Contacts of the helix formed by residues 275 - 286 (chain A) in PDB entry 5MKF
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 SER 275 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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273A LEU* 3.6 8.8 - - - +
274A SER* 1.3 89.8 + - - +
276A MET* 1.3 63.2 + - - +
277A GLU* 3.0 25.1 + - - -
278A ASP* 3.0 34.7 + - - +
279A PHE* 3.4 12.0 + - - +
445A PHE* 6.0 0.2 - - - -
451A VAL* 5.5 0.8 - - - +
311D TYR* 6.3 1.8 - - - -
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Residues in contact with MET 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274A SER 5.4 0.9 - - - +
275A SER* 1.3 72.5 - - - +
277A GLU* 1.3 65.3 + - - +
279A PHE* 2.9 29.8 + - + +
280A TRP* 3.0 18.9 + - + +
415A LEU* 3.6 33.0 - - + +
416A ASP 4.2 6.7 - - - +
417A ARG* 6.0 0.7 - - - -
445A PHE* 4.0 35.2 - - + -
450A GLY 5.8 2.5 - - - +
311D TYR* 3.3 52.5 - - + +
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Residues in contact with GLU 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A SER* 3.0 30.8 + - - +
276A MET* 1.3 77.2 + - - +
278A ASP* 1.3 63.7 + - - +
280A TRP* 3.0 14.8 + - - +
281A LYS* 2.8 35.8 + - + +
410A LYS* 4.9 7.9 - - - +
293D TRP* 6.0 1.7 - - - -
311D TYR* 4.4 13.2 + - - -
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Residues in contact with ASP 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A GLU* 4.6 2.8 - - - +
268A THR* 4.7 16.8 - - + +
273A LEU* 4.4 15.3 - - + +
274A SER* 4.2 8.8 + - - -
275A SER* 3.0 36.5 + - - +
277A GLU* 1.3 79.3 - - - +
279A PHE* 1.3 51.9 + - - +
281A LYS* 2.9 31.3 + - - +
282A PHE* 2.5 37.5 + - - +
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Residues in contact with PHE 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273A LEU* 4.3 14.7 - - + +
275A SER 3.4 6.8 + - - +
276A MET* 2.9 17.7 + - - +
278A ASP* 1.3 77.9 - - - +
280A TRP* 1.3 66.7 + + - +
282A PHE* 3.1 18.3 + + - +
283A THR* 3.0 36.3 + - + +
415A LEU* 4.2 26.2 - - + -
422A THR* 3.6 26.9 - - + -
424A ILE* 4.3 20.2 - - + -
443A VAL* 3.3 44.0 - - + -
445A PHE* 5.0 9.0 - + + -
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Residues in contact with TRP 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276A MET* 3.0 27.5 + - + +
277A GLU* 3.0 12.2 + - - +
279A PHE* 1.3 74.0 - + - +
281A LYS* 1.3 67.1 + - + +
282A PHE 2.9 1.6 + - - -
283A THR* 2.6 30.2 + - + -
284A GLU* 3.1 16.6 - - - +
406A VAL* 3.7 29.8 - - + -
409A LEU* 3.9 8.7 - - + -
410A LYS* 2.9 71.1 - - + +
413A VAL* 5.3 2.2 - - + -
414A TRP* 4.0 24.5 - + - -
415A LEU* 3.2 41.0 - - + +
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Residues in contact with LYS 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263A SER* 5.0 8.6 - - - +
264A LYS* 3.3 24.7 - - - +
266A GLU* 2.6 41.6 + - - -
277A GLU* 2.8 21.4 + - + +
278A ASP* 3.3 29.7 + - - +
280A TRP* 1.3 73.2 - - + +
282A PHE* 1.3 56.4 + - - +
284A GLU* 3.8 11.2 + - - +
285A GLY* 3.0 27.1 + - - -
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Residues in contact with PHE 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257A PHE 3.9 13.2 - - - -
258A LEU 5.2 0.7 - - - -
261A PRO* 6.6 0.2 - - + -
269A ASN 5.7 0.7 - - - -
270A PHE* 3.3 52.0 - + + -
273A LEU* 4.7 8.5 - - + -
278A ASP 2.5 16.5 + - - +
279A PHE* 3.1 22.4 - + - +
280A TRP 2.9 1.0 + - - -
281A LYS* 1.3 71.8 - - - +
283A THR* 1.3 70.4 + - + +
286A SER* 2.8 42.7 + - - -
287A LEU* 3.3 42.2 + - + -
424A ILE* 4.7 10.1 - - + -
441A LEU* 4.6 5.2 - - + -
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Residues in contact with THR 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279A PHE* 3.4 32.3 - - + +
280A TRP* 2.6 20.7 + - + -
282A PHE* 1.3 92.2 - - + +
284A GLU* 1.3 70.7 + - - +
285A GLY 3.0 3.3 + - - -
286A SER 3.3 0.2 + - - -
287A LEU* 3.5 6.4 + - - +
288A LEU* 3.0 24.9 + - - -
321A ILE* 6.0 4.3 - - + -
406A VAL* 4.1 15.7 - - - +
424A ILE* 4.3 15.7 - - + -
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Residues in contact with GLU 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280A TRP* 3.1 33.4 - - - +
281A LYS* 3.8 9.7 + - - +
283A THR* 1.3 80.1 + - - +
285A GLY* 1.3 58.5 + - - +
288A LEU* 3.4 42.1 - - + +
289A ASP* 4.7 1.4 - - - +
403A ALA* 5.6 0.6 - - - +
406A VAL* 3.2 30.9 - - + +
407A ALA* 4.5 7.8 + - - +
410A LYS* 4.2 10.5 - - - -
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Residues in contact with GLY 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263A SER* 4.2 21.9 - - - -
281A LYS* 3.0 22.4 + - - -
282A PHE 3.7 0.2 - - - -
284A GLU* 1.3 81.4 - - - +
286A SER* 1.3 61.0 + - - +
289A ASP* 3.8 19.0 - - - +
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Residues in contact with SER 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A LEU* 4.8 7.6 + - - +
257A PHE* 4.7 5.9 + - - -
260A THR 4.7 11.3 + - - -
261A PRO* 5.6 9.0 - - - -
263A SER* 6.1 0.4 - - - -
282A PHE* 2.8 35.6 + - - -
283A THR 3.3 0.8 + - - -
285A GLY* 1.3 76.8 - - - +
287A LEU* 1.3 61.9 + - - +
288A LEU 3.1 0.9 - - - -
289A ASP* 2.7 8.6 + - - +
290A GLY* 2.3 34.5 + - - -
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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