Contacts of the helix formed by residues 133 - 146 (chain B) in PDB entry 1ZN8
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 GLY 133 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130B LEU* 3.6 23.6 - - - -
131B ALA 3.2 2.4 - - - -
132B THR* 1.3 78.5 - - - +
134B GLY* 1.3 58.2 + - - +
135B THR 3.4 2.2 - - - -
136B MET* 3.5 2.7 + - - -
137B ASN* 2.9 32.4 + - - +
164B GLY* 4.2 7.9 - - - -
167B LYS* 4.0 6.5 - - - -
168B LEU* 4.0 3.1 - - - +
1032B AMP 2.9 12.3 + - - -
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Residues in contact with GLY 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B TYR* 3.7 19.1 - - - +
102B SER 4.8 4.7 - - - -
132B THR* 3.3 10.9 + - - -
133B GLY* 1.3 77.2 - - - +
135B THR* 1.3 56.7 + - - +
137B ASN* 3.4 2.1 + - - +
138B ALA* 3.0 29.8 + - - +
167B LYS* 3.8 19.2 - - - +
1032B AMP 3.3 6.7 + - - -
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Residues in contact with THR 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B LEU* 3.7 22.9 - - + -
65B ASP 5.5 4.3 - - - +
101B TYR* 3.6 30.8 + - - +
103B LEU* 4.6 2.8 - - - +
110B LEU* 3.8 12.9 - - + +
127B ASP* 4.3 8.3 - - - +
134B GLY* 1.3 68.7 - - - +
136B MET* 1.3 67.2 + - - +
138B ALA* 3.1 5.3 + - - +
139B ALA* 3.0 21.5 + - - +
1032B AMP 2.6 44.5 + - - +
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Residues in contact with MET 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B LEU* 4.1 16.6 - - + -
125B VAL* 4.8 3.1 - - + +
126B VAL 4.5 2.0 - - - -
127B ASP* 3.4 29.2 - - + +
129B LEU 4.9 3.8 - - - +
130B LEU* 3.5 26.7 - - + -
133B GLY* 3.5 4.7 + - - +
134B GLY 3.5 0.2 - - - -
135B THR* 1.3 79.3 - - - +
137B ASN* 1.3 58.2 + - - +
139B ALA* 3.2 3.7 + - - +
140B CYS* 2.8 32.6 + - - -
153B CYS* 3.7 28.0 - - + -
154B VAL 3.4 29.8 - - - +
155B SER* 4.1 8.7 - - - -
168B LEU* 3.8 17.0 - - + -
173B PHE* 4.0 5.2 - - - -
1032B AMP 5.4 0.6 + - - +
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Residues in contact with ASN 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B GLY 2.9 19.8 + - - +
134B GLY* 3.7 5.4 - - - +
136B MET* 1.3 76.2 - - - +
138B ALA* 1.3 57.2 + - - +
140B CYS* 3.2 9.1 + - - +
141B GLU* 3.0 28.6 + - - +
167B LYS* 3.7 41.4 + - + +
168B LEU* 3.5 15.3 + - + +
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Residues in contact with ALA 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B ALA* 4.2 11.9 - - + +
100B SER 5.1 0.4 - - - +
101B TYR* 3.7 31.4 - - + -
110B LEU* 4.1 9.0 - - + -
134B GLY 3.0 18.2 + - - +
135B THR 3.1 4.2 + - - +
137B ASN* 1.3 75.4 + - - +
139B ALA* 1.3 64.7 + - - +
141B GLU* 3.4 12.3 - - - +
142B LEU* 3.1 27.2 + - - +
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Residues in contact with ALA 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B LEU* 3.5 32.3 - - + -
86B ILE* 3.7 14.8 - - + -
110B LEU* 4.1 5.5 - - + +
125B VAL* 4.2 10.5 - - + -
135B THR 3.0 11.2 + - - +
136B MET 3.5 8.7 - - - +
138B ALA* 1.3 76.5 - - - +
140B CYS* 1.3 60.9 + - - +
142B LEU* 3.2 7.1 + - - +
143B LEU* 3.0 28.3 + - - +
