Contacts of the helix formed by residues 86 - 109 (chain C) in PDB entry 2PWZ
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 86 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87C ARG* 1.3 74.6 + - - +
88C SER* 3.4 19.2 + - - -
89C ASP* 2.7 32.4 + - - +
90C LEU* 3.3 22.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 87 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81C ARG* 4.7 24.1 - - - +
86C ASP* 1.3 78.8 + - - +
88C SER* 1.3 63.0 + - - +
90C LEU* 3.9 9.9 + - + +
91C PHE* 3.3 23.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 88 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86C ASP* 3.8 16.7 - - - -
87C ARG* 1.3 76.1 - - - +
89C ASP* 1.3 58.8 + - - +
91C PHE* 3.5 5.9 + - - +
92C ASN* 2.8 48.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 89 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86C ASP* 2.7 39.2 + - - +
87C ARG 3.4 0.2 - - - -
88C SER* 1.3 80.2 + - - +
90C LEU* 1.3 57.1 + - - +
92C ASN* 3.4 9.2 + - - +
93C VAL* 3.1 32.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 90 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C VAL* 4.1 18.8 - - + -
80C ALA* 3.6 21.3 - - - +
81C ARG* 3.5 37.9 - - - +
86C ASP 3.3 13.5 + - - +
87C ARG* 3.9 10.1 + - + +
88C SER 3.4 0.2 - - - -
89C ASP* 1.3 76.3 - - - +
91C PHE* 1.3 62.2 + - - +
93C VAL* 3.3 7.4 + - - +
94C ASN* 2.9 42.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 91 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87C ARG 3.3 18.0 + - - +
88C SER* 3.8 5.8 - - - +
89C ASP 3.4 0.2 - - - -
90C LEU* 1.3 80.0 - - + +
92C ASN* 1.3 65.4 + - - +
94C ASN* 3.2 4.5 + - + -
95C ALA* 2.7 57.7 + - + +
120C PRO* 4.1 25.4 - - + -
123C THR* 3.4 34.3 - - + -
124C THR* 5.6 0.7 - - + -
127C ILE* 4.8 1.6 - - + -
305C LEU* 3.7 37.7 - - + -
309C PHE* 4.3 13.9 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 92 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88C SER* 2.8 39.5 + - - +
89C ASP* 3.6 8.7 + - - +
91C PHE* 1.3 84.8 - - - +
93C VAL* 1.3 57.6 + - + +
95C ALA* 4.1 0.5 - - - +
96C GLY* 3.1 24.4 + - - -
309C PHE* 3.8 26.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 93 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C VAL* 4.5 14.1 - - + -
89C ASP 3.1 17.7 + - - +
90C LEU* 3.6 10.8 - - - +
91C PHE 3.1 0.2 - - - -
92C ASN* 1.3 76.0 - - + +
94C ASN* 1.3 73.0 + - - +
96C GLY* 3.3 1.8 + - - -
97C ILE* 3.0 41.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 94 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78C GLY* 3.4 8.0 - - - -
79C VAL* 3.0 47.7 + - - +
90C LEU* 2.9 28.9 + - - +
91C PHE* 4.0 4.7 - - - +
93C VAL* 1.3 78.1 - - - +
95C ALA* 1.3 61.6 + - - +
97C ILE* 3.4 7.5 + - - +
98C VAL* 3.1 28.1 + - - +
118C THR* 4.0 11.7 - - + +
119C ASN* 3.3 27.5 + - - +
120C PRO* 5.3 3.1 - - + -
124C THR* 5.2 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 95 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91C PHE* 2.7 34.6 + - + +
94C ASN* 1.3 73.1 - - - +
96C GLY* 1.3 57.7 + - - +
98C VAL* 3.3 4.4 + - - +
99C LYS* 3.0 29.8 + - - +
124C THR* 5.0 4.0 - - - +
127C ILE* 3.5 29.8 - - + +
309C PHE* 3.6 27.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 96 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92C ASN 3.1 18.8 + - - -
93C VAL 3.7 1.1 - - - -
95C ALA* 1.3 75.4 - - - +
97C ILE* 1.3 56.9 + - - +
99C LYS* 3.3 4.9 + - - +
100C ASN* 3.0 30.9 + - - +
309C PHE* 3.6 13.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 97 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C ALA* 3.5 35.4 - - + +
78C GLY* 4.0 20.0 - - - +
79C VAL* 5.2 1.6 - - + +
93C VAL* 3.0 34.0 + - + +
94C ASN* 3.6 8.5 - - - +
95C ALA 3.4 0.2 - - - -
96C GLY* 1.3 72.2 - - - +
98C VAL* 1.3 66.0 + - + +
100C ASN* 3.4 4.7 + - - +
101C LEU* 2.9 33.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 98 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75C ILE* 4.7 9.0 - - + -
94C ASN 3.1 17.3 + - - +
95C ALA 3.3 4.2 + - - +
97C ILE* 1.3 77.3 - - + +
99C LYS* 1.3 59.1 + - - +
101C LEU* 4.2 3.3 - - - +
102C VAL* 2.9 52.5 + - + +
116C ILE* 4.9 7.4 - - + -
118C THR* 3.6 34.3 - - + +
124C THR* 3.7 38.6 - - + +
