +
290R ILE* 1.4 103.1 - - + +
292R ALA* 1.3 58.8 + - - +
294R PHE* 4.1 7.0 - - + +
295R ALA* 2.9 30.7 + - - +
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Residues in contact with ALA 292 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186R SER* 6.1 3.1 - - - +
268R TYR* 5.2 4.9 - - - -
288R MET 5.2 5.6 - - - +
289R THR 4.0 9.2 - - - +
290R ILE 3.3 0.6 - - - -
291R PRO* 1.3 79.9 - - - +
293R PHE* 1.3 58.5 + - - +
295R ALA* 3.1 9.3 + - - +
296R LYS* 2.9 41.1 + - - +
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Residues in contact with PHE 293 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40R LEU* 5.8 10.8 - - + -
43R TYR* 3.3 35.0 - + - -
44R MET* 4.9 10.7 - - + +
289R THR* 3.2 43.7 - - + -
290R ILE* 3.6 25.6 - - + -
292R ALA* 1.3 76.8 - - - +
294R PHE* 1.3 64.8 + + + +
295R ALA 3.3 0.2 - - - -
296R LYS* 3.3 25.0 - - + +
297R SER* 2.9 28.0 + - - -
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Residues in contact with PHE 294 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263R ILE* 3.8 31.9 - - + -
264R CYS* 4.0 19.5 - - + -
267R PRO* 4.8 15.3 - - + -
268R TYR 6.2 0.9 - - - -
290R ILE* 2.9 26.2 + - + +
291R PRO* 4.1 7.0 - - + +
293R PHE* 1.3 82.6 - + + +
295R ALA* 1.3 59.0 + - - +
297R SER* 2.4 32.0 + - - -
298R ALA* 3.0 12.2 + - + +
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Residues in contact with ALA 295 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264R CYS 5.3 2.5 - - - +
265R TRP* 5.6 12.7 - - + -
268R TYR* 5.1 14.6 - - + -
291R PRO 2.9 20.5 + - - +
292R ALA* 3.4 5.6 - - - +
294R PHE* 1.3 77.2 - - - +
296R LYS* 1.3 60.0 + - + +
298R ALA* 3.2 11.1 + - - +
299R ALA* 2.9 25.1 + - - +
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Residues in contact with LYS 296 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44R MET* 4.8 18.4 - - + -
91R PHE* 3.5 44.5 - - + -
94R THR* 5.1 13.0 - - + +
186R SER* 5.2 11.9 + - - +
292R ALA* 2.9 22.6 + - - +
293R PHE* 3.3 38.8 - - + +
294R PHE 3.3 0.2 - - - -
295R ALA* 1.3 75.7 - - + +
297R SER* 1.3 59.0 + - - +
299R ALA* 3.1 9.6 + - - +
300R ILE* 3.0 28.1 + - - +
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Residues in contact with SER 297 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47R LEU* 5.8 3.6 - - - -
293R PHE* 2.9 14.2 + - - -
294R PHE* 2.4 43.6 + - - -
296R LYS* 1.3 74.8 - - - +
298R ALA* 1.3 57.2 + - - +
300R ILE* 3.3 13.0 - - - +
301R TYR* 2.9 28.3 + - - +
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Residues in contact with ALA 298 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264R CYS* 3.8 39.7 - - + +
265R TRP* 5.5 8.7 - - + -
294R PHE* 3.0 14.4 + - + +
295R ALA* 3.2 12.1 + - - +
297R SER* 1.3 78.1 + - - +
299R ALA* 1.3 57.5 + - - +
301R TYR* 3.3 8.6 - - - +
302R ASN* 3.0 37.7 + - - +
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Residues in contact with ALA 299 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83R ASP* 3.2 29.9 - - - +
91R PHE* 4.4 17.0 - - + -
121R GLY* 6.2 4.0 - - - -
265R TRP* 6.4 0.4 - - - -
295R ALA 2.9 12.9 + - - +
296R LYS* 3.1 13.2 + - - +
298R ALA* 1.3 77.3 - - - +
300R ILE* 1.3 59.4 + - - +
302R ASN* 3.8 12.4 + - - +
303R PRO* 3.5 6.6 - - - +
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Residues in contact with ILE 300 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47R LEU* 3.3 55.0 - - + +
48R ILE* 5.4 0.7 - - - -
50R LEU* 5.1 2.7 - - + -
51R GLY* 3.8 20.4 - - - +
55R ASN* 6.4 0.2 - - - +
83R ASP* 5.1 0.7 - - - -
87R VAL* 6.0 8.7 - - + -
91R PHE* 5.5 4.0 - - + -
