Contacts of the helix formed by residues 267 - 278 (chain B) in PDB entry 2R8K
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 THR 267 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26B ILE* 4.7 1.1 - - - -
265B SER* 3.0 5.6 + - - -
266B SER* 1.3 85.1 + - - +
268B LYS* 1.3 71.9 + - - +
269B ASN* 3.3 24.9 - - + +
270B VAL* 2.9 22.4 + - + +
271B CYS* 2.8 23.0 + - - -
380B GLY* 3.1 19.4 + - - -
381B ARG* 3.9 2.1 - - - -
382B TYR* 3.3 37.7 + - + +
383B GLY* 4.2 4.0 + - - -
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Residues in contact with LYS 268 (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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26B ILE* 3.9 20.3 - - + +
150B GLU* 2.8 35.5 + - - +
158B PHE* 3.5 46.1 - - + -
267B THR* 1.3 70.7 - - - +
269B ASN* 1.3 69.2 + - - +
271B CYS* 2.8 9.7 + - - +
272B LYS* 2.8 20.8 + - - +
306B TRP* 5.4 11.5 - - + +
384B LEU* 3.5 41.1 + - + +
385B PRO 3.5 9.8 + - - -
386B LEU* 3.7 16.4 - - + -
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Residues in contact with ASN 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B THR* 3.5 6.9 - - + +
268B LYS* 1.3 83.4 - - - +
270B VAL* 1.3 65.2 + - + +
272B LYS* 3.1 20.2 + - - +
273B LEU* 3.3 12.6 + - - +
305B PHE* 4.6 9.9 - - + -
306B TRP* 3.5 33.1 + - - +
307B THR* 4.5 5.7 - - - +
377B LEU* 3.8 23.5 - - + +
382B TYR* 3.1 41.2 + - - -
384B LEU* 4.2 10.6 - - - +
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Residues in contact with VAL 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265B SER* 3.4 18.2 - - - +
267B THR* 2.9 21.6 + - + +
269B ASN* 1.3 74.0 - - + +
271B CYS* 1.3 61.8 + - - +
273B LEU* 3.3 12.5 + - + +
274B ALA* 3.1 20.1 + - - +
286B VAL* 4.4 3.1 - - + -
291B LEU* 3.7 22.4 - - + -
294B PHE* 3.9 22.8 - - + -
295B LEU* 4.4 6.5 - - + -
305B PHE* 5.8 3.1 - - + -
377B LEU 5.9 0.7 - - - +
380B GLY* 3.3 34.8 - - - +
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Residues in contact with CYS 271 (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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26B ILE* 3.1 36.8 - - - -
27B ALA 4.1 0.9 - - - -
28B HIS* 3.7 19.5 - - + -
158B PHE* 4.5 0.4 - - + -
263B GLY* 3.5 11.8 - - - +
265B SER* 2.9 29.7 + - - -
267B THR 2.8 14.1 + - - -
268B LYS* 2.8 10.9 + - - +
270B VAL* 1.3 73.6 - - - +
272B LYS* 1.3 66.9 + - - +
274B ALA* 2.9 7.2 + - - +
275B SER* 2.9 25.1 + - - -
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Residues in contact with LYS 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B HIS* 3.6 30.1 - - + +
152B ALA* 6.0 0.4 - - - -
156B GLU* 3.5 30.9 + - - -
158B PHE* 4.6 9.6 - - + -
268B LYS 2.8 14.5 + - - +
269B ASN* 3.3 14.8 - - - +
271B CYS* 1.3 71.4 - - - +
273B LEU* 1.3 66.5 + - + +
275B SER* 3.2 14.6 + - - -
276B ASN* 3.6 13.3 + - - +
304B SER 5.8 1.8 - - - +
305B PHE 6.0 0.2 - - - -
306B TRP* 4.3 41.9 - - + +
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Residues in contact with LEU 273 (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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269B ASN 3.7 12.1 - - - +
270B VAL* 3.3 8.7 + - + +
271B CYS 3.0 0.8 - - - -
272B LYS* 1.3 79.7 - - + +
274B ALA* 1.3 66.5 + - - +
276B ASN* 3.0 8.8 + - - +
277B TYR* 3.0 19.9 + - - +
294B PHE* 4.0 15.5 - - + -
295B LEU* 4.6 11.4 - - + -
300B PHE* 3.4 47.2 - - + -
304B SER* 3.3 31.0 - - - +
305B PHE* 4.1 26.2 - - + +
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Residues in contact with ALA 274 (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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262B CYS 4.5 0.3 - - - +
263B GLY* 3.7 17.7 - - - -
264B LEU 4.4 2.2 - - - +
270B VAL 3.1 10.5 + - - +
271B CYS* 2.9 9.8 + - - +
273B LEU* 1.3 80.7 - - - +
275B SER* 1.3 61.5 + - - +
277B TYR* 3.1 18.8 + - - +
278B LYS 4.1 0.9 + - - -
284B THR* 3.4 29.5 + - + +
286B VAL* 4.1 9.2 - - + -
294B PHE* 3.7 15.8 - - + -
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Residues in contact with SER 275 (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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28B HIS* 3.0 38.9 + - - -
30B ASP* 4.6 5.4 - - - +
261B SER* 3.1 32.4 - - - -
262B CYS* 3.8 7.6 - - - -
263B GLY* 3.6 22.5 - - - +
271B CYS 2.9 11.5 + - - -
272B LYS* 3.2 8.8 + - - -
274B ALA* 1.3 74.5 - - - +
276B ASN* 1.3 64.2 + - - +
277B TYR 3.2 0.7 + - - -
278B LYS 3.6 5.2 - - - +
279B LYS* 4.2 0.3 - - - +
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Residues in contact with ASN 276 (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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272B LYS* 3.6 14.6 + - - +
273B LEU* 3.0 10.1 + - - +
275B SER* 1.3 79.7 + - - +
277B TYR* 1.3 64.0 + - - +
278B LYS 3.3 1.2 + - - -
279B LYS* 3.4 40.2 + - - +
300B PHE* 6.1 2.8 - - - -
4001B DTP 5.3 1.4 + - - -
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Residues in contact with TYR 277 (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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222B PHE* 3.4 36.3 - + - -
273B LEU 3.0 11.0 + - - +
274B ALA* 3.1 20.8 + - - +
276B ASN* 1.3 79.4 - - - +
278B LYS* 1.3 63.3 + - + +
284B THR* 3.5 23.8 - - + +
294B PHE* 4.1 6.5 - + + -
297B CYS* 4.4 8.0 - - - +
299B LYS* 4.0 40.3 + - + -
300B PHE* 4.1 19.5 - + - -
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Residues in contact with LYS 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B ASP* 3.4 34.7 + - + +
261B SER* 3.2 20.6 + - - -
274B ALA 4.1 1.6 + - - -
275B SER 3.6 2.6 + - - +
276B ASN 3.3 0.2 - - - -
277B TYR* 1.3 88.5 - - + +
279B LYS* 1.3 67.8 + - - +
280B PRO 6.0 0.2 - - - -
282B ALA* 3.6 30.9 - - + +
283B GLN 6.4 0.2 - - - -
284B THR* 4.1 14.1 - - - +
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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