Contacts of the helix formed by residues 64 - 78 (chain B) in PDB entry 1JQE
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 64 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B GLY 3.2 12.7 + - - -
62B GLY 3.3 1.2 - - - -
63B ALA* 1.3 78.2 - - - +
65B GLU* 1.3 66.6 + - - +
66B ILE 3.4 2.5 - - - -
67B ASP* 3.2 4.4 + - - +
68B LEU* 3.0 28.2 + - - +
98B TYR* 3.7 28.0 - - - -
101B LEU* 3.7 4.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 65 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B LEU* 5.8 0.7 - - - +
29B HIS* 2.5 46.2 + - + +
63B ALA* 3.5 7.2 + - + +
64B GLY* 1.3 76.9 - - - +
66B ILE* 1.3 68.3 + - + +
68B LEU* 3.3 4.7 + - - +
69B GLN* 3.3 26.0 + - + +
101B LEU* 3.7 14.2 - - + +
401B SAH 5.6 1.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 66 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B HIS* 3.7 38.1 - - + +
32B MET* 4.0 22.7 - - + -
33B GLN* 5.6 1.3 - - - +
36B MET* 4.6 11.4 - - + -
61B GLY 6.1 0.2 - - - +
64B GLY 3.4 0.2 - - - -
65B GLU* 1.3 78.8 - - + +
67B ASP* 1.3 69.0 + - - +
69B GLN* 3.0 22.6 + - + +
70B ILE* 3.0 18.6 + - + +
142B ILE* 3.4 34.1 - - + -
401B SAH 3.7 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 67 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B SER* 2.5 28.3 + - - -
61B GLY* 3.7 14.7 + - - +
64B GLY 3.2 7.9 + - - +
66B ILE* 1.3 80.1 - - - +
68B LEU* 1.3 57.9 + - - +
70B ILE* 3.3 10.8 + - - +
71B LEU* 2.9 31.7 + - + +
85B ASN* 4.9 4.1 - - - +
98B TYR* 2.7 41.8 + - + +
140B HIS* 3.1 23.3 + - + +
142B ILE* 5.3 0.5 - - - +
401B SAH 5.2 2.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 68 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B GLY 3.0 20.8 + - - +
65B GLU* 3.8 4.7 - - - +
66B ILE 3.2 0.2 - - - -
67B ASP* 1.3 74.2 - - - +
69B GLN* 1.3 65.0 + - - +
71B LEU* 3.4 12.8 + - + +
72B SER* 3.0 27.7 + - - -
98B TYR* 4.3 4.5 - - + -
101B LEU* 3.7 34.3 - - + -
102B VAL* 4.3 13.2 - - + -
105B ILE* 4.0 22.0 - - + -
108B LEU* 5.5 6.3 - - + -
113B PHE* 3.8 32.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 69 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B GLN* 3.1 37.2 + - - +
36B MET* 4.0 18.6 - - + -
65B GLU* 3.3 17.6 + - + +
66B ILE* 3.0 17.2 + - + +
68B LEU* 1.3 78.7 - - - +
70B ILE* 1.3 65.0 + - - +
72B SER* 2.7 28.5 + - - -
73B LYS* 3.3 17.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 70 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B MET* 3.8 24.0 - - + -
40B LEU* 3.8 14.6 - - + -
56B ILE* 5.0 5.2 - - + -
66B ILE* 3.0 18.0 + - + +
67B ASP* 3.5 6.7 - - - +
69B GLN* 1.3 76.8 - - - +
71B LEU* 1.3 62.3 + - + +
73B LYS* 3.1 5.2 + - - +
74B VAL* 3.1 28.0 + - + +
138B PHE* 3.6 31.2 - - + -
140B HIS* 3.6 28.7 - - + +
142B ILE* 3.6 30.5 - - + -
169B LEU* 4.9 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 71 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B ILE* 3.5 28.5 - - + -
67B ASP 2.9 16.3 + - - +
