Contacts of the helix formed by residues 280 - 294 (chain B) in PDB entry 3RK6
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 280 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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234B ASP* 2.5 36.3 + - - -
279B CYS* 1.3 75.1 - - - +
281B ARG* 1.3 65.2 + - - +
282B ASP* 3.4 20.6 - - - -
283B VAL* 3.2 4.6 + - - +
284B LYS* 3.1 20.9 + - - +
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Residues in contact with ARG 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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279B CYS 3.7 1.6 + - - -
280B SER* 1.3 72.0 - - - +
282B ASP* 1.3 59.5 + - - +
284B LYS* 3.1 12.3 + - + +
285B GLN* 2.8 51.6 + - + +
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Residues in contact with ASP 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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280B SER* 3.4 17.3 - - - -
281B ARG* 1.3 78.3 - - - +
283B VAL* 1.3 68.2 + - - +
285B GLN* 3.4 8.3 + - - +
286B MET* 2.9 46.9 + - + +
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Residues in contact with VAL 283 (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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234B ASP* 3.9 23.3 - - + +
237B LEU* 3.5 46.2 - - + -
238B ILE* 3.8 31.4 - - + -
241B VAL* 5.7 0.7 - - + -
279B CYS* 4.2 3.8 - - - -
280B SER* 3.6 7.6 - - - +
281B ARG 3.2 0.6 - - - -
282B ASP* 1.3 88.1 + - - +
284B LYS* 1.3 67.7 + - - +
286B MET* 3.1 14.8 + - + +
287B LEU* 2.9 25.1 + - + +
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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
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273B VAL 3.9 4.4 + - - -
274B VAL* 2.9 47.9 + - + +
275B LEU 4.5 3.0 + - - -
276B ASP 4.5 1.8 - - - -
277B ALA 2.6 32.8 + - - +
279B CYS* 3.5 33.7 - - - +
280B SER 3.1 9.7 + - - +
281B ARG* 3.6 11.2 - - + +
283B VAL* 1.3 76.4 - - - +
285B GLN* 1.3 56.5 + - - +
287B LEU* 3.2 11.9 + - + +
288B LEU* 2.9 34.3 + - + +
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Residues in contact with GLN 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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281B ARG* 2.8 41.1 + - + +
282B ASP* 3.6 9.2 - - - +
284B LYS* 1.3 71.1 - - - +
286B MET* 1.3 63.0 + - - +
288B LEU* 3.2 21.7 + - - +
289B LYS* 3.1 43.6 + - + +
292B GLU* 5.0 0.3 - - - +
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Residues in contact with MET 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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238B ILE* 4.3 25.6 - - + -
241B VAL* 4.1 30.6 - - + +
245B LYS* 5.9 3.4 - - - +
282B ASP* 2.9 39.5 + - + +
283B VAL* 3.2 23.3 - - + +
285B GLN* 1.3 75.4 - - - +
287B LEU* 1.3 61.3 + - - +
289B LYS* 3.3 17.7 + - - +
290B LEU* 3.4 14.9 + - - +
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Residues in contact with LEU 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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229B PHE* 4.0 25.8 - - + -
237B LEU* 4.2 17.3 - - + +
241B VAL* 3.8 21.3 - - + -
270B ILE* 3.7 23.9 - - + +
273B VAL* 3.7 32.5 - - + -
274B VAL* 3.9 11.9 - - + -
283B VAL* 2.9 24.0 + - + +
284B LYS* 3.4 11.0 - - - +
286B MET* 1.3 71.1 - - - +
288B LEU* 1.3 62.9 + - - +
290B LEU* 3.1 23.0 + - + +
291B VAL* 3.2 14.0 + - - +
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Residues in contact with LEU 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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271B GLU* 5.7 4.7 - - + -
274B VAL* 4.0 33.7 - - + -
284B LYS* 2.9 19.6 + - + +
285B GLN* 3.2 25.5 + - - +
287B LEU* 1.3 75.8 - - - +
289B LYS* 1.3 62.7 + - - +
291B VAL* 3.0 29.0 + - + +
292B GLU* 3.0 20.9 + - + +
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Residues in contact with LYS 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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285B GLN* 3.1 35.9 + - + +
286B MET* 3.3 11.2 + - - +
288B LEU* 1.3 75.0 - - - +
290B LEU* 1.3 64.8 + - + +
292B GLU* 3.0 40.3 + - - +
293B LEU* 3.1 37.3 + - + +
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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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241B VAL* 3.9 38.6 - - + -
244B LEU* 4.0 30.1 - - + -
245B LYS* 4.3 26.5 - - + +
270B ILE* 4.8 9.6 - - + -
286B MET 3.4 9.6 + - - +
287B LEU* 3.1 17.2 + - + +
289B LYS* 1.3 76.4 - - + +
291B VAL* 1.3 61.2 + - - +
293B LEU* 3.3 13.4 + - + -
294B ARG* 2.9 47.1 + - + +
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Residues in contact with VAL 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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267B ILE* 4.3 22.5 - - + +
270B ILE* 3.7 23.8 - - + -
271B GLU* 3.7 31.2 - - + +
287B LEU 3.5 13.9 - - - +
288B LEU* 3.0 21.8 + - + +
290B LEU* 1.3 75.2 - - - +
292B GLU* 1.3 66.7 + - - +
294B ARG 4.0 9.0 + - - -
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Residues in contact with GLU 292 (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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285B GLN* 5.0 0.9 - - - +
288B LEU* 3.0 14.7 + - + +
289B LYS* 3.0 47.8 + - - +
290B LEU 3.3 0.2 - - - -
291B VAL* 1.3 79.0 - - + +
293B LEU* 1.3 68.3 + - + +
294B ARG 4.9 1.4 - - - -
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Residues in contact with LEU 293 (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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245B LYS* 6.5 0.2 - - + -
252B GLU* 4.7 1.7 - - - +
289B LYS* 3.1 31.6 - - + +
290B LEU* 3.3 16.4 + - + +
292B GLU* 1.3 89.7 - - + +
294B ARG* 1.3 86.4 + - + +
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Residues in contact with ARG 294 (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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244B LEU* 4.5 11.7 + - + -
245B LYS* 5.6 2.2 + - - +
248B GLY* 3.6 20.5 - - - -
249B SER* 3.5 34.6 - - - +
252B GLU* 3.2 48.2 + - - +
263B MET* 3.5 40.0 - - + +
267B ILE* 3.1 27.1 - - + +
290B LEU* 2.9 35.6 + - + +
291B VAL 4.4 5.8 - - - -
292B GLU 3.6 1.5 - - - -
293B LEU* 1.3 97.4 + - + +
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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