Contacts of the helix formed by residues 253 - 271 (chain B) in PDB entry 3DYQ
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 253 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246B TYR* 3.8 11.4 - - - -
247B ARG 3.5 15.9 - - - +
248B ASN* 4.8 2.7 - - - -
249B ASN 2.9 28.4 + - - +
250B PRO 3.2 17.2 + - - -
251B PHE 2.9 9.3 + - - +
252B HIS* 1.3 73.6 - - - +
254B PHE* 1.3 65.6 + - - +
255B ARG* 3.2 10.9 + - - +
256B HIS* 2.9 31.4 + - - +
257B CYS 3.1 8.8 + - - -
416B TRP* 3.9 6.5 - - - -
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Residues in contact with PHE 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B PRO* 4.1 13.0 - - + -
211B MET* 4.0 34.8 - - + -
212B LEU* 3.6 24.0 - - + -
215B LEU* 3.8 19.3 - - + -
239B LEU* 6.3 0.2 - - + -
242B VAL* 5.1 2.9 - - + -
243B HIS* 3.6 49.4 - + + +
246B TYR* 3.8 24.7 - + + +
247B ARG 4.5 0.6 + - - -
253B ASN* 1.3 75.4 - - - +
255B ARG* 1.3 58.0 + - - +
257B CYS* 3.1 24.1 + - - +
258B PHE* 2.9 25.3 + - + +
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Residues in contact with ARG 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B VAL* 2.9 30.4 + - + +
204B TRP* 3.6 44.5 + - - +
206B TRP 2.8 28.9 + - - -
207B GLU* 5.0 2.6 - - - +
208B PRO* 5.2 4.0 - - - +
211B MET* 3.4 31.4 - - + +
253B ASN* 3.1 10.9 + - - +
254B PHE* 1.3 77.1 - - - +
256B HIS* 1.3 65.7 + - - +
258B PHE* 3.1 8.2 + - - +
259B CYS* 2.9 22.9 + - - -
416B TRP* 3.8 15.0 - - + -
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Residues in contact with HIS 256 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251B PHE* 3.2 47.3 - + - +
252B HIS* 4.3 9.2 - + - -
253B ASN* 2.9 11.7 + - - +
255B ARG* 1.3 75.2 - - - +
257B CYS* 1.3 66.4 + - - +
259B CYS* 2.9 15.1 + - - +
260B VAL* 2.9 31.8 + - + +
292B HIS* 3.4 7.7 + + - -
293B ASP* 3.2 21.1 + - + -
402B ASP* 3.0 20.3 + - - -
405B ASN* 4.6 11.2 + - - -
416B TRP* 3.5 13.7 - - + -
901B NA 2.7 21.8 - - - -
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Residues in contact with CYS 257 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B LEU* 5.0 3.1 - - - -
246B TYR* 3.3 41.3 - - + +
253B ASN 3.1 2.4 + - - +
254B PHE* 3.1 28.4 + - - +
256B HIS* 1.3 83.7 - - - +
258B PHE* 1.3 67.0 + - - +
260B VAL* 3.2 2.6 + - - +
261B ALA* 3.0 22.3 + - - +
289B ALA 4.3 2.9 - - - +
290B ILE* 3.4 31.6 - - - +
292B HIS* 4.7 7.0 - - - -
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Residues in contact with PHE 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B LEU* 4.1 5.2 - - + -
201B PHE* 4.0 28.9 - + - -
203B VAL* 4.2 25.6 - - + -
206B TRP* 4.8 1.3 - + - -
211B MET* 3.6 48.7 - - + -
214B CYS* 3.5 34.3 - - + -
215B LEU* 4.0 14.1 - - + -
218B MET* 4.1 12.1 - - + -
254B PHE* 2.9 16.7 + - + +
255B ARG* 3.1 8.7 + - + +
257B CYS* 1.3 79.3 - - - +
259B CYS* 1.3 58.0 + - - +
261B ALA* 3.3 4.3 + - - +
262B GLN* 2.8 38.3 + - + +
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Residues in contact with CYS 259 (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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203B VAL* 3.9 26.0 - - - -
255B ARG 2.9 19.0 + - - -
