Contacts of the helix formed by residues 276 - 291 (chain A) in PDB entry 3M2K
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 ASP 276 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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219A ALA* 3.1 42.8 - - + +
220A LEU* 3.9 4.8 - - + +
244A ARG* 2.9 35.7 + - - +
274A TYR* 3.6 12.2 - - - +
275A ASP* 1.3 71.1 + - - +
277A LYS* 1.3 60.6 + - + +
278A LEU 2.9 7.0 + - - -
279A ILE* 3.5 15.7 + - - +
280A ALA 3.4 8.8 + - - -
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Residues in contact with LYS 277 (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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40A PHE* 3.9 11.5 - - + -
219A ALA 4.5 1.6 - - - -
275A ASP* 2.9 23.2 + - - +
276A ASP* 1.3 77.6 - - + +
278A LEU* 1.3 57.3 + - - +
280A ALA* 3.6 13.7 - - + +
281A GLU* 2.8 54.2 + - + +
284A LYS* 4.8 6.6 - - - +
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Residues in contact with LEU 278 (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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36A LEU* 3.6 24.5 - - + +
37A GLU* 5.2 0.2 - - - -
40A PHE* 3.5 42.6 - - + -
42A ALA* 4.1 20.6 - - + -
44A LEU* 4.0 20.6 - - + -
265A SER* 3.9 28.9 - - - +
275A ASP 3.0 15.3 + - - +
277A LYS* 1.3 77.9 - - - +
279A ILE* 1.3 61.7 - - + +
281A GLU* 4.7 0.6 - - - +
282A ALA* 2.9 33.0 + - - +
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Residues in contact with ILE 279 (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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220A LEU* 3.8 25.6 - - + -
221A ILE* 4.2 4.0 - - + -
244A ARG* 3.2 48.7 - - + +
245A ASN* 4.9 0.2 - - - -
246A ASP* 3.9 21.3 - - + -
263A VAL* 3.6 34.1 - - + -
265A SER* 3.6 11.0 - - - +
275A ASP 5.2 0.9 - - - +
276A ASP* 3.9 10.3 - - - +
278A LEU* 1.3 78.0 - - + +
280A ALA* 1.3 62.7 + - - +
282A ALA* 3.7 3.6 - - - +
283A THR* 2.7 31.5 + - - -
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Residues in contact with ALA 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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219A ALA 3.9 7.9 - - - +
220A LEU 3.7 19.2 + - - +
223A ALA* 3.8 23.1 - - + +
224A GLY* 3.6 6.7 - - - -
276A ASP 3.4 7.0 + - - +
277A LYS* 3.5 17.7 + - + +
278A LEU 3.3 1.0 - - - -
279A ILE* 1.3 77.7 - - - +
281A GLU* 1.3 58.7 + - - +
283A THR* 3.2 5.3 - - - -
284A LYS* 2.9 26.6 + - - +
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Residues in contact with GLU 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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36A LEU* 3.9 24.7 - - + -
40A PHE* 4.7 5.4 - - + -
277A LYS* 2.8 51.2 + - + +
278A LEU 4.7 0.2 - - - +
280A ALA* 1.3 70.8 - - - +
282A ALA* 1.3 60.3 + - - +
283A THR 3.0 1.6 - - - -
284A LYS* 2.6 61.5 + - - +
285A VAL* 2.8 18.6 + - + +
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Residues in contact with ALA 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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33A PHE* 3.7 6.7 - - - -
36A LEU* 3.8 13.3 - - + +
44A LEU* 4.4 19.5 - - + -
46A ILE* 4.6 4.0 - - + -
263A VAL* 4.0 20.9 - - + -
278A LEU 2.9 21.7 + - - +
279A ILE 3.7 3.6 - - - +
281A GLU* 1.3 76.7 - - - +
283A THR* 1.3 56.6 + - - +
285A VAL* 3.3 3.9 + - - +
286A VAL* 2.9 33.9 + - - +
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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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221A ILE* 3.7 37.9 - - + +
224A GLY* 3.6 25.4 - - - +
225A VAL* 4.6 2.7 - - + -
250A ILE* 5.4 0.2 - - + -
261A LEU* 4.4 9.0 - - + +
263A VAL* 4.1 7.6 - - - +
279A ILE 2.7 16.5 + - - -
280A ALA* 3.2 11.0 - - - -
281A GLU 2.9 0.4 + - - -
282A ALA* 1.3 74.6 - - - +
284A LYS* 1.3 67.4 + - - +