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Residues in contact with CYS 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125B VAL* 4.9 2.2 - - - -
136B MET 2.8 21.9 + - - +
137B ASN* 3.2 13.7 + - - +
139B ALA* 1.3 71.7 - - - +
141B GLU* 1.3 56.9 + - - +
143B LEU* 3.4 2.0 + - - +
144B GLY* 2.9 27.4 + - - -
150B VAL* 4.0 29.5 - - + +
153B CYS* 3.5 28.7 - - - -
168B LEU* 4.5 6.7 - - - -
171B VAL* 4.3 17.0 - - + -
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Residues in contact with GLU 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B TRP 4.6 0.2 - - - +
99B ALA* 3.4 28.8 - - + +
100B SER 4.8 5.5 - - - +
137B ASN* 3.0 13.3 + - - +
138B ALA* 3.4 12.8 - - - +
140B CYS* 1.3 75.5 - - - +
142B LEU* 1.3 61.6 - - - +
144B GLY* 3.4 2.4 + - - -
145B ARG* 3.1 52.8 + - + +
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Residues in contact with LEU 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86B ILE* 4.1 12.1 - - + -
97B LEU* 3.5 42.0 - - + +
98B TRP 3.6 16.8 - - - +
99B ALA* 3.9 7.4 - - + +
110B LEU* 3.8 35.7 - - + -
111B GLU* 3.9 12.8 - - - +
112B ILE* 4.2 10.4 - - + +
138B ALA 3.1 14.2 + - - +
139B ALA* 3.2 5.1 + - - +
141B GLU* 1.3 77.9 - - - +
143B LEU* 1.3 68.4 + - + +
145B ARG* 3.2 18.2 + - - +
146B LEU* 3.4 15.6 + - - +
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Residues in contact with LEU 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B ALA* 4.4 2.9 - - + -
86B ILE* 3.8 14.4 - - + -
112B ILE* 3.6 21.5 - - + -
117B LEU* 3.4 30.5 - - + -
123B VAL* 4.4 12.1 - - + -
125B VAL* 3.3 34.1 - - + -
139B ALA 3.0 18.5 + - - +
140B CYS 3.9 0.2 - - - +
142B LEU* 1.3 75.9 - - - +
144B GLY* 1.3 63.6 + - - +
146B LEU* 3.0 14.5 + - + +
148B ALA* 3.1 26.0 + - + +
150B VAL* 3.8 22.0 - - + -
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Residues in contact with GLY 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140B CYS 2.9 16.7 + - - -
141B GLU 3.4 2.7 + - - -
142B LEU 3.2 0.2 - - - -
143B LEU* 1.3 75.6 - - - +
145B ARG* 1.3 58.4 + - - +
147B GLN* 3.0 21.3 + - - +
148B ALA 3.9 11.6 + - - -
150B VAL* 5.0 1.1 - - - +
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Residues in contact with ARG 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B LEU* 3.5 35.2 - - + +
98B TRP 3.0 27.1 + - - -
141B GLU* 3.1 40.4 + - + +
142B LEU* 3.6 15.8 - - - +
143B LEU 3.1 0.4 - - - -
144B GLY* 1.3 73.6 - - - +
146B LEU* 1.3 57.0 + - - +
147B GLN* 3.1 13.1 + - - +
1030B CL 3.5 24.4 - - - +
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Residues in contact with LEU 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B LEU* 3.6 22.9 - - + -
112B ILE* 3.9 31.4 - - + -
113B GLN 3.9 11.4 - - - +
114B LYS* 3.6 29.2 - - + +
117B LEU* 4.0 32.4 - - + +
118B GLU 4.1 1.6 - - - -
119B PRO* 3.7 19.8 - - - +
142B LEU 3.4 10.0 + - - +
143B LEU* 3.0 10.1 + - + +
145B ARG* 1.3 75.8 - - - +
147B GLN* 1.3 71.0 + - - +
148B ALA* 3.4 5.1 + - + +
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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
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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