Contacts of the helix formed by residues 57 - 72 (chain A) in PDB entry 5JZV
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 ASP 57 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A LEU 3.1 25.9 + - - +
44A TYR 4.1 10.9 - - - +
45A ASP* 4.0 22.0 - - + +
55A ILE 3.4 1.4 + - - -
56A LEU* 1.3 70.1 - - - +
58A GLU* 1.3 64.0 + - - +
59A ASP* 3.5 8.3 + - - +
60A ARG* 3.3 41.1 + - + +
61A VAL* 3.2 22.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 58 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A LEU* 3.6 17.8 + - + +
57A ASP* 1.3 71.6 + - - +
59A ASP* 1.3 66.7 + - - +
61A VAL* 3.3 7.4 + - - +
62A VAL* 3.2 25.6 + - - +
82A ASP* 4.8 3.4 - - - +
83A PHE* 3.5 59.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 59 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A ASP* 3.5 7.0 + - - +
58A GLU* 1.3 80.0 - - - +
60A ARG* 1.3 58.0 + - + +
62A VAL* 3.5 8.3 + - - +
63A ASP* 3.2 34.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 60 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A GLU 4.4 4.4 + - - -
42A GLN 3.4 20.6 + - - -
43A LEU* 3.9 35.1 - - + +
44A TYR 4.5 8.7 + - - +
57A ASP* 3.3 34.8 + - + +
59A ASP* 1.3 75.7 - - + +
61A VAL* 1.3 66.7 + - - +
63A ASP* 3.9 10.2 - - - +
64A GLU* 3.0 27.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 61 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A VAL* 4.2 21.8 - - + +
37A LEU* 4.8 4.9 - - + -
38A ALA* 5.0 1.1 - - + -
43A LEU* 4.0 22.7 - - + -
56A LEU* 3.8 28.7 - - + -
57A ASP 3.2 14.1 + - - +
58A GLU* 3.3 9.8 + - - +
60A ARG* 1.3 77.8 - - - +
62A VAL* 1.3 62.4 + - - +
64A GLU* 3.3 3.5 + - - +
65A LEU* 3.2 37.8 + - + +
83A PHE* 4.3 13.9 - - + -
84A PHE* 4.6 7.0 - - + -
88A TRP* 5.5 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 62 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A GLU 3.2 15.2 + - - +
59A ASP* 3.8 9.6 - - - +
60A ARG 3.4 0.2 - - - -
61A VAL* 1.3 74.1 - - - +
63A ASP* 1.4 63.5 + - - +
65A LEU 3.4 1.0 + - - -
66A ASP* 3.0 34.3 + - + +
83A PHE* 3.7 32.8 - - + +
84A PHE* 4.7 1.3 - - + -
85A PRO* 3.8 31.9 - - + -
87A ARG* 5.8 0.7 - - - +
88A TRP* 3.6 15.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 63 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A ASP* 3.2 21.8 + - - +
60A ARG* 3.9 9.1 - - - +
62A VAL* 1.4 76.4 - - - +
64A GLU* 1.3 67.3 + - - +
65A LEU 3.4 0.2 + - - -
66A ASP* 3.7 12.5 + - - +
67A ASN 5.1 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 64 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A LEU* 4.3 25.6 - - + +
41A GLU* 3.9 30.2 - - - +
43A LEU* 4.3 15.8 - - + +
60A ARG 3.0 18.9 + - - +
61A VAL* 3.5 8.1 - - - +
62A VAL 3.3 0.2 - - - -
63A ASP* 1.3 79.5 - - - +
65A LEU* 1.3 62.8 + - + +
66A ASP 3.9 0.2 + - - -
67A ASN 5.2 0.7 + - - -
68A GLN* 5.7 2.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 65 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A ILE* 3.8 35.0 - - + -
34A VAL* 4.6 10.1 - - + -
37A LEU* 3.8 32.5 - - + -
61A VAL* 3.2 20.2 + - + +
64A GLU* 1.3 80.7 - - + +
66A ASP* 1.3 67.2 + - - +
67A ASN 3.2 3.0 + - - -
68A GLN* 3.3 17.5 + - + +
69A MET* 3.1 27.0 + - + +
76A VAL* 4.9 11.4 - - + -
88A TRP* 3.7 30.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 66 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A VAL* 3.0 21.1 + - + +
63A ASP* 3.7 8.6 + - - +
64A GLU 3.6 2.0 - - - -
65A LEU* 1.3 78.2 - - - +
67A ASN* 1.3 62.1 + - - +
69A MET* 3.3 2.9 + - - +
70A ARG* 3.0 53.7 + - - +
85A PRO* 4.8 1.2 - - - +
87A ARG* 3.0 28.1 + - - -
88A TRP* 3.1 24.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 67 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A ASP 5.1 1.4 + - - -
64A GLU 5.2 0.8 + - - -
65A LEU 3.4 0.8 - - - -
66A ASP* 1.3 79.1 - - - +
68A GLN* 1.3 63.3 + - - +
70A ARG* 3.2 18.4 + - - +
71A GLU* 3.1 49.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 68 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A LYS* 4.4 17.6 - - - +
32A ILE* 3.7 29.3 - - + +
64A GLU 5.7 1.4 - - - +
65A LEU* 3.3 19.7 + - + +
67A ASN* 1.3 77.1 - - - +
69A MET* 1.3 63.9 + - + +
71A GLU* 3.3 21.3 + - - +
72A GLY 3.3 10.9 + - - +
74A VAL* 3.9 24.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 69 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ASN* 3.0 46.2 + - + +
65A LEU* 3.1 26.9 + - + +
66A ASP 3.6 7.2 - - - +
68A GLN* 1.3 73.0 - - - +
70A ARG* 1.3 66.7 + - - +
72A GLY* 3.2 6.2 + - - -
74A VAL* 3.8 29.6 - - + +
76A VAL* 3.8 10.8 - - + -
88A TRP* 3.6 47.8 - - + +
89A PHE* 3.6 32.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 70 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A LEU* 6.2 0.2 - - - +
66A ASP* 3.0 39.8 + - - +
67A ASN* 3.2 21.9 + - - +
69A MET* 1.3 76.8 - - + +
71A GLU* 1.3 62.0 + - + +
72A GLY* 3.6 0.7 + - - -
87A ARG* 3.3 31.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 71 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET 5.8 0.3 - - - +
2A LEU* 6.0 2.2 - - - +
3A LEU* 5.4 4.2 + - - +
67A ASN* 3.1 40.7 + - - +
68A GLN* 3.7 15.0 - - - +
69A MET 3.2 0.6 - - - -
70A ARG* 1.3 79.7 - - + +
72A GLY* 1.3 62.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 72 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A LEU* 6.3 1.1 - - - -
3A LEU* 3.6 21.8 - - - +
5A ASN* 3.5 14.4 - - - -
68A GLN 3.3 7.9 + - - +
69A MET 3.2 11.3 + - - -
70A ARG 3.4 1.3 - - - -
71A GLU* 1.3 81.9 - - - +
73A GLY* 1.3 62.9 + - - -
74A VAL* 3.6 4.0 - - - +
----------------------------------------------------------
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