Contacts of the helix formed by residues 54 - 73 (chain B) in PDB entry 1JQO
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 GLY 54 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B LEU 4.6 0.2 - - - +
50B GLN* 3.4 19.4 + - - -
53B HIS* 1.3 81.4 - - - +
55B PRO* 1.3 69.2 - - - +
56B SER* 3.0 13.9 + - - -
57B LEU* 3.4 11.4 + - - +
58B ARG 3.7 6.6 + - - -
925B LEU 5.3 0.4 - - - -
927B LYS* 5.7 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 55 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B GLN* 3.3 33.0 - - + +
54B GLY* 1.3 81.9 - - - +
56B SER* 1.3 59.4 + - - +
58B ARG* 3.8 3.8 - - - +
59B GLU* 2.8 42.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 56 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B GLY* 4.3 2.9 + - - -
55B PRO* 1.3 80.7 - - - +
57B LEU* 1.3 64.1 + - - +
59B GLU* 2.9 12.7 + - - +
60B PHE* 2.7 34.5 + - - +
925B LEU* 2.7 36.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 57 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B LEU* 4.4 12.6 - - + -
53B HIS* 3.8 24.7 - - + +
54B GLY 3.4 7.9 + - - +
56B SER* 1.3 83.9 + - - +
58B ARG* 1.3 64.2 + - - +
60B PHE* 3.6 3.4 - - + +
61B VAL* 3.0 35.2 + - + +
94B ASP* 3.8 7.4 - - - +
97B LEU* 3.7 37.0 - - + -
98B VAL* 3.6 30.1 - - + +
101B SER* 5.4 0.4 - - - +
925B LEU* 3.8 28.0 - - + +
926B SER* 4.0 2.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 58 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B ASP* 4.9 7.1 + - - -
46B LEU* 3.8 30.7 - - + +
47B ASN* 2.9 41.0 - - - +
49B LEU* 3.9 14.3 - - + +
50B GLN* 3.2 55.3 + - + +
54B GLY 3.7 3.2 + - - -
55B PRO 3.8 7.2 - - - +
57B LEU* 1.3 78.3 - - - +
59B GLU* 1.3 66.0 + - + +
61B VAL* 3.6 4.0 + - - +
62B GLN* 3.1 35.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 59 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B PRO* 2.8 33.3 - - - +
56B SER* 2.9 10.9 + - - +
58B ARG* 1.3 82.8 - - + +
60B PHE* 1.3 67.4 + - - +
62B GLN* 2.7 11.9 + - - +
63B GLU* 2.7 23.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 60 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B SER 2.7 13.2 + - - +
57B LEU* 3.6 7.2 - - - +
59B GLU* 1.3 71.2 - - - +
61B VAL* 1.3 66.2 + - + +
63B GLU* 2.9 28.2 + - - +
64B CYS* 2.9 42.8 + - - -
86B LYS* 3.8 28.0 - - + -
87B LEU* 3.8 8.3 - - + -
90B LEU* 3.6 34.5 - - + -
98B VAL* 3.4 37.9 - - + -
922B GLN* 6.0 1.6 - - - -
925B LEU* 3.5 27.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 61 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B LEU* 5.0 3.6 - - + -
49B LEU* 4.0 18.4 - - + -
57B LEU* 3.0 25.0 + - + +
58B ARG 3.7 4.7 - - - +
60B PHE* 1.3 79.0 - - + +
62B GLN* 1.3 64.4 + - - +
64B CYS* 3.5 7.6 + - - +
65B TYR* 3.4 17.7 + - - +
98B VAL* 4.7 15.5 - - + -
101B SER* 4.2 15.5 - - - +
102B ILE* 4.3 18.9 - - + +
105B MET* 4.0 27.1 - - - -
897B TYR* 4.9 4.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 62 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B LEU* 3.5 33.0 - - - +
58B ARG* 3.1 32.3 + - - +
59B GLU* 2.7 18.4 + - - +
61B VAL* 1.3 77.6 - - - +
63B GLU* 1.3 54.5 + - - +
65B TYR* 3.0 10.2 + - - +
66B GLU* 2.8 28.0 + - + +
897B TYR* 5.7 3.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 63 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B GLU 2.7 13.8 + - - +
60B PHE* 3.3 19.4 - - - +
62B GLN* 1.3 72.6 - - - +
64B CYS* 1.3 50.8 + - - +
66B GLU* 2.7 24.2 + - - +
67B VAL* 2.6 47.2 + - + +
82B GLU* 4.7 4.5 - - - +
86B LYS* 2.8 34.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 64 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B PHE* 2.9 61.2 + - - +
