Contacts of the helix formed by residues 276 - 291 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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219B ALA* 3.6 36.6 - - + +
220B LEU* 4.4 5.8 - - + +
244B ARG* 3.0 34.8 + - - -
274B TYR* 3.3 11.9 - - - -
275B ASP* 1.3 72.8 + - - +
277B LYS* 1.3 56.4 + - - +
278B LEU 2.8 1.1 - - - -
279B ILE* 2.8 32.3 + - - +
280B ALA 3.3 8.5 + - - -
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Residues in contact with LYS 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B PHE* 4.1 14.3 - - + -
219B ALA 4.8 1.6 - - - -
275B ASP* 2.8 24.9 + - - +
276B ASP* 1.3 74.2 - - - +
278B LEU* 1.3 62.1 + - - +
280B ALA* 4.6 11.0 - - + +
281B GLU* 2.9 61.7 + - + +
284B LYS* 3.6 16.2 - - - +
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Residues in contact with LEU 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B LEU* 4.4 18.3 - - + +
37B GLU* 6.0 0.4 - - - -
40B PHE* 4.0 42.3 - - + -
42B ALA* 4.3 21.3 - - + -
43B LYS 5.4 0.7 - - - +
44B LEU* 4.0 26.0 - - + -
244B ARG* 6.2 0.2 - - + -
265B SER* 3.8 27.6 - - - +
275B ASP* 2.7 18.6 + - + +
277B LYS* 1.3 82.3 - - - +
279B ILE* 1.3 62.0 + - + +
281B GLU* 3.3 2.1 + - - +
282B ALA* 3.0 25.5 + - - +
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Residues in contact with ILE 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B LEU* 5.8 0.4 - - + -
220B LEU* 4.1 25.6 - - + -
221B ILE* 4.3 5.4 - - + +
244B ARG* 3.6 48.0 - - + +
245B ASN 4.8 0.7 - - - +
246B ASP* 4.2 12.8 - - + -
263B VAL* 3.7 29.4 - - + +
265B SER* 4.0 14.4 - - - +
275B ASP 5.0 0.4 - - - +
276B ASP* 2.8 17.7 + - - +
278B LEU* 1.3 79.0 - - + +
280B ALA* 1.3 54.3 + - - +
282B ALA* 3.5 6.5 - - - +
283B THR* 2.6 39.1 + - - -
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Residues in contact with ALA 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219B ALA 3.9 13.7 - - - +
220B LEU 3.4 23.7 + - - +
223B ALA* 3.9 16.4 - - + +
224B GLY* 3.6 1.8 - - - +
276B ASP 3.3 3.9 + - - +
277B LYS* 4.0 19.3 - - + +
279B ILE* 1.3 78.6 - - - +
281B GLU* 1.3 60.9 + - + +
283B THR* 3.3 6.3 - - - -
284B LYS* 3.0 30.4 + - - +
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Residues in contact with GLU 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B LEU* 3.8 26.6 - - + +
40B PHE* 5.2 4.7 - - + -
277B LYS* 2.9 53.1 + - + +
278B LEU* 3.9 1.6 - - - +
280B ALA* 1.3 73.0 - - - +
282B ALA* 1.3 70.4 + - - +
283B THR 2.8 2.2 + - - -
284B LYS* 3.0 38.2 + - - +
285B VAL* 3.1 12.6 + - + +
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Residues in contact with ALA 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B PHE* 3.8 10.0 - - + -
36B LEU* 3.7 15.1 - - + +
44B LEU* 4.1 17.5 - - + -
46B ILE* 4.6 2.0 - - + -
263B VAL* 3.8 22.7 - - + -
278B LEU 3.0 16.6 + - - +
279B ILE 3.5 8.5 - - - +
281B GLU* 1.3 73.3 - - - +
283B THR* 1.3 56.3 + - - +
285B VAL* 3.1 4.9 + - - +
286B VAL* 2.9 32.6 + - - +
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Residues in contact with THR 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221B ILE* 3.8 32.3 - - + +
224B GLY* 3.8 24.9 - - - +
225B VAL* 4.0 11.9 - - + -
261B LEU* 4.1 14.7 - - + +
263B VAL* 4.5 3.9 - - - +
279B ILE 2.6 20.5 + - - -
280B ALA* 3.3 10.1 - - - -
281B GLU 2.8 0.8 + - - -