127C ILE* 4.3 8.5 - - + -
128C ALA* 4.4 1.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 99 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95C ALA 3.0 16.7 + - - +
96C GLY* 3.5 6.5 - - - +
97C ILE 3.2 0.2 - - - -
98C VAL* 1.3 77.2 - - - +
100C ASN* 1.3 60.3 + - - +
103C GLN* 3.3 28.5 + - - +
127C ILE* 3.9 15.2 - - + +
131C VAL* 3.8 22.6 - - + +
134C LYS* 6.2 0.2 - - - +
309C PHE* 3.8 24.4 + - + -
310C VAL* 4.4 28.4 + - + +
312C LYS* 6.4 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 100 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C GLU 5.6 0.4 + - - -
96C GLY 3.0 16.8 + - - +
97C ILE* 3.8 5.6 - - - +
99C LYS* 1.3 74.7 - - - +
101C LEU* 1.3 73.0 + - + +
103C GLN* 3.1 9.5 + - - +
104C GLN* 2.8 48.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 101 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C LEU* 4.1 31.4 - - + +
7C GLY 5.1 0.2 - - - +
33C TYR* 3.8 31.0 - - + +
63C ALA* 4.6 3.4 - - + -
75C ILE* 4.1 14.8 - - + -
77C ALA* 3.6 31.6 - - + -
97C ILE* 2.9 29.2 + - + +
98C VAL 4.2 0.7 - - - +
100C ASN* 1.3 80.8 - - + +
102C VAL* 1.3 58.6 + - - +
104C GLN* 3.0 15.3 + - - +
105C VAL* 2.9 30.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 102 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75C ILE* 3.8 19.5 - - + -
98C VAL* 2.9 29.1 + - + +
99C LYS 4.3 0.2 - - - +
101C LEU* 1.3 76.1 - - - +
103C GLN* 1.3 52.6 + - - +
105C VAL* 3.2 10.4 + - + +
106C ALA* 2.7 32.6 + - - +
114C ILE* 5.1 5.4 - - + -
116C ILE* 4.8 3.1 - - + -
128C ALA* 3.6 46.2 - - + +
131C VAL* 4.0 11.2 - - + -
132C LEU* 3.8 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 103 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99C LYS* 3.3 22.2 + - - +
100C ASN* 3.1 13.4 + - - +
102C VAL* 1.3 73.7 - - - +
104C GLN* 1.3 64.7 + - + +
106C ALA* 3.4 3.4 + - - +
107C LYS* 3.2 22.3 + - - +
131C VAL* 3.6 23.3 + - - +
134C LYS* 5.9 2.2 - - - +
135C ALA* 4.3 20.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 104 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C TYR* 4.7 0.6 + - - -
61C GLU 3.2 21.1 + - - -
62C ASP* 3.4 11.4 - - - +
63C ALA* 2.7 33.0 + - + +
64C THR* 3.9 2.2 + - - +
67C LEU* 3.6 17.3 - - + +
100C ASN* 2.8 36.0 + - - +
101C LEU* 3.0 18.7 + - - +
103C GLN* 1.3 74.8 - - + +
105C VAL* 1.3 65.2 + - - +
107C LYS* 3.2 7.3 + - - +
108C THR* 3.0 26.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 105 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C LEU* 4.1 9.9 - - + -
67C LEU* 3.6 10.0 - - + +
73C VAL* 3.7 30.3 - - + -
75C ILE* 4.4 5.2 - - + -
101C LEU 2.9 17.1 + - - +
102C VAL* 3.4 13.9 - - - +
104C GLN* 1.3 75.7 - - - +
106C ALA* 1.3 63.9 + - - +
109C CYS* 3.0 46.8 + - - +
110C PRO* 5.1 0.9 - - + -
114C ILE* 3.6 34.5 - - + -
132C LEU* 4.9 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 106 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C VAL 2.7 19.6 + - - +
103C GLN* 3.7 12.3 - - - +
104C GLN 3.2 0.4 - - - -
105C VAL* 1.3 73.0 - - - +
107C LYS* 1.3 61.4 + - - +
110C PRO* 3.4 22.5 - - - +
131C VAL* 5.1 1.1 - - + +
132C LEU* 4.1 13.5 - - + -
135C ALA* 3.8 28.4 - - + +
137C VAL* 3.9 18.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 107 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C THR* 5.3 5.6 - - - +
103C GLN 3.2 12.4 + - - +
104C GLN* 3.2 9.7 + - - +
106C ALA* 1.3 78.0 - - - +
108C THR* 1.3 69.1 + - - +
110C PRO* 4.3 3.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 108 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C THR* 3.5 28.0 + - + +
67C LEU* 3.8 13.0 - - + +
68C GLU* 3.6 46.2 - - + +
69C GLY 5.3 3.1 + - - -
104C GLN* 3.0 14.5 + - - -
107C LYS* 1.3 88.9 - - - +
109C CYS* 1.3 59.0 + - - +
110C PRO* 3.4 6.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 109 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C LEU* 3.4 40.8 - - - +
69C GLY* 5.0 2.2 - - - +
70C ALA* 3.8 19.3 - - - +
73C VAL* 3.7 29.2 - - - -
105C VAL* 3.0 21.7 + - - +
108C THR* 1.3 79.2 - - - +
110C PRO* 1.4 58.5 - - - +
111C LYS 3.2 2.5 - - - -
112C ALA* 3.0 24.1 + - - +
----------------------------------------------------------
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