Contacts of the helix formed by residues 60 - 74 (chain B) in PDB entry 2JG1
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 60 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B ILE* 1.3 76.2 - - - +
61B GLY* 1.3 67.3 - - - +
63B LEU 4.2 0.9 + - - -
64B GLY* 3.1 9.5 + - - -
82B ASN* 4.1 4.0 - - - -
83B ILE* 3.8 12.8 - - - +
85B GLY 3.4 20.4 - - - -
86B GLU* 3.7 0.3 - - - +
87B THR* 3.0 27.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 61 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A GLU 5.0 6.8 + - - +
98A GLN* 6.5 2.0 - - - -
60B GLY* 1.3 76.7 - - - +
62B GLU* 1.3 67.2 + - - -
63B LEU 3.3 0.2 - - - -
64B GLY* 3.1 5.4 + - - -
65B GLN* 3.2 20.9 + - - +
82B ASN* 4.7 3.9 + - - +
83B ILE 4.7 2.6 + - - -
85B GLY 3.8 3.4 + - - -
86B GLU* 3.7 19.1 - - - -
69C LYS* 6.2 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 62 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B GLY* 1.3 74.7 - - - -
63B LEU* 1.3 61.0 + - + +
65B GLN* 3.2 14.2 - - - +
66B PHE* 3.1 20.3 + - - +
86B GLU* 3.1 19.3 + - - +
62C GLU* 3.4 39.7 - - + +
63C LEU* 5.5 0.9 - - + -
65C GLN* 3.0 35.4 + - - +
66C PHE* 3.6 30.6 - - + +
69C LYS* 3.1 31.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 63 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B VAL* 3.5 28.4 - - + +
60B GLY 4.2 1.1 + - - +
61B GLY 3.3 0.4 - - - -
62B GLU* 1.3 77.9 - - + +
64B GLY* 1.3 62.6 + - - +
66B PHE* 3.2 9.3 + - + +
67B ILE* 3.1 19.8 + - - +
86B GLU* 5.3 3.9 + - + +
87B THR* 3.3 33.7 - - - +
88B ARG 3.9 6.7 - - - +
89B ASN* 3.3 37.5 - - - +
33C LYS* 4.2 7.2 - - + +
62C GLU* 5.8 0.9 - - + -
63C LEU* 4.0 27.1 - - + -
66C PHE* 6.4 2.5 - - + -
89C ASN* 6.0 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 64 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B ILE* 3.8 30.3 - - - +
60B GLY 3.1 19.0 + - - -
61B GLY 3.1 4.7 + - - -
63B LEU* 1.3 74.7 - - - +
65B GLN* 1.3 61.6 + - - +
67B ILE* 3.2 6.4 + - - +
68B ALA* 3.1 18.0 + - - +
87B THR* 3.6 13.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 65 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A GLU* 3.5 40.6 + - + +
98A GLN* 3.3 14.6 + - - -
59B ILE* 5.6 0.2 - - - -
61B GLY* 3.2 14.6 + - - +
62B GLU* 3.2 17.4 - - - +
63B LEU 3.2 0.2 - - - -
64B GLY* 1.3 73.5 - - - +
66B PHE* 1.3 56.8 + - - +
68B ALA* 3.4 8.2 + - - +
69B LYS* 3.0 27.2 + - - +
62C GLU* 3.8 18.7 - - + +
65C GLN* 2.7 44.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 66 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B VAL* 3.7 31.6 - - + -
33B LYS* 3.5 32.3 - - + -
34B THR 4.0 9.9 - - - -
62B GLU 3.1 11.8 + - - +
63B LEU* 3.2 15.7 + - + +
65B GLN* 1.3 73.2 - - - +
67B ILE* 1.3 65.1 + - + +
69B LYS* 3.2 9.2 + - - +
70B LYS* 2.9 66.2 + - + +
62C GLU* 3.8 26.9 - - + +
86C GLU* 3.9 17.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 67 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B PRO* 3.7 23.6 - - + -
10B SER 4.1 11.7 - - - +
11B VAL* 4.1 9.4 - - + -
35B ALA* 4.3 19.0 - - + +
40B LEU* 4.3 20.0 - - + -
59B ILE* 4.3 15.9 - - + -
63B LEU 3.1 6.8 + - - +
64B GLY* 3.2 7.4 + - - +
66B PHE* 1.3 76.1 - - + +
68B ALA* 1.3 61.9 + - - +
70B LYS* 3.3 2.9 + - - +
71B LEU* 3.2 33.7 + - + +
80B PHE* 4.5 7.0 - - + -
87B THR* 3.4 32.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 68 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B ILE* 4.8 10.7 - - + +
64B GLY 3.1 12.3 + - - +
65B GLN* 3.6 11.4 - - - +
66B PHE 3.3 0.2 - - - -
67B ILE* 1.3 76.7 - - - +
69B LYS* 1.3 58.4 + - - +
71B LEU* 3.4 1.2 + - - +
72B ASP* 2.8 38.6 + - - +
78B HIS* 3.6 30.5 + - + +
80B PHE* 6.0 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 69 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B GLN 3.0 14.5 + - - +
66B PHE* 3.2 17.3 + - + +
68B ALA* 1.3 75.4 - - - +
70B LYS* 1.3 69.5 + - + +
72B ASP* 3.2 8.0 + - - +
73B HIS* 3.0 62.7 + - + +
61C GLY* 5.5 0.8 - - - -
62C GLU* 3.1 32.0 + - - +
86C GLU* 2.6 38.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 70 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B LYS 3.5 14.0 + - - -
34B THR* 4.8 2.2 - - - +
35B ALA* 3.9 22.4 - - + +
66B PHE* 2.9 55.6 + - + +
67B ILE 3.3 7.6 + - - +
69B LYS* 1.3 87.7 - - + +
71B LEU* 1.3 62.4 + - + +
73B HIS* 3.4 15.2 + - + +
74B ALA* 3.2 21.3 + - - +
86C GLU* 5.6 2.6 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
35B ALA* 4.8 11.4 - - + -
40B LEU* 4.2 21.1 - - + -
43B THR* 5.4 1.1 - - + -
44B ARG* 4.9 9.4 - - + +
55B ALA* 4.3 5.4 - - + -
67B ILE* 3.2 20.1 + - + +
68B ALA 3.8 0.2 - - - +
70B LYS* 1.3 74.3 - - - +
72B ASP* 1.3 65.7 + - - +
74B ALA* 3.0 8.2 + - + +
76B ILE* 2.9 57.9 + - + +
78B HIS* 3.8 25.8 - - + -
80B PHE* 3.7 33.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 72 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B ALA* 2.8 26.2 + - - +
69B LYS* 3.2 9.5 + - - +
71B LEU* 1.3 75.6 - - - +
73B HIS* 1.3 67.1 + - + +
75B ASP* 3.3 18.3 + - - +
76B ILE 4.6 3.6 - - - +
78B HIS* 2.8 29.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 73 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B LYS* 3.0 55.4 + - + +
70B LYS* 3.7 15.9 + - + +
71B LEU 3.2 0.2 - - - -
72B ASP* 1.3 83.7 - - + +
74B ALA* 1.3 57.2 + - - +
75B ASP* 3.3 6.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 74 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B ARG* 6.3 0.7 - - + -
47B ALA* 5.8 0.9 - - - +
70B LYS 3.2 14.3 + - - +
71B LEU* 3.0 6.9 + - + +
73B HIS* 1.3 76.8 - - - +
75B ASP* 1.3 68.3 + - - +
76B ILE* 3.2 24.9 + - + +
----------------------------------------------------------
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