Contacts of the helix formed by residues 453 - 464 (chain B) in PDB entry 6B5G
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 453 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452A ASN* 3.4 21.9 - - - +
454A ILE* 4.8 0.7 - - - -
298B ASP* 3.9 14.3 + - - +
451B THR* 3.2 12.0 + - - +
452B ASN* 1.3 75.8 - - - +
454B ILE* 1.3 61.7 + - - +
455B ASN* 3.5 18.7 + - - +
456B LYS* 3.4 37.1 + - + +
457B ALA* 2.9 30.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 454 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451A THR 4.1 2.0 - - - +
452A ASN* 2.9 28.1 + - - +
453A ASP 5.0 0.2 - - - -
454A ILE* 4.2 30.5 - - + -
457A ALA* 4.1 23.6 - - + -
458A LEU* 5.1 6.1 - - + -
471A ILE* 4.4 6.3 - - + -
472A ASN* 4.1 13.5 - - - +
452B ASN 3.5 0.6 + - - -
453B ASP* 1.3 72.1 - - - +
455B ASN* 1.3 76.4 + - - +
457B ALA* 3.3 0.9 + - - +
458B LEU* 2.9 47.0 + - + +
511C VAL* 4.2 22.4 - - + -
512C LYS 5.9 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 455 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A ASP* 5.7 1.2 + - - -
452A ASN* 3.3 24.9 + - - -
472A ASN* 4.8 6.2 + - - +
431B MET* 5.6 0.9 - - - -
453B ASP* 3.3 12.1 + - - +
454B ILE* 1.3 86.7 - - - +
456B LYS* 1.3 56.1 + - + +
458B LEU* 4.1 2.8 - - - +
459B THR* 2.8 36.0 + - - -
512C LYS 4.1 11.4 - - - +
513C ILE* 4.9 0.7 - - - -
514C PRO* 4.0 30.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 456 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296B PHE* 3.7 40.5 - - + -
298B ASP* 3.2 22.8 + - - -
329B GLU* 5.2 3.8 - - - -
431B MET* 3.6 31.9 - - + -
449B VAL* 5.4 0.2 - - - -
451B THR* 4.1 9.0 - - + +
453B ASP* 3.4 27.1 + - + +
454B ILE 3.3 0.2 - - - -
455B ASN* 1.3 74.9 - - + +
457B ALA* 1.3 65.9 + - - +
460B VAL* 2.9 30.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 457 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454A ILE* 3.7 24.9 - - + -
449B VAL* 4.2 8.6 - - - +
451B THR* 3.5 19.9 - - + +
453B ASP 2.9 18.8 + - - +
454B ILE 3.3 4.2 + - - +
456B LYS* 1.3 75.7 - - - +
458B LEU* 1.3 58.4 + - - +
461B SER* 2.8 30.3 + - - -
471B ILE* 3.9 16.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 458 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454A ILE* 5.4 3.4 - - + -
454B ILE* 2.9 39.9 + - + +
455B ASN* 4.1 3.6 - - - +
457B ALA* 1.3 78.8 - - + +
459B THR* 1.3 64.5 + - - +
460B VAL 3.3 0.2 - - - -
461B SER* 3.4 9.6 - - - +
462B SER* 3.1 33.0 + - - +
471B ILE* 4.7 10.8 - - + -
169C PHE* 4.6 24.2 - - + -
511C VAL* 4.0 20.2 - - + -
512C LYS 5.2 1.3 - - - +
513C ILE* 4.1 23.3 - - + -
514C PRO* 5.6 2.0 - - + -
171D PHE* 5.0 9.4 - - + -
511D VAL* 6.3 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 459 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431B MET* 3.6 28.0 - - - +
432B ASP* 5.6 2.7 - - - +
435B ILE* 4.2 9.4 - - + -
455B ASN 2.8 27.3 + - - -
456B LYS 3.9 2.5 - - - -
458B LEU* 1.3 73.4 - - - +
460B VAL* 1.3 61.3 + - - +
462B SER* 4.1 2.9 - - - -
463B ALA* 3.2 24.2 + - + +
514C PRO* 3.5 26.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 460 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294B ILE* 3.9 22.4 - - + -
296B PHE* 4.1 17.3 - - + -
431B MET* 3.9 28.5 - - + -
434B VAL* 5.5 0.2 - - + -
435B ILE* 4.1 13.7 - - + -
448B ALA 5.9 0.2 - - - -
449B VAL* 3.8 26.2 - - + -
456B LYS 2.9 20.2 + - - +
457B ALA 4.3 0.9 - - - +
459B THR* 1.3 74.4 - - - +
461B SER* 1.3 65.8 + - - +
463B ALA* 3.2 2.6 + - - +
464B MET* 3.0 38.3 + - + +
469B VAL* 6.0 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 461 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449B VAL* 5.1 0.4 - - - -
457B ALA 2.8 24.8 + - - -
458B LEU* 3.3 17.3 + - - +
460B VAL* 1.3 78.0 - - - +
462B SER* 1.3 61.2 + - - +
463B ALA 3.5 0.3 + - - -
464B MET* 3.5 2.2 + - - -
469B VAL* 3.5 32.3 - - - +
471B ILE* 4.2 5.6 - - - +
171D PHE* 5.7 0.5 - - - -
173D ARG* 6.2 0.2 - - - -
507D LYS* 2.8 30.2 + - - +
509D VAL* 4.2 19.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 462 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458B LEU* 3.1 23.6 + - - +
459B THR* 4.1 3.4 - - - -
461B SER* 1.3 79.2 + - - +
463B ALA* 1.3 57.9 + - - +
464B MET 4.2 0.2 - - - +
513C ILE* 6.0 2.3 - - - +
517C ASN 6.3 0.9 - - - -
90D LEU* 5.9 1.2 - - - +
173D ARG* 3.6 43.4 + - - +
175D GLU* 3.7 3.6 - - - +
507D LYS* 3.2 12.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 463 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435B ILE* 3.6 27.8 - - + -
439B ASN* 2.8 25.0 + - - -
459B THR* 3.2 18.7 + - + +
460B VAL 3.2 4.3 + - - +
462B SER* 1.3 76.2 - - - +
464B MET* 1.3 62.0 + - - +
465B GLN* 3.4 2.6 + - - +
90D LEU* 3.8 28.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 464 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B PRO* 3.6 31.0 - - + -
294B ILE* 4.3 15.3 - - + -
435B ILE* 5.1 7.9 - - - -
438B ALA* 3.6 19.7 - - + +
439B ASN* 3.4 21.1 - - - +
447B ALA* 3.7 17.7 - - + -
448B ALA 5.8 1.1 - - - +
460B VAL* 3.0 30.9 + - + +
461B SER* 3.9 1.3 - - - +
462B SER 3.4 1.4 - - - +
463B ALA* 1.3 79.9 - - - +
465B GLN* 1.3 62.3 + - - +
466B ALA* 4.5 3.6 - - + +
469B VAL* 3.8 25.4 - - + -
175D GLU* 4.7 2.4 - - - +
507D LYS* 2.5 32.2 + - - -
----------------------------------------------------------
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