Contacts of the helix formed by residues 349 - 369 (chain B) in PDB entry 6B0Z
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 349 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B ILE* 4.6 0.9 - - - +
6B SER 2.7 29.5 + - - -
7B GLY* 4.4 3.6 + - - -
344B ALA* 2.8 24.9 + - - +
347B ASP* 3.2 12.1 + - + +
348B ASN* 1.3 69.1 - - - +
350B LYS* 1.3 63.5 + - - +
351B GLU* 3.2 17.0 - - - +
352B LEU* 3.0 37.2 + - + +
353B ALA* 2.9 20.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 350 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348B ASN 3.4 7.1 + - - +
349B ASN* 1.3 73.2 + - - +
351B GLU* 1.3 76.0 + - - +
353B ALA* 3.3 6.2 + - - +
354B PHE* 3.0 24.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 351 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B ILE* 3.8 26.1 - - + +
349B ASN* 3.2 13.5 - - - +
350B LYS* 1.3 86.0 + - - +
352B LEU* 1.3 63.6 + - - +
354B PHE* 3.3 7.6 + - - +
355B PHE* 3.0 22.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 352 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B ILE* 3.9 11.1 - - + +
7B GLY* 3.5 26.2 - - - +
35B VAL* 4.2 27.8 - - + -
340B LEU* 3.5 48.7 - - + +
343B ARG* 3.7 13.7 - - + -
344B ALA* 3.8 7.0 - - + +
349B ASN* 3.0 27.3 + - + +
351B GLU* 1.3 76.3 - - - +
353B ALA* 1.3 57.8 + - - +
355B PHE* 3.2 5.1 + - + +
356B ALA* 2.9 27.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 353 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341B ALA* 5.3 4.6 - - + +
344B ALA* 3.5 15.4 - - + +
345B LYS 5.7 0.2 - - - +
349B ASN 2.9 19.0 + - - +
350B LYS* 3.7 5.6 - - - +
352B LEU* 1.3 76.8 - - - +
354B PHE* 1.3 61.9 + - - +
356B ALA* 3.4 6.4 + - - +
357B ASN* 3.2 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 354 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350B LYS 3.0 16.7 + - - +
351B GLU* 3.6 7.4 - - - +
352B LEU 3.3 0.2 - - - -
353B ALA* 1.3 76.2 - - - +
355B PHE* 1.3 67.4 + - - +
357B ASN* 3.9 7.1 + - - +
358B ALA* 3.0 33.2 + - + +
408B LYS* 5.7 3.4 - - + -
409B LEU* 4.4 17.5 - - + -
412B ALA* 4.1 28.9 - - + -
413B LYS* 6.1 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 355 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B ILE* 3.7 24.2 - - + -
30B LEU 3.2 25.6 - - - -
31B ILE* 4.2 8.1 - - + -
34B TYR* 3.6 25.4 - + + -
35B VAL* 3.8 24.9 - - + -
337B THR* 6.0 0.2 - - + -
340B LEU* 4.0 21.3 - - + -
351B GLU 3.0 6.3 + - - -
352B LEU* 3.2 11.0 + - + +
354B PHE* 1.3 81.4 - - + +
356B ALA* 1.3 68.5 + - - +
358B ALA* 3.1 6.2 + - - +
359B LEU* 3.0 36.9 + - + +
405B LEU* 4.4 5.6 - - + -
409B LEU* 3.7 29.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 356 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337B THR* 3.6 34.4 - - - +
340B LEU* 4.3 7.9 - - + -
341B ALA* 3.9 22.0 - - + +
352B LEU 2.9 16.3 + - - +
353B ALA 3.8 4.3 - - - +
354B PHE 3.4 0.2 - - - -
355B PHE* 1.3 84.8 - - - +
357B ASN* 1.3 60.6 + - - +
359B LEU 3.3 0.5 + - - -
360B GLU* 3.3 26.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 357 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353B ALA 3.2 13.5 + - - +
354B PHE* 4.1 7.5 + - - +
356B ALA* 1.3 78.8 - - - +
358B ALA* 1.3 59.4 - - - +
360B GLU* 3.2 15.7 + - - +
361B GLU* 2.8 59.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 358 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354B PHE* 3.0 30.6 + - + +
355B PHE 3.6 3.8 - - - +
357B ASN* 1.3 78.8 - - - +
359B LEU* 1.3 57.1 + - - +
361B GLU* 3.4 12.8 + - - +
362B VAL* 2.8 33.6 + - - +
405B LEU* 4.9 0.9 - - - -
408B LYS* 4.2 13.5 - - + -
409B LEU* 3.9 25.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 359 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B ILE* 6.0 0.4 - - + -
30B LEU* 4.2 25.1 - - + -
31B ILE* 4.0 26.0 - - + -
333B ILE* 4.0 12.3 - - + +
337B THR* 3.8 20.4 - - + -
340B LEU* 6.1 0.2 - - + -
355B PHE* 3.0 29.3 + - + +
356B ALA 3.8 4.9 - - - +
357B ASN 3.2 0.2 - - - -
358B ALA* 1.3 73.9 - - - +