61B VAL* 3.8 7.9 - - - +
62B GLN 3.4 0.2 - - - -
63B GLU* 1.3 75.2 - - - +
65B TYR* 1.3 57.1 + - - +
67B VAL 4.0 0.2 - - - -
68B SER* 3.1 28.2 + - - -
83B LEU* 3.5 30.6 - - + +
86B LYS* 4.7 1.1 - - - -
87B LEU* 4.4 5.8 - - - -
98B VAL* 4.9 2.5 - - - -
102B ILE* 5.1 4.0 - - + -
900B THR* 3.2 20.5 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 65 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B VAL 3.4 7.7 + - - +
62B GLN* 3.0 12.0 + - - +
63B GLU 3.0 0.4 - - - -
64B CYS* 1.3 76.7 - - - +
66B GLU* 1.3 61.7 + - - +
67B VAL 3.1 1.1 - - - -
68B SER* 3.9 2.2 - - - -
69B ALA* 2.6 50.5 + - + +
892B VAL 4.2 3.3 + - - -
893B LEU* 3.6 23.4 + - + +
896B PRO* 3.0 42.6 - - + +
897B TYR* 3.5 53.2 - + + +
900B THR* 4.5 2.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 66 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B GLN* 2.8 14.6 + - + +
63B GLU* 2.7 26.1 + - - +
65B TYR* 1.3 81.8 - - - +
67B VAL* 1.3 66.5 + - - +
69B ALA* 3.3 14.6 - - - +
70B ASP* 3.5 6.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 67 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B GLU* 2.6 42.1 + - + +
64B CYS* 4.0 5.8 - - - +
66B GLU* 1.3 71.1 - - + +
68B SER* 1.3 56.9 + - - +
69B ALA 3.0 4.0 - - - -
70B ASP* 2.7 36.7 + - - +
71B TYR* 3.5 2.4 + - - +
79B LYS* 4.3 31.1 - - + +
80B LEU* 6.5 0.2 - - + -
82B GLU* 3.7 29.4 - - - +
83B LEU* 3.8 17.7 - - + -
86B LYS* 4.5 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 68 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B CYS 3.1 8.7 + - - -
65B TYR 3.9 1.3 - - - -
67B VAL* 1.3 79.9 - - - +
69B ALA* 1.3 61.2 + - - +
71B TYR* 3.3 8.0 + - - +
72B GLU* 3.2 24.9 + - - +
80B LEU* 5.3 2.0 - - - -
83B LEU* 3.9 11.2 - - - -
896B PRO* 2.9 20.1 + - - -
899B THR* 3.1 27.7 - - - +
900B THR* 3.1 23.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 69 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B TYR* 2.6 40.8 + - + +
66B GLU* 3.3 9.9 - - - +
68B SER* 1.3 73.0 - - - +
70B ASP* 1.3 62.3 + - - +
72B GLU* 3.8 3.0 + - - +
73B GLY* 3.1 18.7 + - - -
74B LYS* 5.5 0.2 + - - -
896B PRO* 3.9 12.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 70 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B GLU 3.5 5.3 + - - +
67B VAL* 2.7 18.1 + - - +
69B ALA* 1.3 77.9 - - - +
71B TYR* 1.3 50.7 + - - +
73B GLY 3.0 3.8 + - - -
74B LYS* 2.6 73.2 + - - +
76B ASP* 4.5 1.7 - - - +
79B LYS* 4.2 21.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 71 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B VAL 3.5 2.4 + - - +
68B SER* 3.3 8.4 + - - +
70B ASP* 1.3 78.3 - - - +
72B GLU* 1.3 86.5 - - + +
74B LYS* 2.7 9.0 + - - -
75B GLY* 2.6 65.1 + - - +
76B ASP* 4.2 11.0 + - - +
77B THR* 3.9 10.3 - - + -
79B LYS* 5.3 6.1 - - + +
80B LEU* 3.6 39.0 - - + -
837B ASP* 2.8 22.8 + - - -
839B GLY* 3.3 24.4 - - - -
840B ILE* 3.7 15.9 - - + -
899B THR* 3.9 6.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 72 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B SER 3.2 15.7 + - - +
69B ALA* 4.0 5.8 - - - +
71B TYR* 1.3 98.3 - - + +
73B GLY* 1.3 58.2 + - - +
74B LYS 3.4 0.9 + - - -
785B ARG* 3.7 8.1 + - - -
837B ASP* 3.9 6.5 - - - +
895B ASN* 3.1 30.5 - - - +
896B PRO* 3.8 20.0 - - + -
899B THR* 2.7 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 73 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B ALA 3.1 12.1 + - - -
70B ASP 3.0 9.2 + - - -
71B TYR 3.0 0.8 - - - -
72B GLU* 1.3 77.2 - - - +
74B LYS* 1.3 75.1 + - - +
----------------------------------------------------------
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