Contacts of the helix formed by residues 344 - 367 (chain B) in PDB entry 6KJV
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 344 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340B MET* 3.8 14.6 - - + +
341B CYS* 3.3 31.3 + - - +
343B THR* 1.3 90.4 - - - +
345B ILE* 1.3 69.0 + - + +
346B ALA* 3.3 7.4 - - + +
347B PHE* 3.3 3.7 + - - +
348B ARG* 3.1 25.4 + - - +
1091B ASP* 4.0 10.2 - - - +
1092B ALA* 3.5 41.3 + - + +
1093B VAL* 6.1 1.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 345 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B ARG* 4.1 29.8 - - - +
254B LEU* 4.7 22.0 - - + -
344B ASP* 1.3 72.1 - - + +
346B ALA* 1.3 69.1 + - - +
348B ARG* 3.3 27.6 - - - +
349B LEU* 2.8 30.3 + - + +
408B GLU* 3.8 10.5 - - - +
1093B VAL* 4.1 19.1 - - + -
1155B GLY 3.9 20.0 - - - +
1156B THR* 4.8 11.7 - - + -
1157B TRP* 5.9 2.0 - - + +
2001B 97Y 5.6 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 346 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251B LEU* 3.9 6.4 - - - +
254B LEU* 4.4 25.1 - - + +
255B LEU* 3.8 15.7 - - + +
340B MET* 3.7 24.7 - - + -
344B ASP* 3.3 4.9 - - + +
345B ILE* 1.3 83.1 - - + +
347B PHE* 1.3 56.9 + - - +
349B LEU* 4.7 0.2 - - - -
350B ALA* 2.9 30.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 347 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331B VAL* 3.9 17.9 - - + -
335B LEU* 3.8 21.8 - - + -
340B MET* 3.8 19.3 - - - -
341B CYS 3.8 10.8 - - - +
342B LYS* 3.3 55.9 - - + -
344B ASP 3.3 5.0 + - - +
345B ILE 3.1 0.6 - - - -
346B ALA* 1.3 78.0 - - - +
348B ARG* 1.3 59.2 + - - +
350B ALA* 3.3 6.6 + - + +
351B LYS* 2.8 54.6 + - + +
2001B 97Y 3.7 37.0 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 348 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342B LYS 4.0 13.7 - - - +
343B THR* 3.4 25.7 + - - +
344B ASP* 3.1 16.2 + - - +
345B ILE* 3.3 23.3 - - - +
347B PHE* 1.3 75.8 - - - +
349B LEU* 1.3 59.4 + - - +
351B LYS* 3.0 32.4 + - - +
352B SER* 3.0 10.4 + - - -
407B ASN* 3.2 45.8 - - - +
408B GLU* 2.7 29.5 + - - -
2001B 97Y 3.4 37.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 349 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B ARG* 3.8 25.6 - - + -
180B HIS* 4.0 18.4 - - + +
247B GLU* 4.2 3.8 - - - +
250B TYR* 4.0 17.3 - - + -
251B LEU* 4.0 14.6 - - + -
254B LEU* 3.9 24.5 - - + -
345B ILE* 2.8 17.3 + - + +
346B ALA 3.9 2.2 - - - +
348B ARG* 1.3 74.8 - - - +
350B ALA* 1.3 59.5 + - - +
352B SER* 3.2 1.8 + - - +
353B THR* 2.9 38.6 + - - +
402B TYR* 4.0 24.0 - - + -
2001B 97Y 4.2 10.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 350 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251B LEU* 3.7 25.0 - - + +
255B LEU* 5.6 0.9 - - + -
327B VAL* 4.6 0.7 - - + -
331B VAL* 4.3 19.7 - - + -
346B ALA 2.9 18.9 + - - +
347B PHE* 3.6 6.7 - - + +
349B LEU* 1.3 76.2 - - - +
351B LYS* 1.3 58.2 + - - +
354B LEU* 2.9 50.9 + - + +
2001B 97Y 5.9 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 351 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342B LYS 5.3 1.1 - - - -
347B PHE* 2.8 43.3 + - + +
348B ARG* 3.0 21.6 + - - +
350B ALA* 1.3 76.7 - - - +
352B SER* 1.3 56.2 + - - +
