Contacts of the helix formed by residues 468 - 482 (chain B) in PDB entry 4B92
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 PRO 468 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B ASN* 4.3 7.2 - - + +
185B GLY 3.4 11.2 - - - +
187B ILE* 3.9 24.2 - - + -
383B LYS 4.1 9.9 - - - +
384B LEU* 3.4 28.9 - - - +
386B ASN* 3.5 17.7 - - + +
465B ARG 4.1 4.0 - - - +
466B SER* 3.5 4.2 - - - -
467B PHE* 1.3 87.5 - - - +
469B ASP* 1.3 65.4 + - - +
470B THR* 3.0 6.0 + - + +
471B VAL* 3.2 3.0 + - + +
472B TYR* 3.1 24.1 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 469 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383B LYS 5.1 0.8 + - - -
386B ASN* 4.0 8.6 + - - +
465B ARG* 3.0 28.0 + - - -
467B PHE 3.0 7.7 + - - +
468B PRO* 1.3 70.1 - - - +
470B THR* 1.3 61.7 + - - +
471B VAL 3.3 0.7 + - - -
472B TYR* 4.7 0.9 - - - +
473B LYS* 3.2 64.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 470 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268B LEU* 5.6 0.7 - - + -
383B LYS* 3.4 51.2 + - + +
384B LEU* 3.9 13.5 - - + +
468B PRO* 3.0 3.2 + - + +
469B ASP* 1.3 78.2 - - - +
471B VAL* 1.3 68.4 + - + +
474B LYS* 4.1 17.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 471 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B ILE* 3.8 15.0 - - + -
242B PRO* 3.2 35.9 - - + -
266B VAL* 3.7 11.7 - - + -
268B LEU* 3.3 33.2 - - + -
384B LEU* 4.5 2.5 - - + -
468B PRO* 3.2 7.6 + - + +
470B THR* 1.3 87.0 - - + +
472B TYR* 1.3 70.1 + - + +
473B LYS 3.4 2.5 - - - -
474B LYS* 3.4 27.2 - - - +
475B LEU* 3.7 11.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 472 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A ASP* 5.5 2.5 - - - -
182B LYS* 3.7 26.3 - - + -
185B GLY 3.5 16.8 - - - -
186B ALA 2.4 36.5 + - - -
187B ILE* 4.3 2.7 - - + -
242B PRO* 3.4 30.9 - - + +
467B PHE* 3.6 45.8 - + + +
468B PRO* 3.1 20.7 + - + +
469B ASP* 5.2 0.4 - - - -
471B VAL* 1.3 82.6 - - + +
473B LYS* 1.3 59.3 + - - +
474B LYS 3.4 0.4 - - - -
475B LEU* 3.7 14.6 - - + +
476B VAL* 3.0 32.6 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
469B ASP* 3.2 51.7 + - - +
471B VAL 3.4 1.2 - - - -
472B TYR* 1.3 76.3 - - - +
474B LYS* 1.3 63.3 + - - +
476B VAL* 3.3 22.1 - - + +
477B GLN* 3.4 8.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 474 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266B VAL* 4.2 30.1 - - + +
470B THR 4.1 16.9 + - - +
471B VAL* 3.4 17.9 - - - +
473B LYS* 1.3 78.1 - - - +
475B LEU* 1.3 65.1 + - - +
477B GLN* 3.0 7.5 + - - +
478B ARG* 2.7 40.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 475 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240B HIS* 3.6 26.9 - - + +
241B CYS 5.6 0.2 - - - -
242B PRO* 3.6 32.8 - - + -
266B VAL* 3.9 27.6 - - + -
471B VAL* 3.7 22.8 + - + +
472B TYR* 3.5 19.5 + - + +
473B LYS 3.5 0.4 - - - -
474B LYS* 1.3 82.3 - - - +
476B VAL* 1.3 64.5 + - - +
478B ARG* 3.8 15.9 - - - +
479B GLU* 3.0 39.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 476 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A GLU 4.6 2.9 - - - +
107A THR* 4.5 23.9 - - + -
108A SER* 5.0 4.5 - - - +
111A ASP* 4.4 17.3 - - + +
115A LYS* 4.8 14.4 - - - +
467B PHE* 6.4 0.7 - - + -
472B TYR* 3.0 16.5 + - + +
473B LYS* 3.3 18.2 - - + +
474B LYS 3.2 0.2 - - - -
475B LEU* 1.3 77.8 - - - +
477B GLN* 1.3 73.0 + - + +
479B GLU* 3.5 15.7 + - + +
480B LYS* 3.7 14.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 477 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473B LYS 3.7 9.2 - - - +
474B LYS* 3.0 10.4 + - - +
476B VAL* 1.3 84.8 - - + +
478B ARG* 1.3 57.2 + - - +
480B LYS* 2.9 69.2 + - - +
481B THR* 3.9 7.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 478 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237B ASN* 3.6 23.4 + - - +
240B HIS* 6.1 1.2 + - - -
263B GLN 5.2 2.8 + - - -
264B GLY* 2.5 35.3 + - - -
265B LYS* 4.3 2.2 - - - +
266B VAL* 3.9 17.0 - - - +
474B LYS* 2.7 23.1 + - + +
475B LEU* 3.8 17.8 - - - +
477B GLN* 1.3 73.9 - - - +
479B GLU* 1.3 60.2 + - + +
481B THR* 3.2 13.9 + - - +
482B LEU* 2.9 29.2 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
106A GLU 4.7 4.3 - - - +
108A SER* 5.0 6.1 - - - -
111A ASP* 5.2 2.9 - - - +
140A LYS* 3.1 25.4 + - - +
182B LYS* 4.1 18.2 + - - +
240B HIS* 3.1 56.3 - - + +
475B LEU* 3.0 30.5 + - + +
476B VAL* 3.7 10.7 - - - +
477B GLN 3.2 0.2 - - - -
478B ARG* 1.3 74.8 - - + +
480B LYS* 1.3 66.1 + - - +
481B THR 3.4 0.2 - - - -
482B LEU* 3.3 26.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 480 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A ASP* 5.3 3.6 - - - +
105A LYS 3.6 19.6 + - - -
106A GLU* 3.3 48.8 - - + +
107A THR* 3.6 16.9 - - - +
476B VAL* 3.7 6.3 + - - +
477B GLN* 2.9 54.4 + - - +
479B GLU* 1.3 79.3 - - - +
481B THR* 1.3 64.4 + - + +
482B LEU* 3.2 5.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 481 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477B GLN* 3.9 7.6 + - - +
478B ARG* 3.2 17.2 + - - +
480B LYS* 1.3 79.1 - - + +
482B LEU* 1.3 67.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 482 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A LYS* 4.8 23.8 - - + +
240B HIS* 4.3 28.4 - - - +
478B ARG* 2.9 21.0 + - - +
479B GLU* 3.4 23.2 - - - +
480B LYS 3.0 5.2 - - - +
481B THR* 1.3 86.6 + - - +
----------------------------------------------------------
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