Contacts of the helix formed by residues 74 - 90 (chain A) in PDB entry 1ZP2
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 74 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A GLY 3.8 3.0 + - - -
73A PHE* 1.3 72.5 - - - +
75A LEU* 1.3 55.2 + - - +
76A GLU* 2.8 21.1 + - - +
77A ALA* 2.6 62.7 + - - +
78A LEU* 2.9 10.4 + - - +
109A LEU* 4.5 9.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 75 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A TYR* 3.4 37.2 - - + -
35A GLN* 4.0 27.8 - - + +
38A VAL* 3.8 15.3 - - + -
60A LEU* 4.3 14.8 - - + -
64A MET* 6.0 2.7 - - - -
73A PHE 3.4 4.1 + - - -
74A SER* 1.3 70.7 - - - +
76A GLU* 1.3 67.3 + - - +
78A LEU* 3.5 9.6 - - + +
79A VAL* 2.8 50.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 76 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A TYR* 4.5 12.3 + - - -
38A VAL* 5.0 3.0 - - + +
74A SER* 2.8 22.1 + - - +
75A LEU* 1.3 88.8 + - - +
77A ALA* 1.3 54.5 + - - +
79A VAL* 3.2 3.9 + - - +
80A ALA* 2.7 37.3 + - - +
107A TRP* 3.5 53.9 + - + +
109A LEU* 3.8 20.6 - - + +
113A LEU* 5.1 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 77 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A PHE* 4.9 4.0 - - + -
74A SER* 2.6 35.3 + - - +
76A GLU* 1.3 72.2 - - - +
78A LEU* 1.3 56.0 + - - +
80A ALA* 3.2 3.1 + - - +
81A THR* 2.6 34.4 + - - -
113A LEU* 3.7 32.9 - - + +
118A ILE* 5.4 0.2 - - - +
121A ILE* 3.7 15.6 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
60A LEU* 3.4 28.9 - - + -
63A TYR* 3.9 20.9 - - + -
64A MET* 3.4 28.3 - - + -
73A PHE* 4.1 23.8 - - + +
74A SER 2.9 8.6 + - - +
75A LEU* 3.5 18.4 - - + +
77A ALA* 1.3 72.9 - - - +
79A VAL* 1.3 68.3 + - - +
81A THR* 2.7 6.7 + - - -
82A CYS* 2.7 29.1 + - - +
121A ILE* 3.6 23.3 - - + -
124A GLU* 5.9 0.2 - - + -
125A ILE* 4.8 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A GLN 4.8 0.4 - - - +
38A VAL* 3.8 25.4 - - + +
39A VAL* 3.6 35.7 - - + +
42A PHE* 4.3 3.1 - - + -
60A LEU* 4.0 22.6 - - + +
75A LEU* 2.8 31.1 + - + +
76A GLU* 3.5 4.9 - - - +
78A LEU* 1.3 73.0 - - - +
80A ALA* 1.3 64.2 + - - +
82A CYS* 3.8 7.8 - - + +
83A ILE* 3.0 37.2 + - + +
107A TRP* 4.2 10.1 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
42A PHE* 3.6 22.6 - - + -
76A GLU 2.7 20.7 + - - +
77A ALA 3.4 6.3 - - - +
78A LEU 3.0 0.2 - - - -
79A VAL* 1.3 73.8 - - - +
81A THR* 1.3 56.4 + - - +
83A ILE* 3.3 4.9 + - - +
84A TYR* 3.1 25.1 + - - +
99A ILE* 3.8 15.2 - - + +
103A ALA* 4.6 0.4 - - + -
107A TRP* 4.6 4.0 - - + -
113A LEU* 3.8 23.6 - - + -
118A ILE* 5.1 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A ALA 2.6 20.2 + - - -
78A LEU 2.7 10.0 + - - -
80A ALA* 1.3 68.4 - - - +
82A CYS* 1.3 55.7 + - - -
83A ILE 3.0 1.6 - - - -
84A TYR* 3.1 9.8 + - + +
85A LEU* 2.7 38.3 + - + +
118A ILE* 3.4 34.1 - - + +
121A ILE* 3.2 27.0 - - + +
122A GLU* 3.4 28.0 - - + +
125A ILE* 3.8 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 82 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A VAL* 6.2 1.1 - - + -
56A ALA* 3.1 24.9 - - + +
59A LEU* 4.2 10.9 - - + +
60A LEU* 3.6 49.8 - - + -
63A TYR* 5.6 0.4 - - - -
78A LEU* 2.7 18.0 + - - +
79A VAL* 3.8 8.3 - - - +
81A THR* 1.3 72.2 - - - +
83A ILE* 1.3 57.7 + - - +