355B THR* 2.9 22.0 + - - -
2001B 97Y 2.5 112.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 352 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348B ARG 3.0 5.1 + - - -
349B LEU 3.2 3.3 + - - -
350B ALA 3.1 0.2 - - - -
351B LYS* 1.3 78.8 - - - +
353B THR* 1.3 65.5 + - - +
354B LEU 3.4 0.2 - - - -
355B THR* 3.1 7.3 + - - -
356B LEU* 3.0 24.7 + - - +
401B LEU* 3.0 30.6 + - - +
402B TYR* 3.6 25.4 - - - -
2001B 97Y 3.1 30.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 353 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244B LEU* 4.9 4.3 - - + -
247B GLU* 3.9 16.5 + - + +
248B GLY* 4.3 11.7 - - - +
251B LEU* 4.0 20.2 - - + +
349B LEU* 2.9 22.4 + - - +
352B SER* 1.3 75.5 - - - +
354B LEU* 1.3 57.9 + - - +
356B LEU* 3.1 4.2 + - - +
357B ILE* 3.0 48.2 + - + +
402B TYR* 2.5 28.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 354 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251B LEU* 4.9 3.4 - - + -
324B PHE* 3.2 54.5 - - + +
327B VAL* 3.9 28.9 - - + -
328B ILE* 4.0 10.1 - - + -
331B VAL* 5.0 0.7 - - + -
350B ALA* 2.9 29.7 + - + +
351B LYS 5.2 0.9 - - - +
353B THR* 1.3 75.4 - - - +
355B THR* 1.3 56.6 + - - +
357B ILE* 4.9 4.5 - - + -
358B PRO* 3.0 22.5 - - - +
2001B 97Y 3.9 31.9 - - + +
2002B OLC 3.7 13.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 355 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351B LYS 2.9 18.3 + - - -
352B SER 3.1 11.5 + - - -
353B THR 3.1 1.0 - - - -
354B LEU* 1.3 79.1 - - - +
356B LEU* 1.3 65.5 + - - +
357B ILE 3.3 0.2 - - - -
358B PRO* 3.3 12.0 - - - +
359B LEU* 3.2 28.3 + - + +
401B LEU* 4.0 20.6 - - + -
2001B 97Y 2.9 44.6 + - + -
2002B OLC 5.2 2.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 356 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B LEU* 5.2 1.6 - - + -
244B LEU* 4.2 17.0 - - + -
352B SER 3.0 14.5 + - - +
353B THR 3.1 5.1 + - - +
355B THR* 1.3 77.8 - - - +
357B ILE* 1.3 57.2 + - - +
359B LEU* 3.4 12.4 - - + +
360B LEU* 2.9 53.4 + - + +
394B GLN 5.6 0.2 - - - +
397B MET* 5.0 1.6 - - + +
398B VAL* 4.2 26.5 - - + +
401B LEU* 4.0 23.3 - - + -
402B TYR* 3.4 45.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 357 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244B LEU* 4.4 18.8 - - + +
248B GLY* 5.1 7.2 - - - -
251B LEU* 6.3 0.2 - - + -
320B ASN* 3.4 54.1 - - + +
321B PHE* 4.4 8.5 - - + +
323B ILE* 5.1 3.6 - - + -
324B PHE* 4.0 25.1 - - + +
353B THR* 3.0 36.8 + - + +
354B LEU* 4.9 3.6 - - + -
356B LEU* 1.3 76.6 - - - +
358B PRO* 1.3 67.4 - - + +
361B CYS* 3.0 35.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 358 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321B PHE* 3.9 16.2 - - + -
324B PHE* 3.7 15.7 - - + -
354B LEU 3.0 28.3 - - - +
355B THR* 3.3 8.1 - - - +
357B ILE* 1.3 89.3 - - + +
359B LEU* 1.3 58.1 + - - +
361B CYS 4.2 0.2 - - - -
362B THR* 3.2 27.3 - - - +
2002B OLC 3.5 50.8 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
355B THR* 3.2 28.8 + - + +
356B LEU* 3.1 27.8 + - + +
357B ILE 3.1 1.0 - - - -
358B PRO* 1.3 79.6 - - - +
360B LEU* 1.3 66.1 + - + +
362B THR 4.9 0.4 + - - -
390B PHE* 4.9 19.7 - - + -
394B GLN* 4.9 5.2 + - + +
