Contacts of the helix formed by residues 80 - 98 (chain C) in PDB entry 1ZUM
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 80 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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127A LYS* 5.2 3.1 + - - -
147B ASP* 3.5 36.6 - - - +
148B GLY* 3.1 12.0 + - - -
498B LYS* 2.7 30.6 + - - +
78C ARG 3.5 2.5 + - - +
79C MET* 1.3 78.1 - - - +
81C ALA* 1.3 57.1 + - - +
82C SER* 3.7 7.2 - - - +
83C HIS* 2.8 33.2 + - + +
84C ARG* 3.2 5.4 + - - +
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Residues in contact with ALA 81 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B PRO* 4.4 19.8 + - + +
147B ASP* 4.9 0.6 + - - -
498B LYS* 4.7 4.2 - - - +
79C MET 3.6 2.2 + - - -
80C ASP* 1.3 70.9 - - - +
82C SER* 1.3 63.7 + - - +
84C ARG* 3.0 36.6 + - - +
85C GLY 3.2 7.4 + - - -
136C ALA* 3.3 30.9 - - - +
137C ASP* 3.9 15.0 - - + -
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Residues in contact with SER 82 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A LYS* 5.4 5.1 - - - -
462A GLN* 4.2 5.6 - - - -
145B PRO 5.6 0.4 + - - -
147B ASP* 2.8 33.2 + - - -
80C ASP* 3.7 3.8 - - - +
81C ALA* 1.3 78.1 - - - +
83C HIS* 1.3 59.1 + - - +
85C GLY* 3.2 4.5 + - - +
86C ARG* 3.1 31.3 + - - +
137C ASP* 3.4 27.8 - - - +
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Residues in contact with HIS 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C MET* 3.5 38.9 - - + +
80C ASP* 2.8 21.8 + - + +
82C SER* 1.3 78.3 + - - +
84C ARG* 1.3 62.7 + - - +
85C GLY 3.0 1.8 - - - -
86C ARG* 3.1 20.8 + - + +
87C LEU* 3.0 40.0 + - + +
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Residues in contact with ARG 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500B SER* 3.8 26.3 - - - -
76C TRP* 3.7 35.5 + - + -
79C MET* 4.0 21.9 + - + -
80C ASP 3.2 4.9 + - - +
81C ALA* 3.0 28.1 + - - +
83C HIS* 1.3 74.9 - - - +
85C GLY* 1.3 63.7 + - - +
87C LEU* 3.2 5.1 + - - +
88C LEU* 3.0 27.9 + - - +
136C ALA* 3.4 21.1 + - + -
183C LEU 3.5 16.2 - - - +
184C ALA* 3.0 27.3 + - - +
185C THR* 3.9 8.4 + - - +
186C GLY* 3.4 20.8 - - - +
213C PHE* 4.9 1.2 - - - -
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Residues in contact with GLY 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81C ALA 3.2 4.8 + - - -
82C SER 3.2 7.7 + - - -
83C HIS 3.0 0.4 - - - -
84C ARG* 1.3 80.6 - - - +
86C ARG* 1.3 56.7 + - - +
88C LEU* 3.3 1.3 + - - -
89C ASN* 3.0 37.8 + - - -
133C ALA* 3.4 30.9 - - - +
136C ALA* 3.6 6.2 - - - +
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Residues in contact with ARG 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A ASN* 5.3 2.2 + - - -
93A ASP* 4.8 3.6 + - - -
96A GLU* 4.8 2.0 + - - -
130A ARG* 3.5 59.0 - - - +
82C SER* 3.1 22.1 + - - +
83C HIS* 3.1 29.8 + - + +
85C GLY* 1.3 75.6 - - - +
87C LEU* 1.3 58.3 + - + +
89C ASN* 3.3 25.6 + - - +
90C ARG* 2.9 28.3 + - - +
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Residues in contact with LEU 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76C TRP* 4.0 13.2 - - + -
79C MET* 3.6 37.7 - - + -
83C HIS* 3.0 29.3 + - + +
84C ARG 3.2 5.6 + - - +
86C ARG* 1.3 75.0 - - - +
88C LEU* 1.3 58.5 + - - +
90C ARG* 3.1 5.9 + - + +
91C LEU* 2.9 29.6 + - - +
211C ALA* 3.5 23.5 - - - +
212C GLY* 4.2 13.0 - - - +
213C PHE* 3.5 34.6 - - + -
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Residues in contact with LEU 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84C ARG 3.0 18.1 + - - +
85C GLY* 3.3 7.6 + - - +
87C LEU* 1.3 75.1 - - - +
89C ASN* 1.3 58.0 + - - +
91C LEU* 3.3 9.1 + - + +
92C ALA* 3.0 26.9 + - - +
129C LEU* 4.2 33.6 - - + +
132C TYR* 4.2 1.3 - - + -
133C ALA* 3.7 28.9 - - + +
180C GLY* 4.0 8.1 - - - +
183C LEU* 4.2 27.4 - - + -
184C ALA* 3.8 36.1 - - + +
213C PHE* 4.2 9.2 - - + -
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Residues in contact with ASN 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A ARG* 4.9 3.4 + - - -
89A ASN* 4.8 19.1 + - - +
85C GLY 3.0 22.9 + - - +
86C ARG* 3.7 25.8 - - - +
87C LEU 3.3 0.2 - - - -
88C LEU* 1.3 73.5 - - - +
90C ARG* 1.3 61.2 + - - +
