Contacts of the helix formed by residues 257 - 277 (chain J) in PDB entry 3V6K
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 ASN 257 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255J SER* 2.9 15.3 + - - +
256J ARG* 1.3 74.6 - - - +
258J LEU* 1.3 64.4 + - - +
259J GLU* 3.0 11.1 + - - +
260J GLU* 2.9 42.3 + - - +
261J ILE* 3.2 27.0 + - - +
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Residues in contact with LEU 258 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256J ARG 3.4 5.8 + - - +
257J ASN* 1.3 73.3 + - - +
259J GLU* 1.3 68.9 + - + +
261J ILE* 3.6 5.5 + - - +
262J LYS* 3.1 27.3 + - + +
316J VAL* 4.4 17.9 - - + -
319J LEU* 3.7 26.3 - - + +
320J GLN* 3.7 38.8 - - + +
323J LEU* 4.0 11.7 - - + -
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Residues in contact with GLU 259 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257J ASN* 3.0 6.4 + - - +
258J LEU* 1.3 88.1 - - + +
260J GLU* 1.3 56.8 - - - +
262J LYS* 3.3 18.9 - - - +
263J PRO* 3.4 15.8 - - - +
266J PHE* 5.3 5.4 - - - -
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Residues in contact with GLU 260 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251J MET* 5.4 1.0 - - - +
253J ARG* 4.8 14.0 - - - +
255J SER* 2.6 37.5 + - - -
257J ASN* 2.9 25.4 + - + +
259J GLU* 1.3 78.0 - - - +
261J ILE* 1.3 62.5 + - - +
263J PRO* 3.3 14.5 - - - +
264J TYR* 3.8 13.7 - - + -
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Residues in contact with ILE 261 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251J MET* 3.6 27.6 - - + -
255J SER* 4.3 9.2 - - - +
256J ARG 4.2 9.9 - - - +
257J ASN 3.2 23.6 + - - +
258J LEU* 3.9 3.6 - - - +
260J GLU* 1.3 74.6 - - - +
262J LYS* 1.3 56.2 + - - +
263J PRO* 2.7 0.5 - - - +
264J TYR* 2.7 34.7 + - - +
265J LEU* 3.3 7.2 + - + -
319J LEU* 4.1 23.3 - - + -
323J LEU* 5.5 1.3 - - + -
330J ILE* 3.7 30.1 - - + -
333J ILE* 4.2 31.4 - - + -
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Residues in contact with LYS 262 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258J LEU 3.1 13.3 + - - +
259J GLU* 3.3 31.4 - - - +
261J ILE* 1.3 77.2 - - - +
263J PRO* 1.4 60.7 - - + +
264J TYR 3.3 0.2 - - - -
265J LEU* 3.5 13.6 + - + +
266J PHE* 2.9 51.9 + - + -
316J VAL* 6.2 1.8 - - + -
319J LEU* 5.6 1.1 - - + -
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Residues in contact with PRO 263 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A ASN* 6.0 1.1 - - - +
259J GLU* 3.4 15.3 - - - +
260J GLU* 3.3 19.1 - - - +
262J LYS* 1.4 88.9 - - + +
264J TYR* 1.3 63.4 + - + +
266J PHE* 4.0 11.8 - - + +
267J ARG* 3.1 25.3 + - - +
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Residues in contact with TYR 264 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249J VAL* 4.0 18.8 - - + +
250J THR 4.5 5.2 - - - -
251J MET* 3.5 46.4 - - + -
252J LYS* 3.6 22.7 + - - +
260J GLU* 3.8 16.4 - - + -
261J ILE 2.7 17.7 + - - +
263J PRO* 1.3 83.0 - - + +
265J LEU* 1.3 50.4 + - - +
267J ARG* 2.9 10.5 + - + +
268J ALA* 2.6 34.5 + - - +
333J ILE* 3.9 16.8 - - + -
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Residues in contact with LEU 265 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261J ILE* 3.3 9.2 + - + +
262J LYS* 3.6 15.9 - - - +
264J TYR* 1.3 81.4 - - - +
266J PHE* 1.3 61.1 + - + +
268J ALA* 3.3 6.9 - - + +
269J ILE* 3.0 29.3 + - + +
286J VAL* 4.5 7.4 - - + -
315J SER* 3.2 31.6 - - - +
316J VAL* 4.6 14.6 - - + +
319J LEU* 4.0 25.4 - - + -
333J ILE* 4.2 22.3 - - + +
334J GLY 4.4 5.8 - - - +
335J VAL* 4.0 17.9 - - + -
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Residues in contact with PHE 266 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259J GLU* 5.3 5.4 - - - -
262J LYS* 2.9 42.5 + - + +
263J PRO* 4.0 10.1 - - + +
264J TYR 3.2 0.2 - - - -
265J LEU* 1.3 81.6 - - + +
267J ARG* 1.3 59.8 + - - +
269J ILE* 3.1 10.1 + - + +
270J GLU* 2.9 33.6 + - - +
312J TYR* 3.4 51.5 + + + +
316J VAL* 4.5 21.8 - - + -
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Residues in contact with ARG 267 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A VAL* 6.5 1.1 - - + -
249J VAL* 5.5 7.4 - - + -
263J PRO 3.1 15.7 + - - +
264J TYR* 2.9 16.7 + - + +
266J PHE* 1.3 73.9 - - - +
268J ALA* 1.3 61.5 + - - +
270J GLU* 3.3 6.0 + - - +
271J GLU* 3.2 36.0 + - + +
