Contacts of the helix formed by residues 376 - 399 (chain B) in PDB entry 1T8U
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 ASP 376 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B GLU* 2.9 30.9 + - + +
274B ARG* 4.3 4.1 + - - -
374B GLU 4.2 0.2 + - - -
375B ILE* 1.3 73.0 - - - +
377B ARG* 1.3 66.8 + - - +
378B GLU* 3.1 16.4 + - - +
379B VAL* 3.1 29.8 + - + +
380B VAL* 3.0 19.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 377 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375B ILE 3.2 6.8 + - - +
376B ASP* 1.3 74.6 + - - +
378B GLU* 1.3 57.2 + - - +
380B VAL* 3.3 8.1 + - - +
381B ARG* 2.9 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 378 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274B ARG* 3.7 19.3 - - - +
376B ASP* 3.1 16.3 + - - +
377B ARG* 1.3 78.1 - - - +
379B VAL* 1.3 56.8 + - - +
381B ARG* 2.9 34.6 + - - +
382B ARG* 2.8 59.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 379 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266B PHE* 4.4 6.3 - - + -
267B GLU* 3.6 31.2 - - + -
270B THR* 4.3 20.0 - - + +
271B PHE* 3.6 31.2 - - + -
274B ARG* 4.1 11.9 - - - +
375B ILE* 4.1 13.7 - - + -
376B ASP* 3.1 20.2 + - + +
378B GLU* 1.3 73.5 - - - +
380B VAL* 1.3 66.8 + - - +
382B ARG* 3.2 6.6 + - - +
383B LEU* 3.0 23.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 380 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B VAL* 4.2 10.3 - - + -
250B ILE* 4.8 9.9 - - + -
266B PHE* 6.1 0.4 - - + -
375B ILE* 3.6 30.3 - - + +
376B ASP 3.0 17.6 + - - +
377B ARG* 3.3 9.8 + - - +
379B VAL* 1.3 75.4 - - - +
381B ARG* 1.3 58.7 + - - +
383B LEU* 3.2 8.0 + - + +
384B ARG* 2.9 54.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 381 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377B ARG 2.9 17.0 + - - +
378B GLU* 2.9 39.8 + - - +
379B VAL 3.2 0.2 - - - -
380B VAL* 1.3 78.3 - - - +
382B ARG* 1.3 73.4 + - - +
384B ARG* 3.4 8.0 + - - +
385B GLU* 3.0 60.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 382 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B PHE* 3.6 26.5 - - + -
274B ARG* 2.6 48.4 + - - +
275B THR 4.4 6.5 + - - -
277B GLY* 3.5 18.1 - - - -
279B ILE* 4.0 8.5 - - + +
378B GLU* 2.8 48.4 + - - +
379B VAL 3.8 4.0 - - - +
381B ARG* 1.3 86.8 - - - +
383B LEU* 1.3 58.2 + - - +
385B GLU* 3.3 15.0 + - - +
386B PHE* 2.9 26.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 383 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B VAL* 4.1 22.4 - - + -
249B ALA* 5.2 6.3 - - + -
266B PHE* 3.5 38.4 - - + -
270B THR* 4.0 25.6 - - + +
279B ILE* 4.3 12.8 - - + -
286B ILE* 4.1 18.2 - - + -
379B VAL* 3.0 19.3 + - + +
380B VAL* 3.2 6.5 + - + +
382B ARG* 1.3 76.5 - - + +
384B ARG* 1.3 65.2 + - - +
386B PHE* 3.1 6.2 + - + +
387B TYR* 3.0 41.6 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 384 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244B ASP* 2.8 38.8 + - - -
246B VAL* 3.6 25.7 - - + +
247B THR* 4.3 9.7 - - - +
380B VAL* 2.9 37.6 + - + +
381B ARG* 3.8 6.7 - - - +
383B LEU* 1.3 75.7 - - - +
385B GLU* 1.3 61.5 + - - +
387B TYR* 3.5 3.1 + - - +
388B ARG* 3.0 26.2 + - - +
391B ASN* 5.5 0.2 + - - -
404B TRP* 4.1 14.5 + - - +
405B ASP* 4.4 5.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 385 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381B ARG* 3.0 45.6 + - - +
382B ARG* 3.4 12.2 - - - +
384B ARG* 1.3 79.7 - - - +
386B PHE* 1.3 62.3 + - - +
388B ARG* 3.9 6.3 - - - +
389B PRO* 3.5 15.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 386 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B ILE* 3.4 35.2 - - + -
281B THR* 3.4 31.0 - - + -
286B ILE* 3.9 21.1 - - + -
290B ILE* 4.1 12.6 - - + -
382B ARG 2.9 6.0 + - - +
383B LEU* 3.1 9.6 + - + +
385B GLU* 1.3 77.0 - - - +
387B TYR* 1.3 88.0 + + - +
389B PRO* 3.4 13.3 - - - +
390B PHE* 3.5 39.2 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 387 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B PRO* 3.5 39.2 + - + -
246B VAL* 3.9 15.0 - - + -
249B ALA* 4.6 3.5 - - + +
285B ALA 3.8 4.3 + - - -
286B ILE* 2.6 44.3 + - + +
289B GLY* 3.6 28.2 - - - -
290B ILE* 4.0 5.6 - - + -
383B LEU* 3.0 38.7 + - + +
384B ARG* 4.2 4.0 - - - +
386B PHE* 1.3 92.8 - + - +
388B ARG* 1.3 68.3 + - - +