360B GLU* 1.3 59.9 + - - +
362B VAL* 4.3 10.1 - - + -
363B SER* 2.8 39.3 + - - +
401B LEU* 6.0 1.3 - - + -
405B LEU* 4.0 29.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 360 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334B PHE* 3.5 33.0 - - + -
337B THR* 2.7 37.0 + - + +
338B ARG* 3.1 25.6 + - - +
356B ALA 3.3 12.2 + - - +
357B ASN* 3.2 16.6 + - - +
359B LEU* 1.3 74.2 - - - +
361B GLU* 1.3 65.9 + - + +
363B SER* 3.2 2.9 + - - -
364B ILE* 3.0 31.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 361 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357B ASN* 2.8 43.3 + - - +
358B ALA* 3.6 10.2 - - - +
360B GLU* 1.3 75.9 - - + +
362B VAL* 1.3 55.9 + - - +
364B ILE* 3.2 7.0 + - - +
365B GLU* 2.8 48.0 + - - +
408B LYS* 3.1 24.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 362 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358B ALA 2.8 20.7 + - - +
359B LEU* 3.8 11.4 - - + +
360B GLU 3.3 0.2 - - - -
361B GLU* 1.3 74.9 - - - +
363B SER* 1.3 64.7 + - - +
365B GLU* 3.8 8.4 - - - +
366B THR* 2.9 32.6 + - - +
401B LEU* 3.9 16.8 - - + +
404B ASN* 4.1 13.0 - - + +
405B LEU* 3.9 31.4 - - + +
408B LYS* 3.5 36.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 363 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330B ILE* 3.7 22.9 - - - +
333B ILE* 3.8 21.0 - - - +
334B PHE* 3.9 14.5 - - - -
359B LEU* 2.8 27.2 + - - +
360B GLU 3.5 5.2 - - - -
362B VAL* 1.3 76.4 - - - +
364B ILE* 1.3 63.0 + - - +
366B THR* 3.6 2.1 + - - -
367B ILE* 3.5 26.5 + - - +
401B LEU* 3.8 13.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 364 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B ILE* 4.1 26.5 - - + -
113B ILE 4.1 18.8 - - - +
114B CYS* 4.2 9.2 - - - -
290B MET* 6.0 0.2 - - + -
330B ILE* 6.3 0.2 - - + -
334B PHE* 4.4 9.0 - - + -
360B GLU* 3.0 19.2 + - + +
361B GLU* 3.8 5.6 - - - +
363B SER* 1.3 73.0 - - - +
365B GLU* 1.3 68.0 + - + +
367B ILE* 3.3 4.2 + - - +
368B GLU* 3.0 49.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 365 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361B GLU* 2.8 29.8 + - + +
362B VAL* 3.8 9.9 - - - +
364B ILE* 1.3 75.2 - - + +
366B THR* 1.3 57.6 + - - +
368B GLU* 3.2 11.8 + - - +
369B ALA* 2.8 33.5 + - - +
408B LYS* 2.6 37.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 366 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362B VAL 2.9 19.4 + - - -
363B SER 3.9 2.0 - - - -
364B ILE 3.3 0.2 - - - -
365B GLU* 1.3 77.6 - - - +
367B ILE* 1.3 62.4 + - - +
369B ALA* 3.4 10.1 + - - +
370B GLY 3.5 0.3 + - - -
371B PHE* 3.1 45.3 + - + +
397B PHE* 3.9 13.5 - - + -
400B LYS* 3.9 18.8 - - + -
401B LEU* 3.4 20.0 - - + +
404B ASN* 3.0 25.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 367 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B CYS* 4.0 8.7 - - - -
116B ASN* 2.7 24.8 + - - +
117B ILE* 3.8 35.0 - - + -
290B MET* 3.7 21.3 - - + -
330B ILE* 3.9 17.5 - - + -
363B SER 3.5 15.5 + - - +
364B ILE 3.3 6.5 + - - +
365B GLU 3.3 0.2 - - - -
366B THR* 1.3 76.3 - - - +
368B GLU* 1.3 53.2 + - - +
370B GLY* 3.0 13.2 + - - -
371B PHE 3.2 14.8 - - - +
372B MET* 3.8 7.5 - - + +
376B LEU* 3.6 27.1 - - + -
397B PHE* 3.9 11.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 368 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B ILE 4.4 0.9 - - - +
114B CYS* 3.4 10.4 - - + -
115B LYS* 2.7 60.4 + - + +
116B ASN* 3.2 28.9 + - + +
364B ILE* 3.0 36.8 + - - +
365B GLU* 3.8 9.3 - - - +
367B ILE* 1.3 75.7 - - - +
369B ALA* 1.3 58.9 + - - +
370B GLY 3.6 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 369 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365B GLU 2.8 17.7 + - - +
366B THR* 3.7 7.9 - - - +
367B ILE 3.2 0.6 - - - -
368B GLU* 1.3 76.1 - - - +
370B GLY* 1.3 56.7 + - - +
371B PHE* 3.7 22.9 - - + -
404B ASN* 6.3 0.7 - - - +
----------------------------------------------------------
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