Contacts of the helix formed by residues 280 - 294 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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234A ASP* 2.6 35.4 + - - -
279A CYS* 1.3 76.3 - - - +
281A ARG* 1.3 65.4 + - - +
282A ASP* 3.2 20.9 - - - -
283A VAL* 3.3 4.1 + - - +
284A LYS* 3.1 21.0 + - - +
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Residues in contact with ARG 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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279A CYS 3.8 1.2 + - - -
280A SER* 1.3 73.2 - - - +
282A ASP* 1.3 60.3 + - - +
284A LYS* 3.1 13.3 + - + +
285A GLN* 2.9 50.7 + - + +
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Residues in contact with ASP 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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280A SER* 3.2 18.6 - - - -
281A ARG* 1.3 79.9 - - - +
283A VAL* 1.3 72.5 + - - +
285A GLN* 3.3 9.1 + - - +
286A MET* 3.0 43.5 + - + +
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Residues in contact with VAL 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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234A ASP* 3.7 27.4 - - - +
237A LEU* 3.6 44.0 - - + -
238A ILE* 3.9 28.5 - - + -
241A VAL* 5.7 0.7 - - + -
279A CYS* 4.3 2.7 - - - -
280A SER* 3.6 7.6 - - - +
281A ARG 3.2 0.8 - - - -
282A ASP* 1.3 91.5 + - - +
284A LYS* 1.3 66.6 + - - +
286A MET* 3.1 13.1 + - + +
287A LEU* 2.9 25.8 + - + +
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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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273A VAL 3.7 5.2 + - - -
274A VAL* 2.8 46.8 + - + +
275A LEU 4.3 4.6 + - - -
276A ASP 4.5 0.2 - - - -
277A ALA 2.7 31.9 + - - +
279A CYS* 3.5 28.0 - - - +
280A SER 3.1 11.4 + - - +
281A ARG* 3.1 14.3 + - + +
283A VAL* 1.3 77.3 - - - +
285A GLN* 1.3 56.0 + - - +
287A LEU* 3.2 11.1 + - + +
288A LEU* 2.9 33.8 + - + +
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Residues in contact with GLN 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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281A ARG* 2.9 35.5 + - + +
282A ASP* 3.7 11.2 - - - +
284A LYS* 1.3 74.7 - - - +
286A MET* 1.3 65.0 + - - +
288A LEU* 3.2 21.0 + - - +
289A LYS* 3.1 47.0 + - + +
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Residues in contact with MET 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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238A ILE* 4.3 28.5 - - + -
241A VAL* 4.2 29.1 - - + +
245A LYS* 5.7 6.1 - - - +
282A ASP* 3.0 36.4 + - + +
283A VAL* 3.3 17.5 - - + +
285A GLN* 1.3 75.9 - - - +
287A LEU* 1.3 62.6 + - - +
289A LYS* 3.3 17.7 + - - +
290A LEU* 3.4 14.9 + - - +
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Residues in contact with LEU 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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229A PHE* 4.0 26.0 - - + -
237A LEU* 4.2 18.2 - - + +
241A VAL* 3.7 21.5 - - + -
270A ILE* 3.7 22.4 - - + +
273A VAL* 3.6 33.0 - - + -
274A VAL* 3.9 11.9 - - + -
279A CYS* 5.1 0.2 - - - -
283A VAL* 2.9 20.7 + - + +
284A LYS* 3.2 11.0 + - - +
286A MET* 1.3 76.4 - - - +
288A LEU* 1.3 62.5 + - - +
290A LEU* 3.1 21.0 + - + +
291A VAL* 3.2 15.6 + - - +
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Residues in contact with LEU 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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271A GLU* 5.7 5.6 - - + -
274A VAL* 3.9 34.8 - - + -
284A LYS* 2.9 20.7 + - + +
285A GLN* 3.2 22.8 + - - +
287A LEU* 1.3 76.7 - - - +
289A LYS* 1.3 63.7 + - - +
291A VAL* 3.1 27.1 + - + +
292A GLU* 3.2 19.2 + - - +
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Residues in contact with LYS 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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285A GLN* 3.1 41.4 + - + +
286A MET* 3.6 11.2 - - - +
287A LEU 3.3 0.2 - - - -
288A LEU* 1.3 76.4 - - - +
290A LEU* 1.3 60.8 + - + +
292A GLU* 2.9 39.1 + - - +
293A LEU* 3.4 22.5 + - + +
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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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241A VAL* 4.0 33.7 - - + -
244A LEU* 4.0 36.3 - - + -
245A LYS* 4.3 28.5 - - + +
263A MET* 6.3 0.7 - - + -
267A ILE* 4.8 2.5 - - + -
270A ILE* 4.7 8.5 - - + -
286A MET 3.4 9.4 + - - +
287A LEU* 3.1 17.5 + - + +
289A LYS* 1.3 74.9 - - + +
291A VAL* 1.3 65.3 + - - +
293A LEU* 3.2 13.0 + - + +
294A ARG* 3.1 37.4 + - + +
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Residues in contact with VAL 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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267A ILE* 4.0 25.0 - - + +
270A ILE* 3.7 21.8 - - + -
271A GLU* 3.5 33.7 - - + +
287A LEU 3.5 13.0 - - - +
288A LEU* 3.1 20.0 + - + +
290A LEU* 1.3 78.3 - - - +
292A GLU* 1.3 62.0 + - - +
294A ARG 4.0 9.4 + - - -
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Residues in contact with GLU 292 (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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285A GLN* 5.4 0.2 - - - +
288A LEU* 3.2 14.6 + - - +
289A LYS* 2.9 46.9 + - - +
291A VAL* 1.3 79.1 - - - +
293A LEU* 1.3 70.7 + - + +
294A ARG 3.7 1.4 + - - -
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Residues in contact with LEU 293 (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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252A GLU* 4.7 1.0 - - - +
289A LYS* 3.4 16.6 - - + +
290A LEU* 3.2 15.5 + - + +
292A GLU* 1.3 87.0 - - + +
294A ARG* 1.3 89.6 + - + +
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Residues in contact with ARG 294 (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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244A LEU* 4.8 7.8 + - + -
245A LYS 5.9 1.0 + - - -
248A GLY* 3.6 25.6 - - - -
249A SER* 3.5 29.5 - - - +
252A GLU* 3.1 44.2 + - - +
263A MET* 3.1 43.6 - - + +
267A ILE* 4.0 10.2 - - + +
290A LEU* 3.1 24.7 + - + +
291A VAL 4.5 8.7 - - - -
292A GLU 3.6 1.9 - - - -
293A LEU* 1.3 116.5 + - + +
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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