390B PHE* 2.9 12.2 + + + +
391B ASN* 2.8 38.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 388 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384B ARG 3.0 16.9 + - - +
385B GLU* 3.9 7.6 - - - +
387B TYR* 1.3 74.8 - - - +
389B PRO* 1.3 71.6 - - + +
391B ASN* 3.1 2.3 + - - +
392B LEU* 2.9 52.6 + - + +
405B ASP* 3.6 46.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 389 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385B GLU 3.5 7.6 - - - +
386B PHE 3.4 16.8 - - - +
388B ARG* 1.3 97.0 - - + +
390B PHE* 1.3 74.0 + - + +
392B LEU* 3.3 14.1 + - + +
393B LYS* 3.1 31.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 390 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289B GLY 5.7 0.2 - - - +
290B ILE* 3.8 38.8 - - + -
291B TYR 5.7 0.2 - - - +
292B ALA* 3.8 11.6 + - + +
293B LYS* 4.6 21.3 - - + -
386B PHE* 3.5 55.6 - + - -
387B TYR* 2.9 12.1 + + + +
389B PRO* 1.3 81.9 - - + +
391B ASN* 1.3 68.2 + - - +
393B LYS* 3.3 20.9 + - + +
394B PHE* 3.0 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 391 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244B ASP* 5.4 0.4 + - - -
245B PRO* 3.4 23.6 - - - +
289B GLY 4.8 2.3 - - - +
291B TYR* 5.3 1.4 - - - -
384B ARG 5.5 0.2 + - - -
387B TYR* 2.8 31.6 + - - +
388B ARG 3.4 4.7 - - - +
390B PHE* 1.3 77.4 - - - +
392B LEU* 1.3 56.9 + - - +
394B PHE* 3.0 10.0 + - - +
395B TYR* 2.8 41.5 + - + +
404B TRP* 3.8 24.7 + - + +
405B ASP* 3.0 35.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 392 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388B ARG* 2.9 56.7 + - + +
389B PRO* 3.5 12.6 - - + +
391B ASN* 1.3 77.0 - - - +
393B LYS* 1.3 63.1 + - + +
395B TYR* 3.3 25.8 + - + +
396B GLN* 3.2 21.0 + - - +
401B ASP* 6.0 0.2 - - - +
405B ASP* 5.0 5.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 393 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B ALA* 4.2 11.9 - - + -
389B PRO* 3.1 18.9 + - - +
390B PHE* 3.6 22.9 - - + +
391B ASN 3.2 0.2 - - - -
392B LEU* 1.3 76.8 - - + +
394B PHE* 1.3 57.3 + - - +
396B GLN* 3.3 6.9 + - - +
397B MET* 2.8 39.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 394 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B PHE* 5.4 2.0 - + - -
242B VAL* 3.8 15.9 - - + -
291B TYR* 3.6 26.5 - + + -
292B ALA* 4.0 16.8 - - + +
295B LEU* 4.0 17.0 - - + -
309B PHE* 3.7 21.1 - + - -
390B PHE 3.0 13.1 + - - +
391B ASN* 3.0 10.3 + - - +
393B LYS* 1.3 75.5 - - - +
395B TYR* 1.3 58.7 + + - +
397B MET* 4.3 2.5 - - - -
398B THR* 2.7 57.1 + - + +
402B PHE* 3.6 30.3 - + - -
404B TRP* 3.9 27.4 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 395 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391B ASN* 2.8 24.3 + - + -
392B LEU* 3.6 26.5 - - + +
393B LYS 3.3 0.4 - - - -
394B PHE* 1.3 76.6 - + - +
396B GLN* 1.3 58.7 + - - +
398B THR* 3.8 0.2 - - - -
399B GLY* 2.8 25.6 + - - -
400B HIS 3.0 33.4 + - - +
401B ASP* 3.5 30.1 - - + -
402B PHE* 3.3 22.4 - + + -
404B TRP* 3.0 47.8 + + - +
405B ASP* 3.0 30.4 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 396 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392B LEU 3.2 11.2 + - - +
393B LYS* 3.6 9.0 - - - +
395B TYR* 1.3 77.9 - - - +
397B MET* 1.3 66.6 + - + +
398B THR 3.3 0.3 + - - -
399B GLY* 3.3 10.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 397 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B ALA* 3.7 36.8 - - - +
295B LEU* 3.7 34.5 - - + -
296B GLU* 3.8 24.2 - - + +
299B LEU* 3.9 17.0 - - + +
304B ILE* 3.9 19.7 - - - +
393B LYS* 2.8 31.8 + - + +
394B PHE* 3.8 4.3 - - - +
396B GLN* 1.3 75.2 - - + +
398B THR* 1.3 59.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 398 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B LEU* 4.1 3.1 - - + -
304B ILE* 5.0 4.5 - - - +
309B PHE* 3.5 40.7 - - + -
394B PHE* 2.7 49.6 + - + +
395B TYR 3.4 3.8 + - - -
397B MET* 1.3 78.4 - - - +
399B GLY* 1.3 61.8 + - - +
400B HIS* 3.4 16.5 + - - +
402B PHE* 3.7 11.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 399 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395B TYR 2.8 9.2 + - - -
396B GLN* 3.3 10.4 + - - -
398B THR* 1.3 79.3 - - - +
400B HIS* 1.3 60.3 + - - +
----------------------------------------------------------
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