Contacts of the helix formed by residues 455 - 475 (chain B) in PDB entry 4KPE
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 455 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451B ALA* 3.2 14.3 + - + +
452B ILE 3.8 5.2 - - - +
453B ILE 3.5 3.8 + - - -
454B GLY* 1.3 79.8 - - - +
456B GLU* 1.3 69.6 + - - +
457B ARG* 3.7 13.8 + - - +
458B THR* 2.8 44.4 + - - +
459B MET 2.9 10.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 456 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354B ARG* 2.8 47.1 + - - -
358B LEU* 5.0 3.8 - - - +
453B ILE 5.5 2.8 - - - +
455B ASP* 1.3 72.0 + - - +
457B ARG* 1.3 62.9 + - - +
459B MET* 3.3 15.5 + - - +
460B TYR* 2.9 44.5 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 457 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455B ASP* 3.1 15.2 + - - +
456B GLU* 1.3 78.3 - - - +
458B THR* 1.3 64.1 + - - +
460B TYR* 3.4 5.8 + - - +
461B ASN* 3.0 33.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 458 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448B MET 5.2 0.4 - - - +
451B ALA* 3.8 17.3 - - + +
452B ILE* 3.7 29.4 - - + +
455B ASP* 2.8 34.9 + - - +
457B ARG* 1.3 71.6 - - - +
459B MET* 1.3 60.4 + - - +
461B ASN* 3.3 8.6 + - - +
462B LEU* 3.2 20.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 459 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354B ARG* 3.7 27.6 - - + +
357B ILE* 4.1 17.4 - - + +
358B LEU* 4.0 22.9 - - + -
452B ILE* 3.6 27.5 + - + +
455B ASP 2.9 7.6 + - - +
456B GLU* 3.5 31.4 - - - +
458B THR* 1.3 74.7 - - - +
460B TYR* 1.3 104.7 + - + +
462B LEU* 3.3 6.2 - - - +
463B MET* 3.1 22.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 460 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194B ILE* 3.7 31.3 - - + +
350B ILE* 3.8 25.3 - - + +
351B ALA* 6.1 0.5 - - - -
354B ARG* 3.7 17.6 - - + +
456B GLU* 2.9 45.6 + - + +
457B ARG* 4.0 5.6 - - - +
459B MET* 1.3 96.6 - - + +
461B ASN* 1.3 61.8 + - - +
463B MET* 3.2 14.3 + - + +
464B LYS* 2.8 31.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 461 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457B ARG* 3.0 24.3 + - - +
458B THR* 3.7 8.2 - - - +
459B MET 3.2 0.2 - - - -
460B TYR* 1.3 77.8 - - - +
462B LEU* 1.3 60.6 + - - +
464B LYS* 3.5 27.4 + - - +
465B LYS* 2.9 27.2 + - - +
468B ARG* 5.4 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 462 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357B ILE* 3.7 19.3 - - + -
360B ARG* 3.5 15.9 - - - +
452B ILE* 4.0 24.5 - - + -
458B THR 3.2 11.9 + - - +
459B MET* 3.3 12.8 - - - +
461B ASN* 1.3 75.3 - - - +
463B MET* 1.3 60.2 + - - +
465B LYS* 3.1 17.1 + - + -
466B GLU* 2.9 58.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 463 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194B ILE* 3.0 28.3 - - + -
349B TYR* 5.3 0.4 - - + -
350B ILE* 2.9 56.5 - - + +
353B ARG* 3.7 27.4 - - + +
354B ARG* 4.2 7.6 - - - -
357B ILE* 3.7 16.5 - - + +
459B MET* 3.1 10.8 + - - +
460B TYR* 3.4 21.1 - - + +
462B LEU* 1.3 78.9 - - - +
464B LYS* 1.3 61.0 + - - +
466B GLU* 3.7 3.7 + - - +
467B LEU* 3.1 38.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 464 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B VAL* 3.9 18.8 - - + +
194B ILE* 3.5 39.0 - - + -
195B ASP* 2.9 31.3 + - - +
460B TYR* 2.8 15.1 + - + +
461B ASN* 3.5 27.2 + - - +
462B LEU 3.1 0.2 - - - -
463B MET* 1.3 73.7 - - - +
465B LYS* 1.3 65.9 + - - +
466B GLU 3.1 1.5 + - - -
467B LEU* 3.3 4.7 + - - +
468B ARG* 3.1 57.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 465 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461B ASN 2.9 16.2 + - - +
462B LEU* 3.5 22.2 - - + +
464B LYS* 1.3 74.7 - - - +
466B GLU* 1.3 61.8 + - + +
