Contacts of the helix formed by residues 81 - 94 (chain C) in PDB entry 1ZVM
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 81 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C HIS 3.5 5.0 + - - +
80C VAL* 1.3 72.9 - - - +
82C CYS* 1.3 60.2 + - - +
83C GLN* 3.9 10.7 + - - +
84C SER* 2.5 60.1 + - - +
85C VAL* 3.2 8.1 + - - +
112C LEU* 5.0 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 82 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C LEU* 3.8 20.1 - - + +
67C CYS* 2.1 67.6 - - + +
68C VAL* 3.4 13.2 - - + -
71C THR* 3.9 14.8 - - - -
80C VAL* 3.5 4.5 + - - -
81C ASP* 1.3 73.6 + - - +
83C GLN* 1.3 61.1 + - - +
85C VAL* 3.1 4.8 + - - +
86C TRP* 3.1 18.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 83 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C LEU* 4.0 26.9 - - + +
81C ASP* 3.3 12.1 + - - +
82C CYS* 1.3 78.3 - - - +
84C SER* 1.3 61.2 + - - +
86C TRP* 3.6 16.2 + - - +
87C ASP* 3.0 51.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 84 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81C ASP* 2.5 40.5 + - - +
83C GLN* 1.3 75.6 - - - +
85C VAL* 1.3 63.2 - - - +
87C ASP* 3.5 8.7 + - - +
88C ALA* 3.0 18.0 + - - +
112C LEU* 3.2 26.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 85 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63C VAL* 5.0 4.0 - - + -
67C CYS* 4.1 9.9 - - + -
80C VAL* 3.6 31.0 - - + -
81C ASP 3.2 5.0 + - - +
82C CYS* 3.1 9.1 + - - +
84C SER* 1.3 75.3 - - - +
86C TRP* 1.3 57.2 + - - +
88C ALA* 3.0 5.1 + - - +
89C PHE* 2.7 37.9 + - + +
109C LEU* 3.7 20.5 - - + +
112C LEU* 3.9 23.8 - - + +
113C GLY* 5.3 1.3 - - - +
149C LEU* 5.2 4.0 - - + -
150C LEU* 5.5 0.9 - - + -
153C LEU* 3.7 24.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 86 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C PHE* 3.5 40.6 - + - -
60C PRO* 3.8 38.1 - - + +
63C VAL* 4.1 26.4 - - + +
64C LEU* 4.7 13.0 - - + -
82C CYS 3.1 8.2 + - - +
83C GLN* 3.7 29.8 - - - +
85C VAL* 1.3 81.3 - - - +
87C ASP* 1.3 58.4 + - - +
89C PHE* 3.4 7.1 - - + +
90C LYS* 2.7 76.4 + - + +
93C PHE* 4.8 0.9 - + - -
168C ILE* 4.3 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 87 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83C GLN* 3.0 39.1 + - - +
84C SER* 3.8 7.8 - - - +
85C VAL 3.2 0.2 - - - -
86C TRP* 1.3 84.7 + - - +
88C ALA* 1.3 58.4 + - - +
90C LYS* 4.0 16.6 + - - +
91C GLY* 2.9 26.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 88 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84C SER 3.0 16.9 + - - +
85C VAL 3.0 4.8 + - - +
87C ASP* 1.3 76.5 - - - +
89C PHE* 1.3 64.2 + - - +
91C GLY* 3.5 2.2 + - - -
92C ALA* 3.3 19.8 + - - +
105C ASP 4.9 1.7 - - - +
108C PRO* 4.0 16.6 - - + +
109C LEU* 3.8 32.4 + - - +
112C LEU* 4.1 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 89 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C PHE* 4.0 13.0 - + - -
63C VAL* 3.8 35.0 - - + -
85C VAL* 2.7 20.2 + - + +
86C TRP* 3.4 12.3 - + + +
88C ALA* 1.3 70.9 - - - +
90C LYS* 1.3 66.8 + - - +
92C ALA* 3.1 16.9 + - - +
93C PHE* 3.4 9.5 - + - -
106C TYR* 4.0 12.3 - + - -
109C LEU* 3.8 31.8 - - + +
153C LEU* 4.7 15.7 - - + -
154C ALA* 4.5 7.2 - - + -
159C TRP* 3.8 45.5 - + - -
188C PHE* 4.4 10.8 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 90 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86C TRP* 2.7 59.0 + - + +
87C ASP* 4.0 16.4 + - - +
89C PHE* 1.3 72.8 - - - +
91C GLY* 1.3 62.9 + - - +
92C ALA 3.0 1.4 + - - -
93C PHE* 3.1 13.3 + - + -
94C ILE* 3.0 65.8 + - + +
166C SER 6.0 0.7 - - - +
168C ILE* 5.3 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 91 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87C ASP 2.9 19.2 + - - -
88C ALA* 3.8 3.4 - - - -
89C PHE 3.2 0.4 - - - -
90C LYS* 1.3 76.3 - - - +
92C ALA* 1.3 61.5 - - - +
93C PHE 3.3 0.6 + - - -
94C ILE* 4.0 15.3 + - - +
96C LYS* 3.3 17.7 + - - -
105C ASP 4.9 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 92 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88C ALA 3.3 9.0 + - - +
89C PHE 3.1 13.2 + - - +
90C LYS 3.0 1.4 + - - -
91C GLY* 1.3 79.4 - - - +
93C PHE* 1.3 59.1 + - - +
96C LYS* 3.2 20.4 + - - +
101C ILE* 4.0 5.0 - - - +
105C ASP* 3.1 37.7 - - - +
106C TYR* 3.5 32.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 93 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C PHE* 4.0 22.7 - + - -
86C TRP* 4.8 1.3 - + - -
89C PHE* 3.4 23.6 - + - -
90C LYS* 3.1 14.8 + - - -
92C ALA* 1.3 80.4 - - - +
94C ILE* 1.3 80.1 + - + +
95C SER 3.6 0.2 + - - -
96C LYS* 3.4 21.6 + - - +
101C ILE* 4.2 8.5 - - + +
106C TYR* 4.7 3.6 - - - +
159C TRP* 3.5 29.6 - + + -
160C CYS* 3.6 38.8 - - - -
161C GLY* 3.6 6.9 + - - -
168C ILE* 4.4 14.4 - - + -
184C PRO* 3.9 23.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 94 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90C LYS* 3.0 63.8 + - + +
91C GLY* 4.0 10.3 - - - +
93C PHE* 1.3 91.8 - - + +
95C SER* 1.3 75.0 + - - +
96C LYS* 3.2 13.0 + - - +
161C GLY* 5.0 3.1 - - - -
166C SER* 4.3 21.3 - - - +
167C LYS 5.3 2.7 - - - +
168C ILE* 4.7 8.3 - - + -
----------------------------------------------------------
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