Contacts of the helix formed by residues 73 - 92 (chain A) in PDB entry 1Z0X
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 73 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A CYS* 3.4 25.1 - - - +
72A GLY* 1.3 81.3 - - - +
74A TRP* 1.3 60.5 + - - +
75A TYR* 3.4 2.2 + - + +
76A SER* 4.2 12.6 - - - +
77A ASP* 2.9 31.9 + - - -
119A ILE* 4.8 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 74 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A GLY 3.8 3.4 + - - -
73A GLU* 1.3 72.7 - - - +
75A TYR* 1.3 89.7 + + + +
78A LEU* 3.0 29.7 + - + +
119A ILE* 3.3 26.2 - - + +
120A LEU* 4.0 10.1 - - + -
123A ALA* 3.8 30.3 - - + -
125A PHE* 3.8 24.5 - + - -
208A LEU* 3.4 35.0 - - + -
211A LEU* 3.8 28.7 - - + -
212A GLN* 3.4 26.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 75 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A GLU* 3.4 1.7 - - + -
74A TRP* 1.3 102.1 - + + +
76A SER* 1.3 68.2 + - - +
79A LEU* 3.1 32.3 + - + +
205A LYS* 3.3 34.5 + - + +
208A LEU* 3.3 38.8 - - + +
209A ASP* 2.7 28.9 + - - -
212A GLN* 3.3 25.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 76 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A CYS* 4.2 19.8 - - - -
73A GLU* 3.5 16.6 + - - +
74A TRP 3.4 0.2 - - - -
75A TYR* 1.3 81.9 - - - +
77A ASP* 1.3 60.9 + - - +
79A LEU* 3.1 9.9 + - - +
80A ALA* 2.9 26.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 77 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A ALA 4.4 1.2 - - - +
70A LEU* 3.1 30.5 - - + +
71A CYS* 2.8 27.5 + - - -
72A GLY* 2.8 26.7 + - - -
73A GLU 2.9 25.4 + - - +
76A SER* 1.3 72.8 + - - +
78A LEU* 1.3 62.1 + - - +
80A ALA* 3.2 9.4 + - - +
81A PHE* 3.1 28.6 + - + -
119A ILE* 4.2 22.4 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
74A TRP* 3.0 21.3 + - + +
75A TYR 4.0 2.9 - - - +
77A ASP* 1.3 76.9 - - - +
79A LEU* 1.3 62.0 + - - +
81A PHE* 3.5 5.3 + - - +
82A MSE 3.3 24.4 + - + +
116A MSE 3.7 44.2 - - + +
119A ILE* 4.5 9.3 - - + +
120A LEU* 4.1 25.6 - - + -
133A ALA* 5.5 0.2 - - + -
134A VAL* 5.0 3.1 - - + -
137A LEU* 3.4 31.9 - - + -
204A VAL* 5.6 0.2 - - - -
208A LEU* 3.5 22.9 - - + -
211A LEU* 5.0 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A TYR* 3.1 27.4 + - + +
76A SER* 3.1 8.3 + - - +
78A LEU* 1.3 76.0 - - - +
80A ALA* 1.3 58.9 + - - +
82A MSE 3.2 3.6 + - + +
83A GLU* 2.9 57.6 + - + +
201A ILE* 3.8 19.7 - - + +
204A VAL* 4.2 16.2 - - + -
205A LYS* 3.7 32.5 - - + -
208A LEU* 4.3 15.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 80 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A PRO* 3.8 20.9 - - + -
69A ALA 4.7 8.1 - - - +
70A LEU* 4.6 3.4 - - + -
76A SER 2.9 11.9 + - - +
77A ASP* 3.2 13.4 + - - +
79A LEU* 1.3 78.0 - - - +
81A PHE* 1.3 61.5 + - - +
83A GLU* 3.3 14.3 + - - +
84A ASN* 3.0 31.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A PHE* 3.6 34.7 - + - -
67A GLU* 5.4 0.2 - - - -
68A PRO* 3.9 20.0 - - + -
70A LEU* 4.4 9.0 - - + -
77A ASP 3.1 22.6 + - - -
78A LEU* 3.6 10.5 - - - +
79A LEU 3.2 0.2 - - - -
80A ALA* 1.3 78.3 - - - +
82A MSE 1.3 68.9 + - + +
84A ASN* 3.5 2.3 + - - +
85A TYR* 2.9 35.4 + + - -
112A HIS* 4.4 13.5 - + + -
115A GLN* 3.4 43.5 - - + -
116A MSE 3.4 35.9 - - + -
119A ILE* 4.8 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 82 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A LEU* 3.3 16.5 + - + +
79A LEU* 3.2 5.4 + - + +
81A PHE* 1.3 84.6 - - + +
83A GLU* 1.3 66.6 + - - +
85A TYR* 3.2 20.3 + - + +
86A TYR* 2.9 24.3 + - - +
116A MSE 3.2 34.8 - - - +
134A VAL 5.4 0.4 - - - +
137A LEU* 3.8 45.5 - - + +
138A GLN* 4.0 11.7 - - - +
141A LEU* 5.5 2.7 - - - -
200A PHE* 3.5 24.0 - - + -
204A VAL* 4.3 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 83 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A LEU* 2.9 39.7 + - + +