468B ARG* 3.4 13.8 + - - +
469B GLU* 3.1 41.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 466 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B GLN* 4.5 5.4 - - - +
158B ALA* 5.7 0.6 - - - +
353B ARG* 3.0 19.6 + - - +
357B ILE* 4.2 3.9 - - - +
360B ARG* 2.8 42.6 + - - -
462B LEU* 2.9 36.3 + - + +
463B MET* 4.1 4.3 - - - +
465B LYS* 1.3 76.6 - - + +
467B LEU* 1.3 67.3 + - + +
468B ARG 3.1 2.0 + - - -
469B GLU* 3.2 19.4 + - - +
470B VAL* 3.1 24.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 467 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B ALA 3.9 11.9 - - - +
159B PHE* 4.7 1.8 - - - -
160B PRO* 4.7 1.6 - - + -
187B ILE* 3.2 38.9 - - + +
190B ALA* 4.5 13.5 - - + -
191B VAL* 4.0 14.6 - - + -
194B ILE* 3.9 24.0 - - + -
349B TYR* 3.6 35.0 - - + +
353B ARG* 5.5 3.1 - - + +
463B MET* 3.1 28.6 + - + +
464B LYS 3.9 2.9 - - - +
466B GLU* 1.3 75.8 - - + +
468B ARG* 1.3 57.9 + - - +
470B VAL* 3.4 4.0 + - - +
471B LYS 3.0 22.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 468 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B ILE* 4.9 1.6 - - + -
191B VAL* 3.9 27.9 - - + +
195B ASP* 5.1 1.8 + - - -
461B ASN 5.4 0.6 + - - -
464B LYS* 3.1 61.2 + - - +
465B LYS* 3.7 10.8 - - - +
466B GLU 3.1 0.8 - - - -
467B LEU* 1.3 75.8 - - - +
469B GLU* 1.3 54.1 + - - +
471B LYS* 3.2 24.0 + - - +
472B LYS* 2.8 35.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 469 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B TYR* 6.3 0.4 - - + -
465B LYS* 3.1 39.7 + - + +
466B GLU* 3.4 21.3 - - - +
468B ARG* 1.3 75.6 - - - +
470B VAL* 1.3 57.6 + - + +
472B LYS* 3.3 8.1 + - - +
473B LYS* 3.0 29.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 470 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B TYR* 3.7 34.8 - - + -
132B GLN* 5.8 0.2 - - - +
158B ALA* 3.8 19.1 - - + +
159B PHE* 3.9 21.5 - - + -
183B LEU* 4.2 6.1 - - + -
187B ILE* 3.8 16.4 - - + -
466B GLU 3.1 14.9 + - - +
467B LEU 3.6 7.0 - - - +
469B GLU* 1.3 72.1 - - + +
471B LYS* 1.3 62.8 + - - +
473B LYS* 3.2 1.6 + - - -
474B PHE* 2.9 45.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 471 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B LEU* 4.2 6.7 - - - -
184B ALA* 3.7 30.7 - - + +
187B ILE* 3.8 18.1 - - + +
188B ASP* 3.0 34.4 + - - +
467B LEU 3.0 14.4 + - - +
468B ARG* 3.2 28.5 + - - +
470B VAL* 1.3 72.9 - - - +
472B LYS* 1.3 67.7 + - - +
475B ALA* 2.7 32.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 472 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468B ARG 2.8 17.0 + - - +
469B GLU* 3.7 10.5 - - - +
471B LYS* 1.3 76.4 - - - +
473B LYS* 1.3 60.4 + - + +
475B ALA* 4.4 4.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 473 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B GLU* 2.9 30.7 + - - -
129B TYR* 3.1 29.6 + - + +
469B GLU 3.0 17.0 + - - +
470B VAL 3.2 0.2 + - - -
471B LYS 3.0 0.4 - - - -
472B LYS* 1.3 80.7 - - + +
474B PHE* 1.3 91.5 + - + +
475B ALA 5.4 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 474 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B GLU* 3.5 14.3 - - - +
125B GLU* 4.1 13.2 - - + -
126B ILE* 3.6 48.2 - - + -
129B TYR* 3.3 47.1 - + - -
183B LEU* 4.2 11.3 - - + +
470B VAL* 2.9 37.3 + - + +
473B LYS* 1.3 108.1 - - + +
475B ALA* 1.3 68.1 + - - +
476B THR* 3.4 12.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 475 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B LEU* 4.4 7.8 - - - +
184B ALA* 4.0 22.7 - - + +
471B LYS* 2.7 27.3 + - + +
472B LYS* 4.4 4.3 + - - +
473B LYS 3.6 1.2 - - - +
474B PHE* 1.3 77.1 - - - +
476B THR* 1.3 67.3 + - - +
----------------------------------------------------------
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