282B ALA* 1.3 73.1 - - - +
284B LYS* 1.3 68.0 + - - +
286B VAL* 2.9 8.8 + - - +
287B MET* 2.8 26.9 + - + +
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Residues in contact with LYS 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223B ALA 3.8 17.2 + - - -
224B GLY* 4.1 17.9 - - - +
277B LYS* 3.6 13.7 - - - +
280B ALA* 3.0 19.7 + - - +
281B GLU* 3.0 43.5 + - - +
283B THR* 1.3 72.4 - - - +
285B VAL* 1.3 52.1 + - + +
287B MET* 3.2 3.7 + - - +
288B LYS* 2.8 39.6 + - - +
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Residues in contact with VAL 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B LYS 5.1 2.5 - - - +
32B ASP* 4.1 35.0 - - + +
33B PHE* 3.5 28.7 - - + -
36B LEU* 3.8 22.4 - - + -
281B GLU* 3.1 13.5 + - + +
282B ALA 3.1 7.2 + - - +
284B LYS* 1.3 72.2 - - + +
286B VAL* 1.3 70.9 + - - +
288B LYS* 3.1 16.2 + - + +
289B ALA* 3.2 15.0 + - + +
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Residues in contact with VAL 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B PHE* 3.6 21.5 - - + -
46B ILE* 3.8 11.9 - - + -
48B ALA* 3.5 31.9 - - + -
57B VAL* 4.6 9.1 - - + +
259B VAL* 6.1 0.2 - - + -
261B LEU* 3.5 25.6 - - + -
263B VAL* 5.1 0.9 - - + -
282B ALA* 2.9 24.0 + - + +
283B THR* 2.9 8.3 + - - +
285B VAL* 1.3 81.7 - - - +
287B MET* 1.3 63.4 + - - +
289B ALA* 3.1 11.9 + - - +
290B LEU* 3.2 23.3 + - + +
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Residues in contact with MET 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224B GLY 4.0 17.7 - - - +
225B VAL* 4.3 2.7 - - + -
226B PRO* 4.1 15.7 - - + -
229B TRP* 3.4 38.4 - - + -
250B ILE* 4.2 29.6 - - + -
259B VAL* 5.3 11.2 - - + -
261B LEU* 5.6 2.0 - - - -
283B THR* 2.8 22.4 + - + +
284B LYS* 3.4 9.0 - - - +
286B VAL* 1.3 74.2 - - + +
288B LYS* 1.3 54.2 + - - +
290B LEU* 4.9 6.3 - - - -
291B ASN* 2.7 63.0 + - - +
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Residues in contact with LYS 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B ASP* 4.9 13.7 + - - +
284B LYS 2.8 18.6 + - - +
285B VAL* 3.1 9.4 + - - +
287B MET* 1.3 75.4 - - - +
289B ALA* 1.3 57.4 + - - +
291B ASN* 4.1 9.1 - - - +
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Residues in contact with ALA 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57B VAL* 4.0 19.3 - - + -
285B VAL* 3.2 10.2 + - + +
286B VAL* 3.1 8.3 + - - +
288B LYS* 1.3 76.8 - - - +
290B LEU* 1.3 73.0 + - - +
291B ASN 3.0 8.5 - - - +
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Residues in contact with LEU 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B ALA* 4.2 12.1 - - + +
50B ASP* 4.0 17.2 - - + +
55B ARG* 3.7 44.8 - - + +
56B THR 4.0 10.5 - - - +
57B VAL* 4.5 5.5 - - + +
259B VAL* 4.5 23.6 - - + -
286B VAL* 3.2 32.9 + - + +
287B MET* 4.2 6.3 - - - +
289B ALA* 1.3 79.0 - - - +
291B ASN* 1.3 71.5 + - - +
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Residues in contact with ASN 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226B PRO* 5.4 3.2 - - - +
229B TRP* 3.9 24.2 - - - -
259B VAL* 5.7 3.3 - - - +
287B MET* 2.7 48.5 + - - +
288B LYS* 4.1 8.6 - - - +
289B ALA 3.0 10.8 - - - +
290B LEU* 1.3 89.4 - - - +
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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