Contacts of the helix formed by residues 120 - 136 (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 VAL 120 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116C ILE* 2.7 41.0 + - + +
119C LEU* 1.3 80.0 - - + +
121C ASP* 1.3 71.9 + - - +
123C ASP* 3.2 3.2 + - - +
124C MET* 2.9 53.6 + - + +
296C PHE* 4.1 21.1 - - + -
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Residues in contact with ASP 121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106C GLU* 4.3 11.7 - - + +
112C LYS* 2.7 45.7 + - - +
116C ILE* 3.2 19.2 + - - +
117C SER* 3.5 10.8 - - - +
120C VAL* 1.3 77.1 - - - +
122C LEU* 1.3 63.6 + - + +
124C MET* 3.3 9.8 + - - +
125C VAL* 2.9 33.8 + - + +
170C PHE* 3.4 20.0 - - - +
172C LEU* 5.6 0.7 - - + -
173C LEU* 4.7 9.0 - - + +
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Residues in contact with LEU 122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95C ILE* 3.7 29.6 - - + -
99C ARG* 3.9 30.5 - - + -
102C LEU* 3.8 18.6 - - + -
103C ALA* 3.7 26.5 - - + +
106C GLU* 5.2 0.7 - - + -
117C SER* 2.9 30.2 + - - +
118C TYR 3.8 8.3 - - - +
121C ASP* 1.3 73.6 - - + +
123C ASP* 1.3 65.6 + - - +
125C VAL* 3.3 7.6 + - + +
126C LEU* 3.0 29.5 + - + +
172C LEU* 3.9 23.1 - - + -
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Residues in contact with ASP 123 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99C ARG* 3.7 20.0 + - - +
118C TYR 3.8 3.6 + - - -
119C LEU 3.1 26.4 - - - +
120C VAL* 3.2 2.7 + - - +
122C LEU* 1.3 77.3 - - - +
124C MET* 1.3 64.3 + - - +
126C LEU* 3.3 7.2 + - - +
127C LYS* 3.0 61.0 + - - +
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Residues in contact with MET 124 (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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120C VAL* 2.9 47.8 + - + +
121C ASP* 3.7 7.6 - - - +
123C ASP* 1.3 80.0 - - - +
125C VAL* 1.3 60.0 + - - +
127C LYS* 3.8 8.8 - - + +
128C CYS* 2.9 31.4 + - - +
170C PHE* 5.6 4.0 - - + -
173C LEU* 3.5 36.4 - - + +
177C TRP* 6.2 0.7 - - - -
296C PHE* 5.6 3.6 - - + -
459C PHE* 5.4 19.7 - - - +
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Residues in contact with VAL 125 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95C ILE* 4.1 35.2 - - + -
121C ASP 2.9 19.1 + - - +
122C LEU* 3.3 12.5 + - + +
124C MET* 1.3 75.6 - - - +
126C LEU* 1.3 63.8 + - - +
128C CYS* 3.3 1.7 + - - +
129C LEU* 3.0 28.3 + - + +
172C LEU* 3.5 47.1 - - + +
173C LEU* 3.5 11.9 - - - +
176C ALA* 4.0 14.3 - - + +
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Residues in contact with LEU 126 (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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92C ALA* 3.1 37.7 - - + +
95C ILE* 4.0 15.3 - - + -
96C GLU* 3.8 44.2 - - + +
99C ARG* 4.4 18.8 - - + +
122C LEU* 3.0 18.2 + - + +
123C ASP* 3.5 10.1 - - - +
125C VAL* 1.3 77.9 - - + +
127C LYS* 1.3 58.8 + - + +
128C CYS 3.4 0.2 + - - -
129C LEU* 3.4 1.4 + - - +
130C ARG* 3.0 51.0 + - - +
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Residues in contact with LYS 127 (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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80A ASP* 5.4 2.0 + - - -
82A SER* 5.3 7.2 - - - +
123C ASP* 3.0 51.2 + - - +
124C MET* 4.0 9.0 - - + +
126C LEU* 1.3 78.4 - - + +
128C CYS* 1.3 56.1 + - - +
130C ARG* 4.1 6.4 - - - +
131C TYR* 3.0 30.5 + - - +
461C ALA* 3.9 8.7 - - + +
147D ASP* 3.6 29.7 + - - +
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Residues in contact with CYS 128 (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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124C MET 2.9 20.0 + - - +
125C VAL 3.7 4.0 - - - +
126C LEU 3.2 0.2 - - - -
127C LYS* 1.3 76.1 - - - +
129C LEU* 1.3 67.2 + - - +
131C TYR* 3.2 3.1 + - - +
132C TYR* 3.0 41.1 + - - -
173C LEU* 4.7 0.4 - - + -
176C ALA* 3.4 36.6 - - + -
177C TRP* 3.8 24.2 - - + +
180C GLY* 5.1 0.2 - - - -
461C ALA* 3.9 13.0 - - + +
477C LEU* 4.4 3.4 - - + -
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Residues in contact with LEU 129 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88C LEU* 4.2 27.3 - - + +
