Contacts of the helix formed by residues 730 - 751 (chain B) in PDB entry 5B2R
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 730 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A U 5.0 6.3 + - - -
12A G 5.3 0.7 - - - -
13B THR* 5.8 0.3 - - - +
58B THR* 6.1 0.4 - - - -
729B GLY* 1.3 71.5 - - - +
731B PRO* 1.3 70.6 - - - +
732B ALA* 3.0 14.6 + - - +
733B ILE* 2.8 30.1 + - - +
734B LYS* 3.0 19.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 731 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A G 4.2 15.9 - - - +
13A C 4.2 8.5 - - - +
64A U 5.5 0.2 - - - +
65A A 5.4 7.3 - - - +
56B GLY* 4.3 5.9 - - - -
57B GLU 3.8 22.7 - - - +
58B THR* 3.8 33.0 - - + +
729B GLY 3.6 6.1 - - - +
730B SER* 1.3 82.6 - - - +
732B ALA* 1.3 61.9 + - - +
734B LYS* 3.8 21.1 - - + +
735B LYS* 3.1 21.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 732 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B THR* 4.2 30.5 - - + +
55B SER* 5.1 5.2 - - - -
56B GLY 3.9 24.9 + - - +
58B THR* 5.8 0.4 - - - +
730B SER* 2.9 12.5 - - - +
731B PRO* 1.3 76.6 - - - +
733B ILE* 1.3 64.7 + - - +
735B LYS* 3.1 18.2 + - - +
736B GLY 3.6 3.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 733 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B ILE* 4.4 9.9 - - + +
12B GLY* 4.1 24.2 - - - +
13B THR* 4.3 12.3 - - + +
729B GLY* 4.4 1.8 - - - -
730B SER* 2.8 35.8 + - - +
732B ALA* 1.3 73.7 - - - +
734B LYS* 1.3 70.5 + - + +
736B GLY* 3.2 11.7 + - - +
737B ILE* 3.2 13.9 + - + +
763B MET* 3.8 39.9 - - + -
764B ALA* 5.1 5.4 - - + +
927B ILE* 4.5 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 734 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A G 5.3 6.9 + - - -
66A U 4.8 1.0 + - - -
724B ILE* 3.2 33.5 - - + +
725B ALA* 2.6 28.6 + - - +
727B LEU* 2.9 27.8 + - + +
729B GLY 3.5 19.0 + - - +
730B SER 3.0 14.0 + - - +
731B PRO* 3.8 23.5 - - + +
732B ALA 3.1 0.2 - - - -
733B ILE* 1.3 81.4 - - + +
735B LYS* 1.3 64.9 + - - +
737B ILE* 3.2 23.9 + - + +
738B LEU* 3.4 10.7 + - - +
927B ILE* 5.0 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 735 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A A 5.3 2.4 + - - -
66A U 3.6 38.0 + - - +
67A C 5.3 6.7 - - - -
53B PHE* 3.7 31.0 - - + +
54B ASP* 2.7 27.2 + - - +
55B SER 4.2 2.8 + - - -
56B GLY* 3.6 22.5 - - - +
731B PRO 3.1 13.7 + - - +
732B ALA 3.1 10.7 + - - +
734B LYS* 1.3 77.6 - - - +
736B GLY* 1.3 62.7 + - - +
737B ILE 3.3 0.3 + - - -
738B LEU* 3.4 2.8 + - - +
739B GLN* 3.2 34.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 736 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B ILE* 4.1 5.6 - - - -
12B GLY 4.1 9.2 - - - -
16B VAL* 3.6 6.5 - - - +
53B PHE* 3.6 24.1 - - - -
732B ALA 3.6 4.0 + - - -
733B ILE 3.2 8.8 + - - -
735B LYS* 1.3 78.7 - - - +
737B ILE* 1.3 56.4 + - - +
739B GLN* 3.4 0.4 + - - -
740B THR* 2.8 35.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 737 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B ILE* 4.7 3.4 - - + -
724B ILE* 4.0 22.7 - - + -
727B LEU* 4.4 7.6 - - + -
733B ILE 3.2 15.7 + - - +
734B LYS* 3.2 15.2 + - - +
735B LYS 3.2 1.0 - - - -
736B GLY* 1.3 77.2 - - - +
738B LEU* 1.3 64.8 + - - +
740B THR* 3.2 16.0 + - - -
741B VAL* 3.2 17.5 + - + +
763B MET* 4.2 10.5 - - + -
927B ILE* 3.7 31.4 - - + -
931B VAL* 3.5 38.4 - - + -
934B ILE* 4.5 10.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 738 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A U 3.7 44.6 - - - +
720B LEU* 4.0 21.8 - - + -
721B HIS* 4.3 20.4 - - + -
724B ILE* 3.8 29.1 - - + +
734B LYS 3.4 8.3 + - - +
735B LYS 4.1 4.9 - - - +
737B ILE* 1.3 76.1 - - - +
739B GLN* 1.3 70.8 + - - +
741B VAL* 3.2 3.4 + - + +
742B LYS* 3.2 42.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 739 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A U 4.4 4.8 + - - -
67A C 2.9 36.5 + - - -
68A A 5.6 1.6 + - - -
16B VAL* 4.1 8.3 - - + -
51B LEU* 3.5 31.9 - - + +
53B PHE* 4.4 12.3 - - + -
735B LYS* 3.2 27.6 + - + +
736B GLY* 3.7 4.0 - - - +
738B LEU* 1.3 85.6 - - - +
740B THR* 1.3 58.2 + - - +
742B LYS* 3.1 14.8 + - - +
743B VAL* 2.8 33.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 740 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B LEU* 3.6 32.8 - - + -
11B ILE* 3.4 34.6 - - + +
16B VAL* 3.4 18.1 - - - +