256B HIS* 2.9 13.4 + - - +
258B PHE* 1.3 71.4 - - - +
260B VAL* 1.3 61.7 + - + +
262B GLN* 3.2 2.0 + - - -
263B MET* 2.8 28.5 + - - +
401B CYS 5.1 0.4 - - - -
404B SER* 5.2 1.8 - - - +
405B ASN* 4.2 12.1 - - - +
408B ARG* 2.9 26.8 + - - +
416B TRP* 3.4 33.0 - - - -
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Residues in contact with VAL 260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256B HIS* 2.9 48.9 + - + +
257B CYS 3.8 6.1 - - - +
259B CYS* 1.3 78.1 - - + +
261B ALA* 1.3 62.6 + - - +
263B MET 3.3 0.2 + - - -
264B MET* 3.0 19.9 + - - +
289B ALA* 4.1 16.8 - - + +
292B HIS* 3.6 21.5 - - + +
398B ILE* 4.8 4.9 - - + +
401B CYS* 3.5 19.7 - - + +
402B ASP* 3.6 32.5 - - + +
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Residues in contact with ALA 261 (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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215B LEU* 3.6 29.2 - - + -
218B MET* 4.6 0.9 - - - -
257B CYS 3.0 17.2 + - - +
258B PHE 3.7 0.9 - - - +
260B VAL* 1.3 77.2 - - - +
262B GLN* 1.3 56.2 + - - +
264B MET* 3.1 4.6 + - - +
265B TYR* 2.9 28.5 + - - +
286B MET* 3.7 11.2 - - + +
289B ALA* 4.0 13.8 - - + +
290B ILE* 3.9 18.8 - - + +
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Residues in contact with GLN 262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B LEU* 2.8 38.3 + - + +
198B LYS 2.8 23.5 + - - +
199B PRO* 4.7 0.5 - - - +
201B PHE* 3.5 16.2 - - + +
203B VAL* 4.5 0.9 - - + +
218B MET* 3.9 21.5 - - + -
258B PHE* 2.8 33.6 + - + +
259B CYS* 3.8 3.1 - - - +
261B ALA* 1.3 73.9 - - - +
263B MET* 1.3 57.9 + - - +
265B TYR* 3.4 2.6 + - - +
266B SER* 2.8 40.0 + - - -
408B ARG* 2.8 35.0 + - - +
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Residues in contact with MET 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B PRO* 3.8 24.0 - - + -
259B CYS 2.8 17.5 + - - +
260B VAL 3.7 4.5 - - - +
262B GLN* 1.3 78.4 - - - +
264B MET* 1.3 58.3 + - - +
266B SER* 3.6 4.7 - - - -
267B MET* 2.9 38.1 + - + +
401B CYS* 3.8 13.7 - - + -
404B SER* 3.4 33.0 - - - +
407B VAL* 3.4 30.3 - - + -
408B ARG* 3.6 33.8 - - + +
465B PHE* 6.2 0.2 - - + -
479B MET* 4.3 12.8 - - + -
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Residues in contact with MET 264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260B VAL 3.0 12.6 + - - +
261B ALA 3.1 9.2 + - - +
263B MET* 1.3 75.3 - - - +
265B TYR* 1.3 59.7 + - - +
267B MET* 3.2 7.5 + - - +
268B VAL* 2.9 37.7 + - + +
273B LEU* 5.4 1.1 - - - -
285B LEU* 3.9 51.8 - - + +
286B MET* 3.7 19.1 - - - -
289B ALA* 4.3 7.4 - - + -
397B LEU* 4.4 8.7 - - - -
398B ILE* 3.7 33.4 - - + +
401B CYS* 3.5 23.7 - - + -
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Residues in contact with TYR 265 (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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193B ILE 4.8 0.5 + - - -
196B LEU* 3.2 39.5 - - + -
197B ARG* 3.6 22.2 + - + +
217B HIS* 3.4 16.9 + + - -
218B MET* 3.7 44.9 - - + -
221B ASP* 2.6 27.1 + - - -
222B LEU* 3.8 25.4 - - + -
261B ALA 2.9 12.6 + - - +
262B GLN 3.5 6.3 - - - +
264B MET* 1.3 76.7 - - - +
266B SER* 1.3 61.4 + - - +