91C LEU* 4.1 20.2 - - + -
92C ALA* 4.2 17.7 - - + +
95C ILE* 3.6 30.5 - - + -
125C VAL* 3.0 24.4 + - + +
126C LEU* 4.1 2.9 - - - +
128C CYS* 1.3 76.4 - - - +
130C ARG* 1.3 57.3 + - - +
132C TYR* 3.3 4.7 + - - +
133C ALA* 2.8 29.7 + - - +
176C ALA* 4.1 20.4 - - + +
179C LEU* 4.7 5.6 - - + -
180C GLY* 4.2 19.7 - - - +
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Residues in contact with ARG 130 (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* 3.4 49.0 - - - +
138A LYS* 4.9 0.7 + - - -
89C ASN* 3.5 23.9 + - - +
92C ALA* 3.7 28.7 + - + +
93C ASP* 2.9 27.5 + - - +
96C GLU* 2.7 31.1 + - - -
126C LEU* 3.0 40.4 + - - +
127C LYS* 4.1 4.9 - - - +
129C LEU* 1.3 73.6 - - - +
131C TYR* 1.3 66.3 + - - +
133C ALA* 3.5 3.3 - - - +
134C GLY* 3.4 14.2 + - - -
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Residues in contact with TYR 131 (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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137A ASP* 3.4 32.1 + - - +
138A LYS* 3.0 44.6 + - - +
140A HIS* 4.7 3.8 + - - -
127C LYS 3.0 20.5 + - - +
128C CYS 3.4 4.3 - - - +
130C ARG* 1.3 77.7 - - - +
132C TYR* 1.3 79.6 + + - +
134C GLY 3.2 4.0 + - - -
135C TRP* 2.9 36.1 + + - -
461C ALA* 3.4 28.7 - - + -
462C GLN* 3.4 35.6 + - + +
478C GLY* 3.4 22.3 - - - -
479C GLU 3.7 1.7 + - - -
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Residues in contact with TYR 132 (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* 4.2 2.9 - - + -
128C CYS* 3.0 41.3 + - - +
129C LEU 4.0 2.0 - - - +
131C TYR* 1.3 89.0 - + - +
133C ALA* 1.3 66.6 + - - +
134C GLY 3.1 2.0 - - - -
135C TRP* 3.0 19.4 + + - +
136C ALA 3.3 7.4 + - - -
177C TRP 5.2 0.7 - - - -
180C GLY* 3.5 24.9 - - - +
181C PRO* 3.6 36.5 - - + +
184C ALA* 3.4 10.9 - - + +
477C LEU* 2.9 47.7 + - + -
478C GLY 3.1 11.3 + - - -
481C GLY* 4.1 4.7 - - - -
482C LEU* 3.6 27.4 - - + -
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Residues in contact with ALA 133 (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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85C GLY* 3.4 19.2 - - - +
88C LEU* 3.7 19.0 - - + +
89C ASN* 3.4 34.5 - - - +
129C LEU 2.8 17.7 + - - +
130C ARG 3.5 7.0 - - - +
131C TYR 3.3 0.2 - - - -
132C TYR* 1.3 77.4 - - - +
134C GLY* 1.3 62.0 + - - +
135C TRP 3.3 0.2 + - - -
136C ALA* 3.3 17.7 + - - +
137C ASP* 5.0 1.4 + - - +
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Residues in contact with GLY 134 (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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130A ARG 6.1 0.2 - - - -
134A GLY* 3.9 22.2 - - - -
138A LYS* 3.8 7.4 - - - -
89C ASN* 5.2 0.6 - - - +
130C ARG 3.4 5.2 + - - -
131C TYR 3.2 9.1 + - - -
132C TYR 3.1 0.8 - - - -
133C ALA* 1.3 80.5 - - - +
135C TRP* 1.3 58.9 + - - +
136C ALA 3.3 0.4 + - - -
137C ASP* 3.7 0.9 - - - +
138C LYS* 2.8 36.1 + - - +
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Residues in contact with TRP 135 (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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135A TRP* 4.9 7.9 - + - -
138A LYS* 3.3 42.8 - - + +
140A HIS* 4.3 4.0 - + - -
131C TYR* 2.9 44.0 + + - -
132C TYR* 3.0 21.0 + + + +
134C GLY* 1.3 75.4 - - - +
136C ALA* 1.3 67.9 + - - +
137C ASP 3.1 2.6 + - - -
138C LYS* 3.1 45.0 + - + -
139C TYR* 3.7 17.1 + + - +
184C ALA* 4.7 2.2 - - + -
185C THR* 6.1 0.9 - - - +
479C GLU* 3.4 50.3 - - + +
482C LEU* 3.6 30.4 - - + +
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Residues in contact with ALA 136 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B PRO* 5.3 1.0 - - - +
81C ALA* 3.3 24.5 - - - +
82C SER* 5.1 0.9 - - - -
84C ARG* 3.4 22.2 + - + -
85C GLY* 3.6 14.8 - - - +
132C TYR 3.3 3.8 + - - +
133C ALA* 3.3 15.6 + - - +
134C GLY 3.3 1.0 - - - -
135C TRP* 1.3 77.9 - - - +
137C ASP* 1.3 59.0 + - - +
138C LYS 3.8 0.2 + - - -
139C TYR* 4.8 4.2 + - - +
184C ALA* 3.4 26.2 - - - +
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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