736B GLY 2.8 21.3 + - - -
737B ILE* 3.2 11.2 + - - -
739B GLN* 1.3 77.4 - - - +
741B VAL* 1.3 63.3 + - + +
743B VAL* 3.2 3.0 + - - +
744B VAL* 3.0 23.9 + - + +
931B VAL* 5.1 2.5 - - + -
935B LEU* 4.6 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 741 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
720B LEU* 3.8 17.3 - - + -
724B ILE* 4.5 10.3 - - + -
737B ILE* 3.2 19.2 + - + +
738B LEU* 3.2 7.3 + - + +
740B THR* 1.3 76.6 - - + +
742B LYS* 1.3 58.6 + - + +
744B VAL* 3.3 2.9 + - - +
745B ASP* 3.0 29.2 + - - +
931B VAL* 6.2 1.8 - - + -
934B ILE* 4.0 22.2 - - + -
935B LEU* 4.3 18.4 - - + -
938B ARG* 3.3 38.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 742 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A U 3.6 10.1 + - - -
67A C 2.8 38.1 + - - +
720B LEU* 6.3 0.4 - - + -
738B LEU* 3.2 35.2 + - + +
739B GLN* 3.1 18.2 + - - +
741B VAL* 1.3 74.6 - - + +
743B VAL* 1.3 66.7 + - - +
745B ASP* 3.5 9.3 + - - +
746B GLU* 3.1 22.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 743 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B LEU* 4.3 7.0 - - + -
16B VAL* 4.3 13.2 - - + -
18B TRP* 3.8 42.4 - - + +
51B LEU* 4.5 18.4 - - + -
739B GLN 2.8 20.5 + - - +
740B THR* 3.5 8.7 - - - +
742B LYS* 1.3 77.3 - - + +
744B VAL* 1.3 61.3 + - - +
746B GLU* 3.2 6.4 + - - +
747B LEU* 2.9 32.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 744 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B ILE* 4.4 9.4 - - + -
9B LEU* 3.6 32.8 - - + -
740B THR 3.0 15.2 + - - +
741B VAL 3.3 7.4 + - - +
743B VAL* 1.3 77.5 - - - +
745B ASP* 1.3 64.2 + - - +
747B LEU* 3.2 8.0 + - - +
748B VAL* 3.0 33.8 + - + +
759B ILE* 4.2 17.0 - - + -
935B LEU* 4.2 17.5 - - + -
939B MET* 3.9 26.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 745 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
741B VAL* 3.0 22.5 + - - +
742B LYS* 3.8 8.8 - - - +
744B VAL* 1.3 77.6 - - - +
746B GLU* 1.3 61.9 + - - +
748B VAL* 3.5 6.2 + - - +
749B LYS* 3.2 39.5 + - - +
938B ARG* 2.8 36.2 + - - -
939B MET* 4.7 11.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 746 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A A 5.7 3.5 + - - +
742B LYS 3.1 16.7 + - - +
743B VAL* 3.7 6.3 - - - +
744B VAL 3.2 0.2 - - - -
745B ASP* 1.3 77.8 - - - +
747B LEU* 1.3 60.1 + - + +
749B LYS* 3.1 13.8 + - + +
750B VAL* 2.8 38.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 747 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B TYR* 4.8 1.1 - - - -
7B ILE* 4.0 36.1 - - + -
18B TRP* 3.6 45.3 - - + -
19B ALA 5.0 0.2 - - - +
20B VAL* 4.2 19.7 - - + -
47B LEU* 5.7 2.5 - - + -
743B VAL* 2.9 35.3 + - + +
744B VAL* 3.8 4.0 - - - +
746B GLU* 1.3 78.9 - - + +
748B VAL* 1.3 58.1 + - - +
750B VAL* 3.0 17.9 + - + +
751B MET* 2.9 32.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 748 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B TYR* 3.8 16.6 - - - +
7B ILE* 4.6 3.4 - - + -
744B VAL* 3.0 34.2 + - + +
745B ASP* 3.8 6.5 - - - +
747B LEU* 1.3 76.1 - - - +
749B LYS* 1.3 59.9 + - + +
751B MET* 3.0 9.9 + - - +
753B ARG* 2.8 41.2 + - + +
754B HIS 3.7 14.8 - - - +
755B LYS* 4.7 7.0 - - + -
756B PRO* 4.2 13.9 - - + -
939B MET* 4.4 11.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 749 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
745B ASP* 3.2 26.1 + - - +
746B GLU* 3.1 12.1 + - + +
748B VAL* 1.3 78.4 - - + +
750B VAL* 1.3 63.5 + - + +
752B GLY* 3.3 12.0 + - - -
753B ARG* 4.2 20.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 750 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B LYS* 3.5 19.6 + - + +
32B PHE* 3.8 39.4 - - + -
47B LEU* 4.3 22.9 - - + -
746B GLU* 2.8 33.2 + - + +
747B LEU* 3.0 18.8 + - + +
749B LYS* 1.3 76.0 - - + +
751B MET* 1.3 60.0 + - - +
752B GLY 3.2 4.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 751 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B TYR* 3.5 61.2 - - + +
20B VAL* 4.3 10.5 - - + -
28B PRO* 5.3 5.8 - - + -
30B LYS* 4.1 14.1 - - - +
47B LEU* 3.7 29.6 - - + -
747B LEU 2.9 18.7 + - - +
748B VAL 3.0 3.2 + - - +
750B VAL* 1.3 78.9 - - + +
752B GLY* 1.3 60.4 + - - +
753B ARG 3.3 2.0 - - - -
754B HIS* 3.3 21.2 + - - +
----------------------------------------------------------
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