Contacts of the helix formed by residues 266 - 283 (chain B) in PDB entry 3DGI
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 HIS 266 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B THR* 4.2 5.2 - - + -
149B THR* 2.7 54.8 + - - +
150B LEU* 3.5 21.6 - - + +
153B ILE* 4.1 1.8 - - + -
173B PHE* 5.0 2.2 - + - -
174B ILE* 3.5 29.8 - - + +
177B MET* 4.0 20.0 - - + +
262B LEU 2.6 26.6 + - - +
263B ILE* 3.3 19.5 + - - -
264B ALA 3.2 0.6 + - - -
265B GLY* 1.3 77.9 - - - +
267B GLU* 1.3 83.5 + - - +
268B ALA 3.7 1.3 - - - -
269B THR* 3.6 3.8 + - - -
270B SER* 3.1 13.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 267 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B THR* 4.2 2.4 + - - +
174B ILE* 6.1 0.2 - - - +
177B MET* 3.5 26.1 - - + +
178B VAL* 4.2 9.5 - - - +
263B ILE* 3.3 18.5 + - + +
264B ALA 4.1 0.2 + - - -
266B HIS* 1.3 92.3 + - + +
268B ALA* 1.3 66.5 + - - +
270B SER* 3.1 13.5 + - - -
271B GLY* 3.2 10.4 + - - -
436B THR* 3.9 13.9 + - - +
437B LEU* 5.6 4.3 - - + -
438B THR* 2.9 33.8 + - + +
440B LYS* 2.8 37.5 + - - -
504B DMS 5.4 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 268 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B ALA 4.5 1.2 + - - -
267B GLU* 1.3 78.2 - - - +
269B THR* 1.3 56.3 + - - +
271B GLY 3.4 0.7 + - - -
272B LEU* 3.0 18.5 + - - +
327B THR* 2.7 38.0 + - - +
438B THR* 4.1 8.3 - - + +
501B HEM 3.4 24.5 - - + -
504B DMS 3.1 32.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 269 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B THR* 3.8 18.2 - - + -
265B GLY 4.2 3.5 + - - -
266B HIS 3.6 8.0 + - - -
267B GLU 3.2 0.8 - - - -
268B ALA* 1.3 76.6 - - - +
270B SER* 1.3 60.4 + - - +
272B LEU* 3.2 2.7 + - + +
273B LEU* 3.0 30.0 + - + +
406B ALA* 3.6 27.6 - - + +
409B GLU* 3.9 16.6 - - - +
410B ALA* 4.5 11.2 - - + -
501B HEM 3.6 33.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 270 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B PRO 3.4 5.5 + - - -
145B MET* 3.5 8.1 - - - +
146B THR* 2.5 39.7 + - - -
149B THR* 3.5 24.5 - - - +
266B HIS 3.1 7.9 + - - -
267B GLU* 3.1 8.9 + - - -
269B THR* 1.3 75.0 - - - +
271B GLY* 1.3 62.9 + - - +
273B LEU 3.4 0.3 + - - -
274B SER* 2.9 28.2 + - - -
440B LYS* 3.5 10.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 271 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B GLU 3.2 8.6 + - - -
268B ALA 3.7 4.3 - - - -
269B THR 3.2 0.2 - - - -
270B SER* 1.3 78.8 - - - +
272B LEU* 1.3 54.9 + - - +
274B SER* 3.2 4.3 + - - -
275B PHE* 2.8 34.8 + - - -
327B THR* 3.6 7.0 - - - -
439B LEU 3.6 23.8 - - - -
440B LYS* 3.9 11.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 272 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268B ALA 3.0 14.2 + - - +
269B THR* 3.2 8.7 + - + +
271B GLY* 1.3 73.4 - - - +
273B LEU* 1.3 65.6 + - - +
275B PHE* 3.3 2.5 + - - +
276B ALA* 2.9 25.6 + - - +
318B LEU* 3.6 45.1 - - + +
321B ALA* 3.9 14.6 - - + -
322B LEU* 3.6 27.1 - - + -
327B THR* 3.6 7.0 - - - +
406B ALA 5.2 1.3 - - - +
407B LEU* 4.3 11.9 - - + -
410B ALA* 4.1 15.5 - - + -
501B HEM 4.0 22.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 273 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B MET* 3.7 30.6 - - + +
148B LEU* 4.0 25.1 - - + -
149B THR* 4.3 8.5 - - + -
269B THR* 3.0 20.5 + - + +
270B SER 3.9 2.5 - - - +
272B LEU* 1.3 77.6 - - - +
274B SER* 1.3 57.7 + - - +
276B ALA* 3.6 4.4 - - - +
277B LEU* 3.0 29.1 + - - +
318B LEU* 4.9 2.2 - - + -
409B GLU* 5.3 0.2 - - + -
410B ALA* 3.5 42.2 - - + +
413B VAL* 4.1 11.0 - - + -
414B LEU* 4.1 22.5 - - + +
417B MET* 5.0 4.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 274 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B VAL* 3.9 14.8 - - - -
142B PRO* 3.3 29.4 - - - +
145B MET* 3.6 6.8 - - - +
270B SER 2.9 20.2 + - - -
271B GLY* 3.6 4.3 - - - -
273B LEU* 1.3 74.5 - - - +
275B PHE* 1.3 59.5 + - - +
277B LEU 3.3 1.6 + - - -
278B TYR* 3.0 27.5 + - - +
440B LYS* 5.4 0.2 - - - -
