Contacts of the helix formed by residues 472 - 484 (chain B) in PDB entry 3D0G
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 GLN 472 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468B ILE* 4.3 4.5 - - + -
469B PRO* 3.0 32.5 + - + +
471B ASP* 1.3 96.0 + - - +
473B TRP* 1.3 67.0 + - - +
475B LYS* 3.1 39.4 + - + +
476B LYS* 2.9 34.2 + - + +
495B GLU* 3.3 7.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 473 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B ARG* 3.4 32.5 - - - +
180B TYR* 3.3 37.0 - + + -
181B GLU* 3.6 31.4 - - + -
184B VAL* 3.5 25.6 - - + -
459B TRP* 3.1 41.5 + + + -
463B VAL* 3.6 23.0 - - + +
468B ILE* 3.7 21.2 + - + -
469B PRO 3.2 22.9 + - - -
470B LYS* 3.7 15.3 - - + +
472B GLN* 1.3 77.7 - - - +
474B MET* 1.3 66.9 + - - +
476B LYS* 4.2 0.2 - - - -
477B TRP* 3.3 7.3 + - - +
495B GLU* 3.0 9.2 + - - +
498B CYS* 4.4 5.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 474 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B ARG* 4.4 2.2 - - - -
459B TRP* 5.5 1.8 - - - -
473B TRP* 1.3 76.2 - - - +
475B LYS* 1.3 66.3 + - - +
477B TRP* 3.3 16.3 + - + -
478B TRP* 3.0 34.3 + - + +
493B HIS* 3.7 19.3 - - + +
494B ASP 3.7 11.4 - - - +
495B GLU* 2.8 20.3 + - - +
497B TYR* 3.2 34.1 - - + +
498B CYS* 3.6 11.2 - - - -
499B ASP* 3.0 46.9 - - + +
500B PRO* 3.9 6.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 475 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471B ASP 5.3 1.1 - - - +
472B GLN* 3.1 47.9 + - - +
474B MET* 1.3 79.8 - - - +
476B LYS* 1.3 60.4 + - + +
478B TRP* 3.9 2.6 - - - +
479B GLU* 2.9 53.0 + - + +
493B HIS 5.2 0.6 + - - -
495B GLU* 3.3 11.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 476 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459B TRP* 4.3 0.2 - - - -
462B MET* 4.3 18.3 - - - +
468B ILE* 4.0 33.4 - - + -
472B GLN* 2.9 22.4 + - + +
473B TRP 4.3 1.8 - - - +
475B LYS* 1.3 78.1 - - + +
477B TRP* 1.3 64.9 + - - +
479B GLU* 3.6 24.7 - - - +
480B MET* 3.0 53.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 477 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452B PHE* 5.8 1.1 - + - -
455B MET* 3.4 27.6 - - + +
456B LEU* 3.3 42.8 - - + -
459B TRP* 3.4 37.7 - + + +
473B TRP 3.3 13.9 + - - +
474B MET* 3.3 20.6 + - + +
476B LYS* 1.3 75.7 - - - +
478B TRP* 1.3 86.6 + + - +
480B MET* 2.9 8.2 + - - +
481B LYS* 2.8 58.6 + - + +
499B ASP* 3.8 11.6 - - + +
500B PRO* 3.8 32.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 478 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B TRP* 3.4 40.4 - + - -
169B ARG* 5.0 0.9 - - - -
264B ALA* 4.0 9.6 - - + -
474B MET* 3.0 28.3 + - + +
475B LYS* 4.3 2.5 - - - +
477B TRP* 1.3 91.2 - + - +
479B GLU* 1.3 65.0 + - - +
481B LYS* 3.6 38.7 - - + +
482B ARG* 3.1 33.6 + - - +
487B VAL* 4.7 0.7 - - + -
488B VAL* 4.0 6.1 - - - -
489B GLU* 3.1 53.4 - - + +
493B HIS* 4.1 16.8 - - + +
499B ASP* 2.6 33.3 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 479 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475B LYS* 2.9 52.9 + - + +
476B LYS* 3.6 31.6 - - + +
478B TRP* 1.3 75.4 - - - +
480B MET* 1.3 58.7 + - + +
482B ARG* 3.4 11.5 + - - +
483B GLU* 2.9 37.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 480 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455B MET* 3.6 20.5 - - + +
458B LYS* 3.7 23.8 - - + -
459B TRP* 3.6 39.5 - - + +
462B MET* 4.0 14.1 - - + +
476B LYS* 3.0 48.9 + - + +
477B TRP 2.9 5.4 + - - +
479B GLU* 1.3 74.5 - - - +
481B LYS* 1.3 61.3 + - - +
483B GLU* 4.3 8.3 - - + -
484B ILE* 2.9 48.8 + - + +
485B VAL 3.6 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 481 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B TRP 4.6 4.6 + - - -
452B PHE* 3.1 42.8 + - - -
455B MET* 3.6 18.0 - - - -
477B TRP* 2.8 47.9 + - - +
478B TRP* 3.6 45.1 - - + +
480B MET* 1.3 75.9 - - - +
482B ARG* 1.3 57.1 + - - +
485B VAL* 3.2 18.4 + - + +
486B GLY 2.8 24.6 + - - -
487B VAL* 2.9 23.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 482 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261B CYS* 4.0 7.0 - - - -
478B TRP* 3.1 21.6 + - - +
479B GLU* 3.5 11.8 - - - +
481B LYS* 1.3 73.1 - - - +
483B GLU* 1.3 57.6 + - - +
486B GLY* 3.3 5.9 + - - -
487B VAL 3.5 6.3 - - - +
488B VAL* 3.4 33.2 - - + +
489B GLU* 2.5 35.7 + - - +
606B TRP* 2.7 32.7 + - - -
608B THR* 2.7 50.8 + - + +
609B ASP* 4.3 3.6 + - - +
610B TRP 3.7 3.2 + - - -
611B SER* 3.4 18.2 + - - -
613B TYR* 3.2 12.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 483 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479B GLU* 2.9 28.5 + - + +
480B MET* 4.1 5.4 - - + +
482B ARG* 1.3 75.6 - - - +
484B ILE* 1.3 73.0 + - + +
606B TRP* 3.5 15.2 + - - -
608B THR* 4.1 18.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 484 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230B PHE* 3.8 31.9 - - + -
234B LYS* 6.2 2.9 - - - +
237B TYR* 4.2 4.3 - - - -
451B PRO* 4.0 11.5 - - - +
454B TYR* 3.8 30.5 - - + +
455B MET* 4.1 23.3 - - + -
458B LYS* 5.5 1.3 - - + -
480B MET* 2.9 33.1 + - + +
483B GLU* 1.3 84.9 - - + +
485B VAL* 1.3 62.3 + - - +
606B TRP* 3.9 8.5 - - - -
----------------------------------------------------------
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