Contacts of the helix formed by residues 73 - 86 (chain A) in PDB entry 5ZCJ
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 SER 73 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ARG* 5.0 2.2 - - - -
67A VAL* 5.9 0.2 - - - +
68A ASP 5.0 1.9 - - - +
69A ARG* 5.8 0.4 - - - -
72A TRP* 1.3 78.6 - - - +
74A LEU* 1.3 65.6 + - - +
75A GLU* 3.6 15.8 + - - +
76A ASP* 3.2 31.0 + - - +
77A GLY* 3.2 18.0 + - - -
93A GLU* 6.0 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 74 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ARG* 4.0 30.3 - - + +
18A MET* 3.6 34.8 - - + -
26A HIS* 4.2 7.0 - - - +
28A CYS* 3.8 15.4 - - - -
67A VAL* 4.3 12.1 - - + -
69A ARG* 4.6 10.3 - - + -
73A SER* 1.3 73.9 - - - +
75A GLU* 1.3 59.1 + - - +
77A GLY* 3.9 0.6 - - - +
78A LEU* 2.9 31.0 + - - +
96A TYR* 5.1 1.8 - - + -
111A HIS* 3.7 40.8 - - + +
113A TYR* 3.4 15.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 75 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ARG* 2.8 36.0 + - - -
73A SER* 3.1 13.6 - - - +
74A LEU* 1.3 77.3 - - - +
76A ASP* 1.3 60.4 + - - +
78A LEU* 3.4 5.4 + - - +
79A ASN* 2.9 36.8 + - - +
91A LEU 4.2 9.9 - - - +
92A THR* 3.6 10.1 - - - +
93A GLU* 3.2 38.8 - - + +
113A TYR* 2.4 31.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 76 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A TRP* 4.2 20.6 - - + -
73A SER* 3.2 24.2 + - - +
75A GLU* 1.3 81.4 - - - +
77A GLY* 1.3 56.3 + - - +
79A ASN* 3.4 9.1 + - - +
80A ARG* 2.9 40.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 77 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A VAL* 3.5 18.8 - - - -
68A ASP 5.2 0.7 - - - -
73A SER 3.2 10.7 + - - -
74A LEU 3.9 2.7 - - - -
76A ASP* 1.3 78.4 - - - +
78A LEU* 1.3 62.3 + - - +
80A ARG* 3.2 27.3 + - - +
81A VAL* 3.1 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 78 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A CYS* 3.6 40.8 - - + +
29A HIS* 4.2 10.8 - - - +
30A ALA 4.4 0.4 - - - +
64A GLY* 4.8 1.1 - - - -
67A VAL* 3.8 2.7 - - - +
74A LEU 2.9 18.3 + - - +
75A GLU* 3.7 4.3 - - - +
77A GLY* 1.3 76.1 - - - +
79A ASN* 1.3 59.7 + - - +
81A VAL* 3.2 4.0 + - - +
82A LEU* 2.8 55.7 + - + +
91A LEU* 3.8 27.1 - - + -
113A TYR* 3.6 37.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A GLU* 2.9 23.0 + - - +
76A ASP* 3.9 8.6 + - - +
78A LEU* 1.3 75.8 - - - +
80A ARG* 1.3 57.5 + - - +
82A LEU* 4.0 8.5 - - - +
83A GLY* 2.9 22.5 + - - -
89A LEU 3.9 4.1 - - - +
90A ARG* 3.2 46.8 + - - +
91A LEU* 2.8 52.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 80 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A VAL* 5.2 0.6 - - - +
68A ASP* 3.6 31.1 + - - +
72A TRP* 3.3 47.7 - - - +
76A ASP* 2.9 21.4 + - + +
77A GLY* 3.4 27.0 + - - +
79A ASN* 1.3 77.4 - - + +
81A VAL* 1.3 64.5 + - + +
83A GLY* 3.3 10.0 + - - -
84A LEU* 3.3 21.7 + - + +
90A ARG* 5.0 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A CYS 5.5 0.4 - - - +
64A GLY* 3.4 38.7 + - - +
65A GLY* 3.6 4.3 - - - +
66A PHE 3.6 23.1 - - - +
67A VAL* 4.2 5.8 - - + -
77A GLY 3.1 17.4 + - - +
78A LEU* 3.9 3.8 - - - +
80A ARG* 1.3 74.4 - - + +
82A LEU* 1.3 61.4 + - - +
84A LEU* 3.1 13.5 + - + +
85A GLY* 3.0 25.8 + - - -
134A ASP* 4.7 5.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 82 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A ALA* 4.1 7.9 - - + -
63A PRO* 3.8 33.9 - - + +
64A GLY* 3.9 13.2 - - - +
78A LEU* 2.8 46.3 + - + +
79A ASN* 4.0 11.7 - - - +
81A VAL* 1.3 74.2 - - - +
83A GLY* 1.3 58.3 - - - +
85A GLY* 4.5 1.3 - - - +
86A LEU* 2.8 44.6 + - + +
87A GLY 3.2 5.0 + - - -
88A CYS 4.1 10.2 - - - +
89A LEU* 5.0 9.2 - - + +
91A LEU* 4.0 24.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 83 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A ASN 2.9 18.5 + - - -
80A ARG 3.3 4.0 + - - -
81A VAL 3.2 0.6 - - - -
82A LEU* 1.3 78.1 - - - +
84A LEU* 1.3 49.8 - - - +
87A GLY* 3.2 9.3 + - - -
88A CYS 4.7 5.8 + - - -
90A ARG* 5.1 4.7 - - - -
133A ARG* 2.1 37.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 84 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A ARG* 3.3 15.4 + - + +
81A VAL* 3.1 14.8 + - + +
83A GLY* 1.3 78.4 - - - +
85A GLY* 1.3 57.5 + - - +
86A LEU 3.6 0.2 - - - -
132A SER* 3.4 2.4 + - - -
133A ARG* 3.4 32.8 + - + +
134A ASP* 3.0 45.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 85 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A GLN* 5.1 1.9 - - - +
63A PRO* 6.1 1.1 - - - -
81A VAL 3.0 13.6 + - - -
82A LEU* 4.7 0.4 - - - -
84A LEU* 1.3 77.8 - - - +
86A LEU* 1.3 69.3 + - - +
129A ALA* 4.2 6.2 - - - +
132A SER* 3.3 12.2 + - - -
134A ASP* 3.7 17.2 + - - -
139A VAL* 4.4 19.6 - - - +
142A LEU* 5.0 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 86 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A LEU* 3.8 28.5 - - + -
51A LEU* 5.7 0.2 - - + -
53A GLN* 5.1 0.7 - - - +
63A PRO* 3.9 17.9 - - + -
82A LEU* 2.8 37.1 + - + +
85A GLY* 1.3 88.2 - - - +
87A GLY* 1.3 50.4 + - - +
88A CYS* 3.4 12.9 + - - +
89A LEU* 4.6 7.4 - - + -
125A VAL* 3.9 10.3 - - + -
128A SER* 2.6 40.0 + - - +
129A ALA* 3.3 8.6 + - + +
132A SER* 4.0 4.7 - - - -
142A LEU* 3.9 33.2 - - + -
----------------------------------------------------------
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