80A ALA* 3.7 15.4 - - - +
82A MSE 1.3 75.1 - - - +
84A ASN* 1.3 64.8 + - - +
86A TYR* 3.2 7.2 + - - +
87A ASP* 3.0 31.5 + - - +
197A LYS* 3.8 16.9 - - - +
201A ILE* 3.2 38.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 84 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A PHE* 3.7 22.4 - - + -
66A GLN* 2.7 40.8 + - + +
67A GLU 4.0 1.4 + - - -
68A PRO* 3.9 17.0 - - - +
80A ALA* 3.0 18.8 + - - +
81A PHE 3.8 0.2 - - - +
83A GLU* 1.3 84.4 - - - +
85A TYR* 1.3 59.4 + - - +
87A ASP* 3.4 14.6 + - - +
88A LEU* 3.0 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 85 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A GLU* 2.8 37.5 + - - -
65A PHE* 3.4 31.4 - + - -
81A PHE* 2.9 18.5 + + - +
82A MSE 3.2 30.0 + - + +
84A ASN* 1.3 75.0 - - - +
86A TYR* 1.3 66.2 + - - +
88A LEU* 3.7 7.3 - - + +
89A TYR* 3.1 46.6 + + - -
109A ARG* 3.2 17.3 + - - -
112A HIS* 3.3 17.3 + - - +
116A MSE 3.7 24.3 - - + +
138A GLN* 3.7 8.1 - - - +
141A LEU* 3.9 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 86 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A MSE 2.9 13.7 + - - +
83A GLU* 3.2 10.1 + - - +
85A TYR* 1.3 75.3 - - - +
87A ASP* 1.3 64.9 + - - +
89A TYR* 3.4 6.1 + - - +
90A GLN* 2.9 62.5 + - + +
141A LEU* 3.7 20.4 - - + +
144A MSE 3.9 15.3 - - - -
145A ILE* 4.9 1.6 - - + -
195A HIS 3.3 21.8 + - - -
196A GLN* 4.2 0.2 - - - -
197A LYS* 3.3 44.3 + - + -
200A PHE* 3.5 42.0 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 87 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A GLN* 6.2 3.8 - - + -
83A GLU 3.0 11.9 + - - +
84A ASN* 3.7 17.4 - - - +
85A TYR 3.3 0.4 - - - -
86A TYR* 1.3 79.6 - - - +
88A LEU* 1.3 62.8 + - - +
90A GLN* 3.1 13.7 + - - +
91A GLN* 3.0 31.2 - - - +
197A LYS* 2.7 41.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 88 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A ILE* 3.3 43.5 - - + +
62A GLU* 4.2 8.7 - - - +
64A HIS* 3.6 29.4 - - + +
65A PHE* 3.8 29.8 - - + -
66A GLN 5.7 0.2 - - - +
84A ASN 3.0 16.3 + - - +
85A TYR* 3.7 13.5 - - + +
86A TYR 3.3 0.2 - - - -
87A ASP* 1.3 77.8 - - - +
89A TYR* 1.3 61.0 + - + +
91A GLN* 3.3 19.3 + - + +
92A PHE* 3.6 21.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 89 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A ILE* 4.3 14.6 - - + -
62A GLU* 5.2 0.8 + - - -
85A TYR* 3.1 24.9 + + - +
86A TYR 3.4 1.1 + - - +
87A ASP 3.2 0.6 - - - -
88A LEU* 1.3 89.9 - - + +
90A GLN* 1.3 62.9 + - - +
91A GLN 3.4 0.7 - - - -
92A PHE 3.6 14.2 - - - +
95A ALA* 3.4 36.4 - - + +
96A VAL* 4.4 5.8 - - + -
99A GLU* 4.2 9.0 - - + +
109A ARG* 3.8 23.2 + - - -
138A GLN* 4.0 8.9 + - - -
141A LEU* 3.4 29.6 - - + -
142A PHE* 3.7 19.9 - + - -
145A ILE* 3.1 36.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 90 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A TYR* 2.9 66.0 + - + +
87A ASP* 3.1 10.9 + - - +
89A TYR* 1.3 78.3 - - - +
91A GLN* 1.3 70.0 + - - +
92A PHE 3.5 2.1 + - - -
145A ILE* 4.0 17.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 91 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A GLU* 5.7 0.5 - - - +
64A HIS* 6.3 0.2 - - + -
87A ASP* 3.0 30.6 - - - +
88A LEU* 3.3 14.5 + - + +
90A GLN* 1.3 88.2 + - - +
92A PHE* 1.3 76.8 + - + +
93A PRO* 4.4 2.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 92 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A PHE* 3.8 40.2 - + + -
60A ALA* 4.7 2.2 - - + -
61A ILE* 3.9 20.2 - - + -
64A HIS* 3.4 54.3 - + + -
88A LEU* 3.6 24.4 + - + -
89A TYR 3.6 14.1 - - - +
90A GLN 3.5 1.3 - - - -
91A GLN* 1.3 94.0 - - + +
93A PRO* 1.3 68.6 - - + +
94A CYS 3.5 2.4 + - - -
95A ALA* 3.6 20.4 + - + +
----------------------------------------------------------
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