441B PRO* 3.7 25.6 - - - -
444B PHE* 3.6 7.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 275 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B GLY 2.8 26.2 + - - +
272B LEU* 3.9 3.6 - - - +
274B SER* 1.3 69.9 - - - +
276B ALA* 1.3 61.3 + - - +
278B TYR* 3.3 6.8 + + - +
279B PHE* 2.8 43.9 + + + -
321B ALA* 4.5 11.2 - - + +
325B TRP* 3.8 44.9 - + + +
327B THR* 3.8 12.8 - - + -
431B LEU* 4.1 13.7 - - + -
433B ILE* 3.8 35.0 - - + -
439B LEU* 3.7 29.8 - - + -
440B LYS* 3.8 4.9 - - - -
441B PRO* 3.9 19.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 276 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B LEU 2.9 18.3 + - - +
273B LEU* 3.6 5.4 - - - +
275B PHE* 1.3 77.8 - - - +
277B LEU* 1.3 57.6 + - - +
279B PHE* 3.3 3.3 + - - +
280B LEU* 2.9 34.6 + - - +
317B VAL* 4.3 7.3 - - + +
318B LEU* 3.8 25.1 - - + -
321B ALA* 4.0 15.4 - - + +
414B LEU* 4.0 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 277 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B TRP* 5.0 2.7 - - + -
141B VAL* 3.9 31.9 - - + -
145B MET* 6.5 0.2 - - - -
273B LEU 3.0 17.3 + - - +
274B SER 3.8 3.8 - - - +
276B ALA* 1.3 72.8 - - - +
278B TYR* 1.3 66.1 + - - +
280B LEU* 3.2 18.5 + - + +
281B VAL* 2.9 32.2 + - + +
287B LEU* 5.7 0.2 - - + -
414B LEU* 4.9 1.9 - - + +
417B MET* 4.0 30.7 - - + -
418B LEU* 5.2 1.3 - - + -
423B PHE* 4.1 28.5 - - + -
444B PHE* 3.9 7.6 - - + -
446B VAL* 4.1 16.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 278 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274B SER 3.0 14.1 + - - +
275B PHE* 3.4 13.7 - + - +
277B LEU* 1.3 77.9 - - - +
279B PHE* 1.3 96.1 + + - +
281B VAL* 3.3 4.2 - - - +
282B LYS* 3.1 62.2 + - + +
429B TYR* 3.7 36.3 + + - -
431B LEU* 3.5 40.9 + - + +
441B PRO* 5.0 3.4 - - + -
444B PHE* 3.3 20.7 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 279 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275B PHE* 2.8 36.4 + - + +
276B ALA 3.9 1.8 - - - +
278B TYR* 1.3 96.6 - + - +
280B LEU* 1.3 61.6 + - - +
282B LYS* 3.3 2.1 + - + +
283B ASN* 2.7 36.3 + - - +
321B ALA* 4.3 11.2 - - + -
324B LEU* 3.4 35.2 - - + -
325B TRP* 3.7 32.1 - + - -
372B GLU 5.5 1.3 - - - -
374B PHE* 3.3 49.5 - + + -
431B LEU* 5.5 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 280 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276B ALA 2.9 24.1 + - - +
277B LEU* 3.2 12.3 + - + +
279B PHE* 1.3 74.8 - - - +
281B VAL* 1.3 64.0 + - - +
283B ASN* 3.1 23.8 + - - +
284B PRO 3.8 0.3 - - - -
286B VAL* 3.9 21.3 - - + +
287B LEU* 3.5 43.8 - - + +
290B ALA* 4.2 9.4 - - + -
317B VAL* 4.1 13.9 - - + -
374B PHE* 5.1 1.1 - - + -
414B LEU* 3.9 35.7 - - + -
418B LEU* 4.1 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 281 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B LEU* 2.9 25.3 + - + +
278B TYR* 3.3 14.1 - - - +
280B LEU* 1.3 77.9 - - - +
282B LYS* 1.3 64.7 + - + +
283B ASN 3.5 0.3 + - - -
284B PRO* 4.4 9.6 - - - +
287B LEU* 4.1 10.3 - - + -
423B PHE* 3.9 33.0 - - + +
425B ASP* 3.9 33.7 - - + +
444B PHE* 4.0 19.1 - - + -
446B VAL* 4.3 11.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 282 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B TYR* 3.1 53.8 + - + +
279B PHE* 4.5 2.5 - - + -
281B VAL* 1.3 76.6 - - + +
283B ASN* 1.3 74.3 + - - +
284B PRO* 3.7 6.7 - - - +
425B ASP* 2.7 31.8 + - - +
428B ASN* 3.7 6.5 - - - +
429B TYR* 2.8 33.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 283 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B PHE* 2.7 32.4 + - - +
280B LEU 3.1 6.9 + - - +
282B LYS* 1.3 89.9 - - - +
284B PRO* 1.3 69.1 - - - +
285B HIS 3.2 2.7 - - - -
286B VAL* 3.0 30.4 + - + +
287B LEU 3.1 8.7 + - - -
374B PHE* 3.7 34.5 + - + +
----------------------------------------------------------
Back to top of page
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) + - + + + + + -
------------------------------------------------------------
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