Contacts of the helix formed by residues 284 - 305 (chain B) in PDB entry 5KX8
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 SER 284 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B PRO 3.5 4.1 + - - -
283B LEU* 1.3 77.7 - - - +
285B TRP* 1.3 58.5 + - - +
286B HIS* 3.4 8.5 + - - +
287B MET* 3.0 37.3 + - - +
288B ARG* 2.9 27.9 + - - +
417B LYS 5.8 0.2 - - - -
418B MET* 4.8 4.3 - - - +
419B ASN* 6.2 1.3 - - - -
420B ASP* 3.5 17.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 285 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284B SER* 1.3 68.5 - - - +
286B HIS* 1.3 57.6 + - - +
288B ARG* 3.1 8.5 + - + +
289B CYS* 2.8 59.3 + - - -
380B ILE* 4.5 5.4 - - + -
381B ILE* 4.3 20.2 - - + -
418B MET* 3.8 25.5 - - + -
420B ASP* 2.8 30.9 + - - +
421B ALA* 3.7 20.0 - - + -
422B ASP* 4.5 3.1 - - - -
425B SER* 2.8 28.7 + - - -
426B VAL* 3.6 41.3 - - + -
429B MET* 3.6 35.2 - - + -
457B MET* 4.6 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 286 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284B SER* 3.3 4.7 - - - +
285B TRP* 1.3 80.1 - - - +
287B MET* 1.3 69.7 + - + +
289B CYS* 3.4 6.9 + - - +
290B LYS* 3.3 26.1 + - + +
420B ASP* 3.0 17.5 + - - +
458B THR* 6.3 0.8 - - - +
208D THR* 5.8 3.6 - - + -
247D GLU* 2.7 40.2 + - - -
249D LEU* 3.6 28.5 - - + +
263D VAL* 4.4 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 287 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B PRO 5.3 0.9 - - - +
283B LEU* 4.2 19.1 - - + -
284B SER* 3.0 39.4 + - - +
286B HIS* 1.3 83.0 - - + +
288B ARG* 1.3 56.7 + - - +
290B LYS* 3.2 12.0 + - + +
291B ILE* 2.9 36.7 + - + +
323B PHE* 3.6 46.7 - - + -
247D GLU* 5.0 6.7 - - - +
326D LYS* 6.0 4.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 288 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B LEU* 5.9 0.2 - - + -
274B LEU* 3.8 20.4 + - + +
282B PRO* 4.4 4.0 - - - +
283B LEU* 2.7 52.2 + - + +
284B SER 2.9 13.6 + - - +
285B TRP* 3.4 11.4 - - + +
287B MET* 1.3 77.9 - - - +
289B CYS* 1.4 56.1 + - - +
291B ILE* 3.9 7.7 - - + +
292B ALA* 3.1 27.2 + - - +
380B ILE* 2.9 52.8 + - + +
383B GLY 4.4 0.8 - - - +
415B ASP* 2.8 37.2 + - - +
417B LYS* 3.9 7.1 + - - +
418B MET* 3.4 28.2 - - - +
429B MET* 4.1 0.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 289 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B TRP* 2.8 62.7 + - - +
286B HIS* 3.8 7.6 - - - +
288B ARG* 1.4 67.5 - - - +
290B LYS* 1.3 65.2 + - - +
292B ALA* 3.3 2.4 + - - +
293B GLN* 3.0 30.6 + - - +
425B SER* 5.2 1.1 - - - -
429B MET* 4.1 7.4 - - - -
457B MET* 3.8 23.2 - - + +
458B THR* 4.0 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 290 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286B HIS* 3.3 16.4 + - + +
287B MET* 3.2 14.2 + - + +
289B CYS* 1.3 78.2 - - - +
291B ILE* 1.3 57.8 + - - +
293B GLN* 3.5 13.7 + - - +
294B GLY* 3.0 25.6 + - - -
322B ALA* 2.8 31.8 + - - +
323B PHE* 3.7 16.4 - - + +
324B THR* 3.9 19.1 + - - +
325B ALA 5.5 0.5 + - - -