85A LEU* 4.3 6.4 - - - +
86A SER* 3.1 27.3 + - - -
125A ILE* 4.2 18.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 83 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A VAL* 3.8 18.8 - - + +
42A PHE* 3.7 27.6 - - + -
43A GLY* 4.7 1.3 - - - -
46A LEU* 5.2 3.1 - - + -
48A LEU* 3.4 28.3 - - + -
52A VAL* 4.4 2.0 - - + +
53A LEU* 4.1 18.8 - - + -
56A ALA* 3.7 20.4 - - + -
79A VAL* 3.0 30.1 + - + +
80A ALA 3.5 4.7 - - - +
81A THR 3.0 0.2 - - - -
82A CYS* 1.3 77.0 - - - +
84A TYR* 1.3 67.6 + - - +
86A SER* 3.2 2.1 + - - -
87A CYS* 2.9 28.0 + - - -
99A ILE* 4.8 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 84 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A ALA 3.1 11.4 + - - +
81A THR* 3.4 13.5 - - + +
83A ILE* 1.3 77.7 - - - +
85A LEU* 1.3 63.3 + - - +
87A CYS* 3.3 4.7 + - - +
88A LYS* 3.1 45.9 + - + +
94A VAL 3.6 17.9 - - - -
95A HIS* 5.1 0.4 - - - -
96A ILE* 3.2 37.7 - - + +
99A ILE* 3.3 33.4 - - + -
118A ILE* 3.8 23.3 - - + -
122A GLU* 3.5 34.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 85 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A LEU* 4.4 12.1 - - + -
81A THR 2.7 17.7 + - - +
82A CYS* 4.3 4.3 - - - +
84A TYR* 1.3 73.4 - - + +
86A SER* 1.3 63.9 + - - +
88A LYS* 3.1 14.3 + - + +
89A VAL* 2.9 29.4 + - + +
122A GLU* 3.3 40.2 - - + +
125A ILE* 4.2 29.8 - - + -
126A ILE* 4.0 28.0 - - + -
133A LEU* 4.4 20.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 86 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A VAL* 2.8 36.4 + - - +
55A THR* 3.1 24.3 - - - -
56A ALA* 3.7 9.2 - - - -
59A LEU* 4.4 3.1 - - - +
82A CYS 3.1 20.2 + - - -
83A ILE 3.2 4.0 + - - -
85A LEU* 1.3 80.8 - - - +
87A CYS* 1.3 55.4 + - - +
89A VAL* 4.6 2.7 - - - -
90A GLU* 2.8 31.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 87 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A LEU* 3.7 24.9 - - - -
52A VAL* 3.9 11.9 - - - -
83A ILE* 2.9 24.5 + - - +
84A TYR* 3.6 6.5 - - - +
86A SER* 1.3 73.8 - - - +
88A LYS* 1.3 65.7 + - - +
91A GLU 3.4 1.4 + - - -
92A CYS* 2.8 55.3 + - - +
93A PRO* 3.1 8.4 - - + -
94A VAL* 3.6 25.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 88 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A TYR* 3.1 38.1 + - + +
85A LEU* 3.1 15.3 + - + +
87A CYS* 1.3 82.0 - - - +
89A VAL* 1.3 65.8 + - + +
91A GLU* 3.4 9.7 + - - +
93A PRO* 4.3 14.4 - - + +
122A GLU* 3.0 27.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 89 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A THR* 5.3 2.9 - - + -
59A LEU* 5.2 2.2 - - + -
85A LEU* 2.9 21.4 + - + +
86A SER* 4.0 5.2 - - - +
88A LYS* 1.3 75.7 - - + +
90A GLU* 1.3 64.1 + - + +
91A GLU* 2.7 26.6 + - - +
133A LEU* 4.0 50.5 - - + +
134A ILE* 4.7 13.0 - - + +
135A VAL 5.8 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 90 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A ARG* 2.7 64.9 + - - +
52A VAL* 4.2 14.4 - - + -
55A THR* 2.9 34.2 + - + +
86A SER* 2.8 31.2 + - - +
87A CYS 4.7 0.4 - - - +
89A VAL* 1.3 74.6 - - - +
91A GLU* 1.3 70.0 + - - +
92A CYS* 3.3 3.1 + - - +
135A VAL 4.4 11.3 + - - +
137A HIS* 4.7 1.4 + - - -
----------------------------------------------------------
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