397B MET* 4.6 23.8 - - + -
2001B 97Y 6.4 0.2 - - + -
2002B OLC 3.9 39.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 360 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B LEU* 6.3 0.4 - - + -
187B PHE* 3.9 28.5 - - + -
240B ASN* 5.4 7.0 - - + +
241B TYR* 3.2 32.2 + - + -
244B LEU* 4.0 28.7 - - + -
356B LEU* 2.9 38.5 + - + +
359B LEU* 1.3 94.9 - - + +
361B CYS* 1.3 58.0 + - - +
362B THR 3.7 0.9 - - - -
363B HIS* 5.1 5.8 + - - +
364B GLU* 5.3 1.7 + - - +
394B GLN* 3.4 32.9 + - + +
398B VAL* 5.3 3.1 - - + -
2002B OLC 5.8 3.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 361 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241B TYR* 3.7 16.8 - - - -
244B LEU* 4.7 4.5 - - - -
317B CYS* 2.0 54.8 - - + -
320B ASN* 4.1 15.3 - - - -
321B PHE* 3.5 18.6 - - + -
357B ILE* 3.0 18.7 + - + +
360B LEU* 1.3 76.1 - - - +
362B THR* 1.3 66.3 + - - +
363B HIS 3.4 2.2 - - - -
364B GLU 3.7 3.2 + - - +
365B VAL* 3.5 17.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 362 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321B PHE* 3.9 18.3 - - - -
358B PRO* 3.2 23.3 + - - +
359B LEU 5.2 0.2 - - - +
360B LEU 3.7 0.2 - - - -
361B CYS* 1.3 76.7 - - - +
363B HIS* 1.3 71.1 + - - +
365B VAL* 3.3 3.2 + - - +
366B ILE* 3.0 46.3 + - + +
2002B OLC 3.5 54.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 363 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360B LEU 5.2 4.9 - - - +
361B CYS 3.4 0.6 - - - +
362B THR* 1.3 82.5 - - - +
364B GLU* 1.3 71.1 + - + +
366B ILE* 3.3 6.0 + - - -
367B PHE* 3.2 56.4 + + + +
384B LEU* 5.4 7.0 - - + -
387B GLU* 3.1 34.3 + - + -
2002B OLC 3.6 39.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 364 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241B TYR* 5.3 7.6 + - - +
310B ARG* 3.5 46.7 + - - +
313B ILE* 3.9 27.2 - - + +
314B LEU* 3.7 20.6 - - + +
317B CYS* 4.1 11.9 - - - -
360B LEU 5.3 0.6 + - - +
361B CYS* 3.7 9.9 + - - +
362B THR 3.3 0.8 - - - -
363B HIS* 1.3 87.2 - - + +
365B VAL* 1.3 59.6 + - - +
367B PHE 3.8 3.8 - - - +
368B ALA* 3.4 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 365 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314B LEU* 4.0 15.9 - - + -
317B CYS* 4.0 21.3 - - + -
318B ILE* 4.8 7.9 - - + +
321B PHE* 4.0 18.4 - - + -
361B CYS 3.5 14.0 + - - +
362B THR* 3.3 6.6 + - - +
363B HIS 3.2 0.4 - - - -
364B GLU* 1.3 77.2 - - - +
366B ILE* 1.3 69.0 + - + +
368B ALA* 3.4 15.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 366 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362B THR* 3.0 41.9 + - + +
363B HIS* 3.3 5.4 + - - +
365B VAL* 1.3 81.5 - - + +
367B PHE* 1.3 89.4 + - + +
368B ALA* 3.4 2.6 + - - +
370B VAL* 5.7 0.2 - - - +
2002B OLC 6.1 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 367 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306B TRP* 5.3 0.7 - - - -
363B HIS* 3.2 48.6 + + + +
364B GLU* 3.8 6.3 - - - +
366B ILE* 1.3 95.9 - - + +
368B ALA* 1.3 64.4 + - - +
369B PHE 3.3 2.1 + - - -
370B VAL* 3.6 38.9 + - + +
384B LEU* 5.5 13.0 - - + -
----------------------------------------------------------
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