Contacts of the helix formed by residues 267 - 278 (chain A) in PDB entry 2R8J
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26A ILE* 4.3 4.9 - - - -
265A SER* 2.9 18.9 + - - -
266A SER* 1.3 87.5 + - - +
268A LYS* 1.3 68.5 + - - +
269A ASN* 3.7 13.7 - - + +
270A VAL* 3.9 16.5 - - + +
271A CYS* 3.0 13.9 + - - -
380A GLY 3.5 17.3 + - - -
381A ARG* 4.2 4.9 - - - -
382A TYR 3.0 39.7 - - - +
383A GLY* 3.6 8.0 + - - -
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Residues in contact with LYS 268 (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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26A ILE* 3.8 18.2 - - + +
150A GLU* 3.0 26.5 + - - -
158A PHE* 3.5 42.2 - - + -
267A THR* 1.3 76.0 - - + +
269A ASN* 1.3 59.8 + - - +
271A CYS* 3.3 2.9 + - - +
272A LYS* 3.0 29.5 + - - +
383A GLY* 5.2 0.2 - - - -
384A LEU* 3.3 47.5 - - + +
385A PRO 3.1 19.4 + - - -
386A LEU* 3.7 16.5 - - + +
387A SER* 4.9 0.8 + - - -
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Residues in contact with ASN 269 (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 THR* 3.3 5.3 - - + -
268A LYS* 1.3 78.5 - - - +
270A VAL* 1.3 64.4 + - + +
272A LYS* 3.4 9.3 - - - +
273A LEU* 3.3 27.1 + - - +
305A PHE* 6.0 5.6 - - + -
306A TRP* 3.7 27.5 + - - +
377A LEU* 4.0 21.2 - - + +
382A TYR* 3.0 45.6 + - + -
384A LEU* 4.1 15.7 - - - +
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Residues in contact with VAL 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A SER* 3.4 23.3 - - - +
267A THR* 3.5 19.6 + - + -
268A LYS 3.4 0.2 - - - -
269A ASN* 1.3 74.7 - - + +
271A CYS* 1.3 61.6 + - - +
273A LEU* 3.2 8.5 + - + +
274A ALA* 2.8 27.4 + - - +
286A VAL* 4.1 12.8 - - + -
291A LEU* 4.0 18.6 - - + -
294A PHE* 4.1 16.4 - - + -
295A LEU* 5.0 8.5 - - + -
380A GLY* 4.1 26.2 - - - +
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Residues in contact with CYS 271 (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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26A ILE* 3.4 35.7 - - - -
27A ALA 3.8 0.9 - - - -
28A HIS* 3.8 15.0 - - + -
158A PHE* 4.8 0.4 - - + -
263A GLY* 3.3 25.7 - - - +
265A SER* 3.1 15.8 + - - -
267A THR 3.0 25.7 + - - +
268A LYS* 3.5 7.2 - - - +
270A VAL* 1.3 76.5 - - - +
272A LYS* 1.3 55.0 + - - +
274A ALA* 3.0 5.1 + - - +
275A SER* 2.8 36.2 + - - -
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Residues in contact with LYS 272 (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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28A HIS* 3.3 28.1 + - + +
152A ALA* 6.0 1.1 - - - -
156A GLU* 3.6 26.1 + - - -
158A PHE* 4.3 8.3 - - + -
268A LYS 3.0 14.1 + - - +
269A ASN* 3.4 13.9 - - - +
271A CYS* 1.3 76.2 - - - +
273A LEU* 1.3 62.3 + - + +
275A SER* 3.1 18.8 + - - -
276A ASN* 3.7 21.9 + - - +
306A TRP* 4.4 33.1 - - + -
1501A CA 4.2 5.1 - - - -
13Q G 4.0 15.8 + - - -
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Residues in contact with LEU 273 (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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269A ASN 3.3 14.8 + - - +
270A VAL* 3.2 9.3 + - + +
271A CYS 3.2 0.6 - - - -
272A LYS* 1.3 79.6 - - + +
274A ALA* 1.3 61.1 + - - +
276A ASN* 3.2 8.2 + - - +
277A TYR* 3.0 25.5 + - - +
294A PHE* 3.9 12.1 - - + -
295A LEU* 3.8 21.5 - - + -
300A PHE* 3.9 34.7 - - + -
304A SER* 3.7 23.3 - - - +
305A PHE* 3.7 32.3 - - + -
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Residues in contact with ALA 274 (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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262A CYS 4.3 0.2 - - - +
263A GLY* 3.8 15.5 - - - -
264A LEU 4.6 1.6 - - - +
270A VAL 2.8 17.1 + - - +
271A CYS* 3.0 6.3 + - - +
273A LEU* 1.3 71.6 - - - +
275A SER* 1.3 65.0 + - - +
276A ASN 3.0 2.0 - - - -
277A TYR* 3.1 18.7 + - - +
278A LYS 4.1 0.7 + - - -
284A THR* 3.3 30.6 + - + +
286A VAL* 4.1 15.5 - - + -
294A PHE* 3.8 10.3 - - + -
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Residues in contact with SER 275 (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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28A HIS* 3.2 43.1 + - - -
30A ASP* 4.8 6.3 - - - +
261A SER* 3.3 28.4 - - - -
262A CYS* 3.8 16.6 - - - +
263A GLY* 3.8 2.8 - - - -
271A CYS 2.8 16.0 + - - -
272A LYS* 3.1 13.5 + - - -
274A ALA* 1.3 73.1 - - - +
276A ASN* 1.3 63.6 + - - +
278A LYS 3.8 4.9 - - - +
279A LYS* 4.0 2.3 - - - +
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Residues in contact with ASN 276 (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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30A ASP* 5.5 1.8 + - - -
272A LYS* 3.7 21.5 + - - +
273A LEU* 3.2 10.0 + - - +
274A ALA 3.0 0.8 - - - -
275A SER* 1.3 81.1 + - - +
277A TYR* 1.3 64.3 - - - +
278A LYS* 3.3 3.7 + - - -
279A LYS* 2.8 46.0 + - - +
300A PHE* 6.4 0.2 - - + -
1501A CA 4.3 16.0 - - - -
2001A DCP 5.5 0.8 + - - -
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Residues in contact with TYR 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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222A PHE* 3.2 37.8 - + - -
273A LEU 3.0 11.7 + - - +
274A ALA* 3.1 17.2 + - - +
276A ASN* 1.3 77.1 - - - +
278A LYS* 1.3 63.5 + - + +
284A THR* 3.7 21.1 - - + +
294A PHE* 3.8 16.6 - + + -
297A CYS* 4.5 10.2 - - - +
299A LYS* 3.9 45.0 + - + -
300A PHE* 4.4 11.0 - + - -
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Residues in contact with LYS 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A ASP* 3.7 27.8 + - + +
261A SER* 3.0 19.4 + - - -
274A ALA 4.1 1.4 + - - +
275A SER 3.8 2.1 - - - +
276A ASN 3.3 0.2 - - - -
277A TYR* 1.3 87.6 - - + +
279A LYS* 1.3 71.7 - - - +
280A PRO 5.4 2.7 - - - -
282A ALA* 3.5 30.9 - - + +
284A THR* 4.0 14.5 + - - +
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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