296R LYS 3.0 14.2 + - - +
297R SER* 3.3 18.8 - - - +
299R ALA* 1.3 75.8 - - - +
301R TYR* 1.3 62.3 + - - +
302R ASN 3.3 0.2 - - - -
303R PRO* 3.3 13.9 - - + +
304R VAL* 4.4 7.6 + - - +
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Residues in contact with TYR 301 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260R ALA* 3.9 35.4 - - + +
264R CYS* 4.6 16.2 - - + -
297R SER 2.9 19.5 + - - +
298R ALA* 3.0 11.1 + - - +
300R ILE* 1.3 78.3 - - + +
302R ASN* 1.3 67.0 + - - +
304R VAL* 3.4 20.6 - - + +
305R ILE* 3.3 32.6 - - + +
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Residues in contact with ASN 302 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79R LEU* 5.1 11.0 - - + -
83R ASP* 5.2 1.3 - - - +
124R ALA* 4.5 19.4 - - + +
128R LEU* 4.7 9.9 - - + +
261R PHE* 5.9 0.5 - - - -
264R CYS* 4.6 14.2 - - - -
265R TRP* 4.6 16.2 + - - +
298R ALA 3.0 23.0 + - - +
299R ALA* 3.8 12.7 + - - +
301R TYR* 1.3 80.9 - - - +
303R PRO* 1.4 69.5 - - + +
304R VAL 3.4 0.3 + - - -
305R ILE* 3.5 4.4 - - - +
306R TYR* 3.0 45.5 + - + +
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Residues in contact with PRO 303 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54R ILE* 5.0 10.7 - - + +
55R ASN* 4.6 18.6 - - - +
79R LEU* 4.9 12.1 - - + -
80R ALA* 6.0 4.7 - - + -
83R ASP* 3.2 22.0 - - + +
299R ALA 3.5 11.2 - - - +
300R ILE* 3.3 19.1 - - + +
302R ASN* 1.4 90.3 - - + +
304R VAL* 1.3 56.2 + - - +
306R TYR* 4.6 0.7 - - + +
307R ILE* 2.9 43.9 + - + +
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Residues in contact with VAL 304 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54R ILE* 4.2 25.0 - - + +
300R ILE 4.4 6.7 + - - +
301R TYR* 3.4 28.7 - - + +
303R PRO* 1.3 75.3 - - - +
305R ILE* 1.3 64.3 + - + +
307R ILE* 4.3 0.5 - - - +
308R MET* 3.0 39.9 + - + +
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Residues in contact with ILE 305 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256R ILE* 3.8 29.2 - - + -
257R TYR* 4.9 10.7 - - + -
260R ALA* 5.4 7.4 - - + -
301R TYR* 3.3 44.2 - - + +
302R ASN* 3.5 6.3 - - - +
304R VAL* 1.3 82.1 - - + +
306R TYR* 1.3 79.7 + - + +
308R MET* 3.4 33.0 + - + +
309R MET* 4.1 11.1 + - - +
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Residues in contact with TYR 306 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76R LEU* 4.5 16.6 - - + +
79R LEU* 5.3 9.9 - - + -
128R LEU* 3.6 36.4 - - + +
131R LEU* 4.7 11.0 - - + -
135R ARG* 5.9 0.9 - - - -
223R TYR* 5.7 3.6 - - - -
257R TYR* 4.5 29.8 + + - +
260R ALA* 6.4 1.3 - - + -
261R PHE* 4.3 25.2 + + + +
302R ASN* 3.0 41.4 + - + +
303R PRO* 4.8 1.6 - - + +
305R ILE* 1.3 91.2 - - + +
307R ILE* 1.3 65.6 + - + +
309R MET* 3.3 38.3 - - + +
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Residues in contact with ILE 307 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54R ILE* 5.4 10.8 - - + -
58R THR* 5.0 26.9 - - + +
76R LEU* 4.8 29.2 - - + +
79R LEU* 6.0 4.9 - - + -
80R ALA* 5.4 5.2 - - + -
303R PRO* 2.9 30.1 + - + +
304R VAL* 4.3 1.1 - - - +
306R TYR* 1.3 81.2 - - - +
308R MET* 1.3 59.3 + - - +
309R MET* 2.9 13.1 + - - +
310R ASN* 3.7 13.2 + - - +
313R PHE* 4.6 29.6 - - + +
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Residues in contact with MET 308 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304R VAL* 3.0 28.6 + - + +
305R ILE* 3.4 30.3 - - + +
307R ILE* 1.3 78.1 - - - +
309R MET* 1.3 68.7 + - - +
310R ASN 3.3 7.9 + - - +
314R ARG* 4.9 14.6 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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