92C ALA* 3.4 5.7 + - - +
93C ASP* 3.0 36.9 + - - +
130C ARG* 3.5 27.1 + - - +
133C ALA* 3.4 18.9 - - - +
134C GLY* 5.9 0.2 - - - -
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Residues in contact with ARG 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86C ARG 2.9 14.5 + - - +
87C LEU* 3.1 12.8 + - + +
89C ASN* 1.3 73.6 - - - +
91C LEU* 1.3 65.7 + - - +
93C ASP* 3.0 21.4 + - - +
94C LEU* 2.9 59.5 + - + +
97C ARG* 5.4 0.8 - - - +
210C GLU* 4.6 11.1 + - - +
211C ALA* 3.8 29.6 + - + +
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Residues in contact with LEU 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87C LEU 2.9 12.8 + - - +
88C LEU* 3.5 13.0 - - + +
90C ARG* 1.3 75.6 - - - +
92C ALA* 1.3 63.4 + - - +
94C LEU* 3.2 4.2 + - - +
95C ILE* 3.0 38.2 + - + +
129C LEU* 4.1 22.2 - - + -
179C LEU* 5.0 8.5 - - + -
183C LEU* 5.4 1.6 - - + -
204C VAL* 4.3 4.7 - - + +
207C LEU* 3.8 15.7 - - + +
208C ILE* 3.8 48.7 - - + +
211C ALA* 4.0 7.1 - - + +
213C PHE* 4.2 17.0 - - + -
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Residues in contact with ALA 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88C LEU 3.0 13.8 + - - +
89C ASN 3.6 8.5 - - - +
90C ARG 3.2 0.2 - - - -
91C LEU* 1.3 78.2 - - - +
93C ASP* 1.3 56.5 + - - +
95C ILE* 3.3 1.4 + - - -
96C GLU* 2.9 24.6 + - - +
126C LEU* 3.1 20.4 - - + +
129C LEU* 4.2 19.7 - - + +
130C ARG* 3.7 35.7 - - + +
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Residues in contact with ASP 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A ARG* 4.6 4.3 + - - -
93A ASP* 5.5 2.9 - - - +
89C ASN* 3.0 22.5 + - - +
90C ARG* 3.0 25.2 + - - +
92C ALA* 1.3 75.9 - - - +
94C LEU* 1.3 59.4 + - - +
96C GLU* 3.3 4.4 + - - +
97C ARG* 3.0 26.9 + - - +
130C ARG* 2.9 26.0 + - - +
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Residues in contact with LEU 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90C ARG* 2.9 44.2 + - - +
91C LEU* 3.6 6.7 - - - +
93C ASP* 1.3 76.5 - - - +
95C ILE* 1.3 64.4 + - - +
97C ARG* 3.2 36.9 + - + +
98C ASP* 3.0 27.0 + - - +
207C LEU* 3.7 38.8 - - + +
210C GLU* 3.8 18.4 - - + +
211C ALA* 3.7 26.0 - - + +
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Residues in contact with ILE 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91C LEU* 3.0 28.7 + - + +
92C ALA 3.7 4.3 - - - +
94C LEU* 1.3 75.3 - - - +
96C GLU* 1.3 58.3 + - - +
98C ASP 3.2 2.8 + - - -
99C ARG* 2.9 26.9 + - - +
102C LEU* 3.9 11.8 - - + +
122C LEU* 3.7 24.9 - - + -
125C VAL* 4.1 15.5 - - + -
126C LEU* 4.0 12.8 - - + -
129C LEU* 3.6 31.0 - - + -
172C LEU* 6.2 1.1 - - + -
204C VAL* 4.3 17.5 - - + -
207C LEU* 3.7 21.8 - - + -
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Residues in contact with GLU 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A ARG* 4.6 2.9 + - - -
92C ALA 2.9 16.7 + - - +
93C ASP* 3.6 5.8 - - - +
95C ILE* 1.3 77.5 - - - +
97C ARG* 1.3 63.9 + - - +
99C ARG* 3.2 34.9 + - - +
126C LEU* 3.8 25.1 - - + +
130C ARG* 2.7 35.4 + - - +
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Residues in contact with ARG 97 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90C ARG* 5.4 0.8 - - - +
93C ASP 3.0 14.0 + - - +
94C LEU* 3.4 25.7 + - + +
96C GLU* 1.3 78.5 - - - +
98C ASP* 1.3 89.3 + - - +
99C ARG 3.4 1.9 + - - -
100C THR 5.0 1.0 + - - -
203C TYR* 4.6 2.0 + - - -
207C LEU* 3.6 7.9 - - - +
210C GLU* 2.8 42.0 + - - -
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Residues in contact with ASP 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94C LEU 3.0 9.6 + - - +
95C ILE 3.2 4.7 + - - +
97C ARG* 1.3 113.3 + - - +
99C ARG* 1.3 58.1 + - - +
100C THR 3.4 2.5 - - - -
101C TYR* 3.3 11.3 + - + +
102C LEU* 2.9 32.8 + - + +
203C TYR* 2.7 38.4 + - + -
207C LEU* 3.4 10.4 - - + +
3115C EDO 4.4 11.2 + - - -
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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
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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) + - + + + + + -
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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