68B LEU* 3.6 19.1 - - + +
69B GLN 3.2 0.2 - - - -
70B ILE* 1.3 78.6 - - + +
72B SER* 1.3 57.2 + - - +
74B VAL* 3.1 4.9 + - - +
75B GLN* 2.9 42.0 + - - +
83B ILE* 3.5 22.7 - - + -
85B ASN* 3.5 20.6 - - + +
108B LEU* 5.5 4.3 - - + -
111B VAL* 4.2 7.2 - - + -
113B PHE* 3.5 38.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 72 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B LEU 3.0 13.9 + - - -
69B GLN* 2.7 27.4 + - - -
71B LEU* 1.3 76.0 - - - +
73B LYS* 1.3 69.5 + - - +
75B GLN* 3.5 12.9 + - - +
76B ALA* 3.0 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 73 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B GLN* 5.1 0.2 - - - +
36B MET* 3.5 22.4 - - + +
37B ASP* 2.8 34.1 + - - +
40B LEU* 3.7 18.4 - - + -
41B PRO* 4.5 14.2 - - + +
44B ILE* 3.6 20.4 - - + +
69B GLN* 3.4 18.6 + - - +
70B ILE 3.1 7.7 + - - +
72B SER* 1.3 87.7 + - - +
74B VAL* 1.3 65.6 + - - +
76B ALA* 3.4 8.2 + - + +
77B GLN* 3.2 19.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 74 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B ILE* 3.5 21.8 - - + -
47B ILE* 4.4 12.8 - - + -
54B ILE* 4.0 31.9 - - + -
56B ILE* 3.9 20.9 - - + -
70B ILE* 3.1 20.3 + - + +
71B LEU 3.1 5.8 + - - +
73B LYS* 1.3 77.2 - - - +
75B GLN* 1.3 56.4 + - - +
77B GLN* 3.3 2.7 + - - -
78B TYR* 2.9 33.8 + - + +
83B ILE* 3.9 18.4 - - + -
138B PHE* 5.3 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 75 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B LEU* 2.9 25.8 + - - +
72B SER* 3.9 8.7 - - - +
74B VAL* 1.3 72.3 - - - +
76B ALA* 1.3 66.1 + - - +
78B TYR 3.2 5.8 - - - +
79B PRO* 3.1 26.3 - - - +
81B VAL 5.7 0.4 - - - +
83B ILE* 3.3 20.6 - - + -
108B LEU* 3.9 34.6 - - - +
110B ASN* 4.2 18.2 + - - +
111B VAL* 3.5 20.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 76 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B SER 3.0 19.8 + - - +
73B LYS* 3.5 11.0 - - + +
74B VAL 3.2 0.2 - - - -
75B GLN* 1.3 78.2 - - - +
77B GLN* 1.3 60.0 + - - +
79B PRO* 3.7 9.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 77 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B PRO* 4.9 4.2 - - + +
44B ILE* 4.3 5.6 - - + +
45B GLY* 3.7 30.5 + - - +
49B ASP* 5.4 0.8 + - - -
73B LYS 3.2 10.8 + - - +
74B VAL* 3.3 7.4 + - - +
76B ALA* 1.3 79.7 - - - +
78B TYR* 1.3 90.9 + - + +
79B PRO* 3.3 7.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 78 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B ILE 3.7 10.8 - - - -
45B GLY 2.7 17.3 + - - -
46B ARG* 3.2 3.3 - - - -
47B ILE* 4.4 2.2 - - + -
48B GLY 3.0 43.1 + - - -
49B ASP* 2.6 27.0 + - - -
54B ILE* 3.4 28.9 - - + -
74B VAL* 2.9 20.1 + - + +
75B GLN* 3.2 10.4 - - - +
77B GLN* 1.3 102.6 - - + +
79B PRO* 1.3 67.4 - - - +
80B GLY 3.3 0.5 + - - -
81B VAL* 3.1 30.0 + - + +
83B ILE* 5.7 0.8 - - + +
----------------------------------------------------------
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