241D GLN* 2.8 37.1 + - - +
247D GLU* 5.7 4.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 291 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B LEU* 4.1 30.1 - - + -
283B LEU* 4.0 34.8 - - + -
287B MET* 2.9 28.6 + - + +
288B ARG* 3.9 7.4 - - - +
289B CYS 3.3 0.2 - - - -
290B LYS* 1.3 71.7 - - - +
292B ALA* 1.3 57.7 + - - +
295B ALA* 2.8 34.4 + - + +
317B ILE* 4.5 3.4 - - + -
319B LEU* 3.9 20.2 - - + -
323B PHE* 3.6 24.5 - - + +
325B ALA* 3.5 17.2 - - + +
380B ILE* 4.4 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 292 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B ARG 3.1 18.1 + - - +
289B CYS 3.3 4.5 + - - +
291B ILE* 1.3 76.1 - - - +
293B GLN* 1.3 62.3 + - - +
295B ALA* 3.4 1.5 + - - -
296B ALA* 3.1 20.3 + - - +
373B PHE* 3.6 11.9 - - - -
377B LEU* 3.8 26.5 - - + -
380B ILE* 4.2 10.0 - - + +
429B MET* 3.8 15.5 - - + -
454B LEU* 3.9 10.5 - - + -
457B MET* 5.2 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 293 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289B CYS 3.0 22.0 + - - +
290B LYS* 3.7 13.0 - - - +
292B ALA* 1.3 76.5 - - - +
294B GLY* 1.3 56.2 + - - +
296B ALA* 3.2 4.7 + - - +
297B ASN* 3.0 38.6 + - - +
451B GLN 5.7 0.2 - - - +
454B LEU* 3.0 46.0 + - + +
455B GLN* 3.9 14.1 - - + +
457B MET* 4.5 2.4 - - + +
458B THR* 3.0 33.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 294 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244B ASN* 3.2 34.4 - - - +
290B LYS 3.0 17.1 + - - -
291B ILE 3.8 0.7 - - - -
293B GLN* 1.3 71.6 - - - +
295B ALA* 1.3 65.8 + - - +
297B ASN* 3.1 7.9 + - - -
298B GLY 3.1 17.5 + - - -
325B ALA* 3.9 5.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 295 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244B ASN* 5.3 0.2 - - - -
291B ILE* 2.8 22.8 + - + +
292B ALA* 3.7 1.6 - - - +
294B GLY* 1.3 70.5 - - - +
296B ALA* 1.3 61.3 + - - +
298B GLY* 3.1 3.6 + - - -
299B ILE* 3.0 25.3 + - - +
317B ILE* 4.4 14.1 - - + -
325B ALA* 3.5 12.3 - - + +
327B ILE* 3.6 21.4 - - + +
373B PHE* 3.6 23.6 - - + -
376B VAL* 5.8 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 296 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B ALA 3.1 13.7 + - - +
293B GLN* 3.2 8.7 + - - +
295B ALA* 1.3 75.8 - - - +
297B ASN* 1.3 58.2 + - - +
299B ILE* 4.6 0.7 - - - -
300B ASN* 2.9 29.0 + - - +
373B PHE* 3.9 12.9 - - + -
447B ILE* 3.6 14.9 - - + +
450B VAL* 4.3 9.4 - - + -
451B GLN* 4.4 13.8 + - + -
454B LEU* 3.8 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 297 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242B HIS* 3.8 11.1 + - + -
244B ASN* 3.4 22.8 + - - +
293B GLN* 3.0 25.3 + - - +
294B GLY* 3.1 6.7 + - - +
296B ALA* 1.3 74.6 - - - +
298B GLY* 1.3 58.5 + - - +
300B ASN* 3.4 3.6 + - - +
301B PHE* 3.0 27.4 + - - +
451B GLN* 3.0 34.7 + - - +
455B GLN* 4.3 8.3 + - - +
164D ARG* 6.1 1.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 298 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242B HIS* 4.3 4.7 - - - -