268B VAL* 3.2 13.4 + - - +
269B TRP* 3.1 37.4 + - - -
286B MET* 3.9 7.1 - - - -
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Residues in contact with SER 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B ARG 3.6 15.1 + - - +
198B LYS* 3.2 11.4 - - - -
199B PRO* 3.3 26.7 - - - +
262B GLN* 2.8 40.0 + - - -
263B MET* 3.6 9.4 - - - -
265B TYR* 1.3 75.6 - - - +
267B MET* 1.3 59.1 + - - +
269B TRP* 3.2 4.2 + - - +
270B LEU* 2.8 32.8 + - - +
479B MET* 6.4 0.2 - - - -
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Residues in contact with MET 267 (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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263B MET* 2.9 26.2 + - + +
264B MET* 3.2 10.1 + - - +
266B SER* 1.3 75.1 - - - +
268B VAL* 1.3 60.3 + - - +
270B LEU* 4.2 5.8 - - - -
271B CYS* 2.9 48.1 + - - +
273B LEU* 3.7 10.0 - - + +
397B LEU* 3.8 23.8 - - + -
400B CYS* 3.7 29.6 - - + -
401B CYS* 4.0 13.5 - - - +
465B PHE* 4.4 2.9 - - + -
468B VAL* 5.7 2.7 - - + -
475B VAL* 4.9 3.6 - - - -
479B MET* 2.9 38.1 - - + +
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Residues in contact with VAL 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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222B LEU* 3.8 26.7 - - + -
264B MET* 2.9 27.4 + - + +
265B TYR* 3.2 10.7 + - - +
267B MET* 1.3 75.6 - - - +
269B TRP* 1.3 64.0 + - + +
272B SER* 3.1 7.1 + - - -
273B LEU* 2.8 43.0 + - + -
274B GLN* 3.9 23.1 - - + -
282B ILE* 4.0 27.6 - - + -
285B LEU* 5.5 1.8 - - + -
286B MET* 5.2 3.8 - - + -
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Residues in contact with TRP 269 (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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197B ARG* 3.2 71.9 - - + +
221B ASP* 3.3 22.0 - - - -
222B LEU* 3.6 25.6 - - + -
265B TYR* 3.1 43.7 + + - -
266B SER 3.2 3.4 + - - +
267B MET 3.2 0.2 - - - -
268B VAL* 1.3 78.2 - - + +
270B LEU* 1.3 68.5 + - - +
272B SER* 3.1 16.0 + - - +
274B GLN* 3.9 21.5 - - + -
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Residues in contact with LEU 270 (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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199B PRO* 5.4 4.5 - - + -
266B SER* 2.8 23.2 + - - +
267B MET* 4.0 6.1 - - - +
269B TRP* 1.3 74.6 - - - +
271B CYS* 1.3 63.4 + - - +
272B SER* 3.6 2.8 + - - -
474B MET* 3.3 42.5 - - + +
475B VAL* 4.2 9.9 - - + -
478B ILE* 3.7 36.3 - - + -
479B MET* 3.4 35.7 - - + -
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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
----------------------------------------------------------
267B MET* 2.9 28.1 + - - +
270B LEU* 1.3 81.8 - - - +
272B SER* 1.3 72.5 + - - +
273B LEU* 3.2 18.7 + - + -
276B LYS* 5.3 0.7 - - - +
397B LEU* 5.8 2.5 - - - -
468B VAL* 5.6 0.9 - - - -
472B PHE* 3.5 51.6 - - + -
474B MET* 4.4 6.1 - - - -
475B VAL* 3.7 19.3 - - - -
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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
------------------------------------------------------------
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