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Residues in contact with ALA 268 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247J ARG* 4.0 16.3 - - - +
249J VAL* 4.7 8.2 - - + +
264J TYR 2.6 15.8 + - - +
265J LEU* 3.3 14.8 - - + +
266J PHE 3.2 0.2 - - - -
267J ARG* 1.3 74.4 - - - +
269J ILE* 1.3 54.9 + - - +
271J GLU* 3.7 0.6 + - - -
272J SER* 2.5 33.8 + - - -
333J ILE 4.5 4.3 - - - +
334J GLY* 3.9 28.3 - - - -
335J VAL* 4.0 5.8 - - + -
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Residues in contact with ILE 269 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265J LEU* 3.0 19.3 + - + +
266J PHE* 3.1 12.3 + - + +
268J ALA* 1.3 75.0 - - - +
270J GLU* 1.3 53.8 + - - +
272J SER* 3.1 3.0 + - - -
273J TYR* 2.8 58.0 + - + +
284J ILE* 5.6 0.2 - - + -
308J LYS* 4.4 2.2 - - + -
311J ALA* 3.9 16.8 - - + +
312J TYR* 4.0 27.8 - - + -
315J SER* 3.7 31.2 - - - +
335J VAL* 3.8 24.0 - - + -
337J PHE* 4.4 3.4 - - + -
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Residues in contact with GLU 270 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A SER* 4.6 6.5 - - - +
26A LYS* 4.1 23.1 + - + +
266J PHE 2.9 14.5 + - - +
267J ARG* 4.0 6.1 - - - +
269J ILE* 1.3 72.8 - - - +
271J GLU* 1.3 67.7 + - + +
273J TYR* 3.8 2.3 - - - +
274J TYR* 2.9 24.9 + - - +
308J LYS* 3.3 42.1 + - - +
312J TYR* 2.9 29.9 + - - +
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Residues in contact with GLU 271 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A ASN* 3.2 26.2 + - - +
22A SER* 3.3 26.6 + - - +
23A LEU* 5.8 1.1 - - + +
247J ARG* 2.9 48.2 + - + +
249J VAL* 5.0 5.4 - - - +
267J ARG* 3.2 21.8 + - + +
268J ALA 4.1 2.9 - - - +
270J GLU* 1.3 78.3 - - + +
272J SER* 1.3 61.0 + - - +
274J TYR* 3.4 2.6 + - - +
275J LYS* 3.1 33.1 + - + +
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Residues in contact with SER 272 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245J ILE* 3.6 8.0 - - - +
246J GLY* 4.6 6.5 - - - -
247J ARG* 3.7 14.6 + - - +
268J ALA 2.5 21.4 + - - -
269J ILE* 3.1 9.3 + - - -
271J GLU* 1.3 73.2 - - - +
273J TYR* 1.3 59.0 + - - +
275J LYS* 3.2 10.3 + - - +
276J LEU* 2.8 31.6 + - - +
335J VAL* 3.4 11.6 - - - +
337J PHE* 3.7 25.1 - - - -
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Residues in contact with TYR 273 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269J ILE* 2.8 33.2 + - + +
270J GLU* 3.9 3.8 - - - +
272J SER* 1.3 70.6 - - - +
274J TYR* 1.3 66.3 + - - +
276J LEU* 3.1 29.0 + - + +
277J ASP* 3.3 10.9 + - - +
280J ILE* 5.6 7.4 - - + -
281J PRO* 4.1 6.3 - - + +
306J ILE* 2.5 48.4 + - - +
307J SER* 3.5 2.0 - - - -
308J LYS* 3.6 45.1 - - + -
311J ALA* 3.5 10.3 - - + -
337J PHE* 3.3 31.8 - + - -
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Residues in contact with TYR 274 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A PRO* 3.3 49.2 + - + +
22A SER* 3.6 26.0 - - - -
270J GLU 2.9 14.2 + - - +
271J GLU 3.4 8.3 - - - +
273J TYR* 1.3 78.6 - - - +
275J LYS* 1.3 70.8 + - + +
277J ASP* 3.4 16.6 + - - +
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Residues in contact with LYS 275 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245J ILE* 3.9 24.5 - - + +
246J GLY 2.9 29.5 + - - -
247J ARG* 4.6 7.4 - - - -
271J GLU* 3.1 20.3 + - + +
272J SER* 3.5 6.1 - - - +
274J TYR* 1.3 84.6 - - + +
276J LEU* 1.3 65.3 + - - +
277J ASP* 4.2 4.0 - - - +
7M A 4.2 19.4 + - - -
8M A 3.8 18.9 + - - +
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Residues in contact with LEU 276 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245J ILE* 3.8 20.9 - - + -
272J SER 2.8 19.3 + - - +
273J TYR* 3.1 29.3 + - + +
275J LYS* 1.3 79.3 - - - +
277J ASP* 1.3 68.1 + - - +
279J ARG* 3.2 44.1 + - + +
281J PRO* 3.8 26.2 - - + -
337J PHE* 3.9 20.4 - - + -
340J PHE* 3.7 31.0 - - + -
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Residues in contact with ASP 277 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273J TYR 3.3 8.9 + - - +
274J TYR 3.4 12.7 + - - +
275J LYS 3.3 5.2 - - - +
276J LEU* 1.3 82.4 - - - +
278J LYS* 1.3 77.5 + - - +
279J ARG* 3.5 5.5 + - + +
280J ILE* 4.6 6.6 - - - +
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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
------------------------------------------------------------
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