244B ASN* 3.7 27.0 - - - +
245B LEU* 3.9 6.1 - - - +
294B GLY 3.1 10.7 + - - -
295B ALA 3.1 4.9 + - - -
297B ASN* 1.3 73.5 - - - +
299B ILE* 1.4 62.3 + - - +
301B PHE* 3.3 5.0 + - - +
302B LEU* 3.1 26.4 + - - +
327B ILE* 4.0 8.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 299 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B ALA 3.0 14.7 + - - +
298B GLY* 1.4 72.4 - - - +
300B ASN* 1.3 66.1 + - - +
302B LEU* 3.2 8.9 + - + +
303B HIS* 3.0 49.6 + - + +
309B HIS* 6.2 0.2 - - + -
312B ILE* 3.7 31.4 - - + -
327B ILE* 4.1 9.0 - - + -
369B ASP* 4.6 10.1 - - + +
370B ILE* 5.0 1.3 - - + -
373B PHE* 3.5 42.2 - - + -
447B ILE* 3.6 23.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 300 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296B ALA 2.9 18.5 + - - +
297B ASN 3.5 5.9 + - - +
298B GLY 3.2 0.2 - - - -
299B ILE* 1.3 76.5 - - - +
301B PHE* 1.3 58.2 + - - +
303B HIS* 3.3 1.7 + - - +
304B GLU* 2.8 59.3 + - - +
447B ILE* 3.6 25.4 - - + +
448B LYS* 4.2 10.9 - - - +
451B GLN* 3.3 34.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 301 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239B LYS 5.2 1.8 - - - -
240B CYS* 3.6 34.8 - - + -
241B GLN 3.4 24.7 - - - -
242B HIS* 3.3 39.3 - + + +
245B LEU* 3.8 11.9 - - + -
297B ASN 3.0 13.4 + - - +
298B GLY 3.3 8.9 + - - +
300B ASN* 1.3 79.1 - - - +
302B LEU* 1.3 61.3 + - - +
304B GLU* 3.5 11.0 + - - +
305B ASN* 2.8 49.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 302 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236B VAL* 4.5 6.1 - - + -
240B CYS* 4.5 15.3 - - - -
245B LEU* 4.2 15.3 - - + -
298B GLY 3.1 16.4 + - - +
299B ILE* 3.2 14.6 + - + +
301B PHE* 1.3 76.9 - - - +
303B HIS* 1.3 62.0 + - + +
305B ASN* 3.2 6.0 + - - -
306B HIS 3.2 4.9 + - - -
307B HIS* 2.8 51.7 + - + +
309B HIS* 4.0 26.7 - - + +
327B ILE* 4.3 4.3 - - + -
330B PHE* 4.0 35.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 303 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B ILE* 3.0 34.7 + - + +
300B ASN 3.8 2.9 - - - +
302B LEU* 1.3 74.7 - - + +
304B GLU* 1.4 64.5 + - - +
306B HIS* 3.0 20.0 + - - +
307B HIS 3.3 18.8 - - - +
366B PRO* 3.5 41.3 - - + +
369B ASP* 3.0 27.5 + - + +
370B ILE* 4.1 9.6 - - + +
447B ILE* 3.5 25.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 304 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300B ASN* 2.8 49.2 + - - +
301B PHE* 3.7 15.9 - - - +
303B HIS* 1.4 71.5 - - - +
305B ASN* 1.3 63.4 + - - +
306B HIS* 3.2 20.7 + - - -
448B LYS* 6.0 2.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 305 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239B LYS* 5.4 2.6 - - - +
240B CYS* 4.0 16.1 - - - -
301B PHE* 2.8 51.3 + - - +
302B LEU 3.3 3.4 - - - +
303B HIS 3.2 0.4 - - - -
304B GLU* 1.3 80.8 + - - +
306B HIS* 1.4 73.3 + - - +
307B HIS* 3.0 28.4 + - + +
----------------------------------------------------------
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