Contacts of the helix formed by residues 56 - 76 (chain E) in PDB entry 3J7Y
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 GLU 56 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54E SER* 3.9 1.6 - - - -
55E GLU* 1.3 80.2 - - + +
57E ASN* 1.3 65.9 + - - +
58E VAL 3.5 1.1 - - - -
59E PRO* 3.5 15.7 - - + +
60E PHE* 4.3 4.7 - - - +
141O HIS* 3.5 29.0 + - + +
150O GLN* 4.2 5.9 - - - +
153O ARG* 2.6 35.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 57 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53E LEU* 4.3 6.7 - - + -
54E SER* 3.2 28.7 + - - +
55E GLU 3.6 0.2 - - - -
56E GLU* 1.3 79.3 + - - +
58E VAL* 1.3 61.0 + - - +
60E PHE* 3.2 15.7 + - - +
61E ILE* 2.9 31.0 + - + +
141O HIS* 3.0 30.3 + - - -
146O ASN* 3.2 17.4 + - - +
149O LEU* 3.2 35.3 - - + +
150O GLN* 4.5 7.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 58 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49E TRP* 3.9 6.5 - - + -
50E ASP* 3.1 31.0 - - - +
53E LEU* 3.4 25.8 - - + +
54E SER 3.3 19.9 + - - +
55E GLU 4.8 1.3 - - - +
57E ASN* 1.3 76.6 - - - +
59E PRO* 1.4 65.1 - - + +
61E ILE* 3.2 4.0 + - - +
62E LYS* 2.9 52.7 + - - +
138O ARG* 4.4 7.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 59 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55E GLU 3.8 12.3 - - - +
56E GLU* 3.5 17.7 - - + +
58E VAL* 1.4 98.5 - - + +
60E PHE* 1.3 55.8 + - - +
62E LYS* 3.2 12.8 + - + +
63E GLN* 2.9 41.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 60 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56E GLU* 4.3 6.7 - - - +
57E ASN* 3.2 26.8 + - - +
59E PRO* 1.3 81.3 - - - +
61E ILE* 1.3 71.6 + - + +
63E GLN* 3.2 17.8 + - + +
64E LEU* 2.9 57.0 + - + +
149O LEU* 3.6 15.5 - - + -
152O LEU* 4.7 3.6 - - + -
153O ARG* 3.4 73.8 - - + +
156O LEU* 4.2 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 61 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3127 ILE* 4.4 13.7 - - + -
3157 LYS* 4.8 9.0 - - + +
49E TRP* 4.4 1.1 - - + -
53E LEU* 3.9 17.3 - - + -
57E ASN 2.9 17.1 + - - +
58E VAL 3.2 8.0 + - - +
60E PHE* 1.3 91.6 - - + +
62E LYS* 1.3 58.2 + - - +
64E LEU* 3.2 10.0 + - + +
65E VAL* 2.9 36.9 + - + +
155E PHE* 3.9 25.1 - - + -
149O LEU* 3.4 47.6 - - + -
152O LEU* 5.8 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 62 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3228A U 3.5 51.7 + - - +
49E TRP* 3.6 30.7 - - + -
50E ASP* 5.5 1.5 + - - -
58E VAL* 2.9 28.8 + - + +
59E PRO* 3.3 13.5 - - + +
61E ILE* 1.3 76.8 - - - +
63E GLN* 1.3 58.7 + - + +
65E VAL* 3.2 5.4 + - - +
66E SER* 2.9 28.0 + - - -
155E PHE* 4.9 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 63 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59E PRO* 2.9 26.8 + - - +
60E PHE* 3.3 20.9 - - + +
62E LYS* 1.3 75.7 - - + +
64E LEU* 1.3 53.0 + - - +
66E SER* 2.5 26.0 + - - -
67E ASP* 2.8 31.3 + - - +
153O ARG* 5.2 4.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 64 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3157 LYS* 3.7 34.3 - - + +
60E PHE* 2.9 39.4 + - + +
61E ILE* 3.3 13.7 - - + +
63E GLN* 1.3 75.5 - - - +
65E VAL* 1.3 59.0 + - - +
67E ASP* 3.2 9.2 + - + +
68E GLU* 2.9 43.6 + - + +
152O LEU* 4.8 11.0 - - + -
156O LEU* 3.8 24.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 65 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3117 THR* 4.9 5.8 - - - +
3157 LYS* 3.3 19.1 - - - +
3228A U 3.2 34.1 - - - +
61E ILE* 2.9 21.7 + - + +
62E LYS 3.2 6.7 + - - +
64E LEU* 1.3 75.8 - - - +
66E SER* 1.3 63.6 + - - +
68E GLU* 3.5 2.8 + - - +
69E ASP* 3.2 24.3 + - - +
154E ARG* 3.9 24.9 - - + +