286A VAL* 3.3 8.1 + - - +
287A MET* 3.1 28.1 + - + +
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Residues in contact with LYS 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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223A ALA 4.0 17.3 - - - -
224A GLY* 3.5 24.7 - - - +
277A LYS* 4.8 7.7 - - - +
280A ALA* 2.9 16.8 + - - +
281A GLU* 2.6 51.1 + - + +
283A THR* 1.3 71.0 - - - +
285A VAL* 1.3 60.2 + - - +
287A MET* 3.3 4.8 + - - +
288A LYS* 3.2 27.8 + - + +
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Residues in contact with VAL 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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32A ASP* 4.0 38.8 - - + +
33A PHE* 3.6 26.2 - - + -
36A LEU* 4.2 17.9 - - + -
281A GLU* 2.8 23.8 + - + +
282A ALA 3.6 5.6 - - - +
284A LYS* 1.3 69.6 - - + +
286A VAL* 1.3 57.1 + - - +
287A MET 3.2 0.3 + - - -
288A LYS* 3.3 4.2 + - + -
289A ALA* 2.4 45.4 + - + +
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Residues in contact with VAL 286 (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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33A PHE* 3.9 10.5 - - + -
46A ILE* 3.7 30.3 - - + -
48A ALA* 3.5 30.1 - - + -
57A VAL* 4.4 4.9 - - + +
259A VAL* 5.9 0.9 - - + -
261A LEU* 4.0 20.6 - - + -
263A VAL* 5.4 1.1 - - + -
282A ALA 2.9 24.9 + - - +
283A THR* 3.3 8.3 + - - +
285A VAL* 1.3 73.3 - - - +
287A MET* 1.3 62.5 + - - +
289A ALA* 2.9 8.5 - - - +
290A LEU* 2.9 38.4 + - + +
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Residues in contact with MET 287 (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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224A GLY 4.1 14.4 - - - +
225A VAL* 4.1 11.0 - - + -
226A PRO* 5.3 3.4 - - + -
229A TRP* 3.2 37.0 - - + -
250A ILE* 3.7 30.5 - - + -
252A PRO* 5.9 0.7 - - + -
259A VAL* 5.6 9.0 - - + -
261A LEU* 5.6 0.4 - - - -
283A THR* 3.1 16.8 + - + +
284A LYS* 3.5 10.3 - - - +
285A VAL 3.1 0.2 - - - -
286A VAL* 1.3 83.9 - - - +
288A LYS* 1.3 52.2 + - + +
290A LEU* 2.6 19.5 + - + +
291A ASN* 2.5 49.0 + - - +
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Residues in contact with LYS 288 (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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284A LYS* 3.2 15.2 + - + +
285A VAL* 4.0 4.3 - - + +
287A MET* 1.3 75.4 - - + +
289A ALA* 1.3 57.9 + - - +
290A LEU 2.3 17.3 + - - -
291A ASN* 2.6 31.8 + - + +
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Residues in contact with ALA 289 (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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33A PHE* 5.4 0.9 - - + -
55A ARG* 6.0 1.0 - - - -
57A VAL* 4.1 19.8 - - + +
285A VAL* 2.4 39.9 + - + +
286A VAL* 2.9 16.4 - - - +
288A LYS* 1.3 73.0 - - - +
290A LEU* 1.3 59.9 + - - +
291A ASN* 4.9 0.9 - - - +
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Residues in contact with LEU 290 (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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48A ALA* 4.6 8.1 - - + -
50A ASP* 4.3 9.4 - - + +
55A ARG* 4.3 42.8 + - + +
56A THR 4.6 4.9 - - - +
57A VAL* 3.9 21.3 - - + +
259A VAL* 3.6 41.3 - - + -
286A VAL* 2.9 18.9 + - + +
287A MET* 2.6 25.9 + - + +
288A LYS 2.3 12.1 + - - -
289A ALA* 1.3 72.4 - - - +
291A ASN* 1.3 66.4 + - - +
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Residues in contact with ASN 291 (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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229A TRP* 4.1 26.8 - - - -
255A LYS* 5.0 6.7 + - - +
287A MET* 2.5 37.5 + - - +
288A LYS* 2.6 22.7 + - + +
289A ALA 4.9 0.7 - - - +
290A LEU* 1.3 82.8 - - - +
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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