155E PHE* 3.9 28.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 66 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3228A U 4.6 10.5 - - - +
62E LYS 2.9 12.5 + - - -
63E GLN* 2.5 26.2 + - - -
65E VAL* 1.3 76.4 - - - +
67E ASP* 1.3 66.7 + - - +
69E ASP* 3.2 10.4 + - - +
70E LYS* 2.9 49.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 67 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63E GLN* 2.8 28.7 + - - +
64E LEU* 3.5 9.5 - - + +
66E SER* 1.3 84.1 + - - +
68E GLU* 1.3 57.4 + - - +
70E LYS* 3.2 20.2 + - - +
71E ALA* 2.9 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 68 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3157 LYS* 4.0 20.4 - - - +
3187 GLU* 4.7 8.3 - - - +
64E LEU* 2.9 39.5 + - + +
65E VAL 3.8 4.9 - - - +
67E ASP* 1.3 75.9 - - - +
69E ASP* 1.3 58.0 + - - +
71E ALA* 3.2 9.0 + - - +
72E GLN* 2.9 39.2 + - + +
154E ARG* 3.8 24.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 69 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3228A U 3.5 24.3 - - - +
65E VAL 3.2 15.1 - - - +
66E SER* 3.2 9.9 + - - +
68E GLU* 1.3 77.4 - - - +
70E LYS* 1.3 57.3 + - + +
72E GLN* 3.2 11.1 + - - +
73E LEU* 2.9 37.8 + - + +
152E VAL 5.5 1.0 - - - +
154E ARG* 3.3 27.1 + - - -
171E PRO* 3.7 28.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 70 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66E SER* 2.9 39.3 + - - +
67E ASP* 3.2 17.8 + - - +
69E ASP* 1.3 75.7 - - + +
71E ALA* 1.3 57.1 + - - +
73E LEU* 3.2 15.9 + - + +
74E ALA* 2.9 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 71 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67E ASP 2.9 13.2 + - - +
68E GLU* 3.2 12.1 + - - +
70E LYS* 1.3 76.5 - - - +
72E GLN* 1.3 58.4 + - + +
74E ALA* 3.2 9.1 + - - +
75E SER* 2.9 28.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 72 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68E GLU* 2.9 27.3 + - + +
69E ASP* 3.4 12.6 - - - +
71E ALA* 1.3 76.0 - - + +
73E LEU* 1.3 57.3 + - - +
75E SER* 2.5 26.6 + - - +
76E LYS* 2.9 18.3 + - - +
165E TYR 5.2 0.2 - - - +
166E ARG* 6.0 0.6 + - - +
168E LEU 5.4 1.6 + - - -
169E GLY* 3.1 9.1 - - - -
170E LEU* 2.7 53.0 + - - +
171E PRO* 4.6 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 73 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69E ASP* 2.9 25.3 + - + +
70E LYS* 3.2 14.3 + - + +
72E GLN* 1.3 75.3 - - - +
74E ALA* 1.3 64.4 + - - +
76E LYS* 3.2 15.0 + - - +
77E LEU* 3.5 17.1 + - - +
126E ASP* 3.1 28.0 - - - +
128E HIS* 4.1 18.6 + - + +
151E THR* 5.1 4.0 - - + -
170E LEU* 5.3 1.3 - - + -
171E PRO* 4.2 24.2 - - + -
173E LYS* 4.4 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 74 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70E LYS 2.9 12.6 + - - +
71E ALA* 3.3 12.1 - - - +
73E LEU* 1.3 76.6 - - - +
75E SER* 1.3 63.8 - - - +
77E LEU* 3.3 34.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 75 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71E ALA 2.9 12.7 + - - -
72E GLN* 2.5 25.4 + - - +
74E ALA* 1.3 75.9 - - - +
76E LYS* 1.3 67.9 + - - +
77E LEU 3.2 5.4 + - - -
78E CYS* 4.2 8.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 76 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72E GLN 2.9 15.3 + - - +
73E LEU* 3.2 8.7 + - - +
75E SER* 1.3 87.1 + - - +
77E LEU* 1.3 60.6 + - - +
78E CYS 3.5 3.4 + - - -
79E PRO* 5.5 0.3 - - - +
128E HIS* 4.2 16.6 - - + +
168E LEU* 4.5 6.5 - - - +
169E GLY* 4.1 19.4 - - - +
170E LEU* 3.7 22.0 - - + +
188E LYS* 5.9 2.8 - - - +
189E PRO 4.0 6.5 + - - -
190E GLY* 3.2 40.5 + - - +
192E PRO* 3.4 24.1 - - - +
----------------------------------------------------------
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