Contacts of the helix formed by residues 133 - 146 (chain A) in PDB entry 1ZN7
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130A LEU* 3.7 23.1 - - - -
131A ALA 3.2 3.6 + - - -
132A THR* 1.3 77.8 - - - +
134A GLY* 1.3 57.9 + - - +
135A THR 3.3 2.9 - - - -
136A MET* 4.0 2.1 - - - +
137A ASN* 2.9 33.8 + - - +
164A GLY* 4.2 8.1 - - - -
167A LYS* 4.2 5.1 - - - +
168A LEU* 4.2 2.7 - - - +
502A PRP 3.0 10.0 + - - -
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Residues in contact with GLY 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A TYR* 3.6 20.6 - - - +
102A SER 5.0 4.9 - - - -
132A THR* 3.2 14.7 + - - -
133A GLY* 1.3 78.4 - - - +
135A THR* 1.3 61.5 + - - +
137A ASN* 3.8 1.4 - - - +
138A ALA* 3.1 23.9 + - - +
167A LYS* 4.3 15.0 - - - +
502A PRP 3.6 1.9 + - - -
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Residues in contact with THR 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A LEU* 3.9 12.8 - - + -
65A ASP 5.4 3.1 - - - +
88A LYS* 6.3 0.9 - - - -
101A TYR* 3.5 26.6 + - - +
103A LEU* 4.5 2.1 - - - +
110A LEU* 3.5 20.8 - - + +
127A ASP* 3.9 8.7 - - - +
133A GLY 3.3 0.2 - - - -
134A GLY* 1.3 74.8 - - - +
136A MET* 1.3 66.1 + - - +
138A ALA* 3.3 2.7 + - - -
139A ALA* 3.1 18.7 + - - +
502A PRP 2.6 58.1 + - - +
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Residues in contact with MET 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A LEU* 4.0 17.9 - - + -
125A VAL* 4.7 3.6 - - + +
126A VAL 4.7 1.3 - - - -
127A ASP* 3.5 26.0 - - + +
129A LEU 4.8 2.5 - - - +
130A LEU* 3.1 33.4 - - + -
133A GLY* 3.5 2.5 + - - +
134A GLY 3.4 0.4 - - - -
135A THR* 1.3 82.0 - - - +
137A ASN* 1.3 56.8 + - - +
139A ALA* 3.3 3.5 + - - +
140A CYS* 3.0 31.9 + - - -
153A CYS* 3.9 19.5 - - + -
154A VAL 3.3 30.7 - - - +
155A SER* 3.8 15.5 - - - -
168A LEU* 3.9 15.5 - - + -
173A PHE* 3.9 9.4 - - + -
502A PRP 5.4 0.4 + - - -
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Residues in contact with ASN 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A GLY 2.9 20.0 + - - +
134A GLY 3.8 3.8 - - - +
136A MET* 1.3 76.0 - - - +
138A ALA* 1.3 59.2 + - - +
140A CYS* 3.3 7.8 + - - +
141A GLU* 3.0 29.1 + - - +
167A LYS* 3.7 44.2 + - + -
168A LEU* 3.6 15.3 + - + +
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Residues in contact with ALA 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A ALA* 4.1 15.9 - - + +
100A SER 4.7 1.6 - - - +
101A TYR* 3.8 28.0 - - + -
110A LEU* 4.1 8.5 - - + -
134A GLY 3.1 18.6 + - - +
135A THR 3.6 4.9 - - - +
137A ASN* 1.3 77.9 + - - +
139A ALA* 1.3 61.0 + - - +
141A GLU* 3.3 11.1 + - - +
142A LEU* 3.0 28.5 + - - +
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Residues in contact with ALA 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A LEU* 3.6 33.7 - - + -
86A ILE* 3.8 12.2 - - + +
110A LEU* 4.0 7.5 - - + +
125A VAL* 4.3 8.1 - - + -
135A THR 3.1 12.1 + - - +
136A MET 3.3 8.3 + - - +
138A ALA* 1.3 77.1 - - - +
140A CYS* 1.3 61.7 + - - +
142A LEU* 3.3 6.3 + - - +
143A LEU* 3.0 30.7 + - - +
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Residues in contact with CYS 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A VAL* 4.9 1.6 - - - -
136A MET 3.0 18.4 + - - -
137A ASN* 3.6 12.6 - - - +
139A ALA* 1.3 77.4 - - - +
141A GLU* 1.3 56.9 + - - +
143A LEU* 3.4 1.6 + - - +
144A GLY* 2.9 26.7 + - - -
150A VAL* 4.0 28.8 - - + +
153A CYS* 3.5 29.4 - - - -
168A LEU* 4.4 9.9 - - - -
171A VAL* 4.3 16.2 - - + -
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Residues in contact with GLU 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A ALA* 3.6 21.5 - - - +
100A SER 4.7 6.8 + - - +
137A ASN* 3.0 15.6 + - - +
138A ALA* 3.3 10.3 + - - +
140A CYS* 1.3 74.5 - - - +
142A LEU* 1.3 58.4 + - - +
144A GLY* 3.4 1.8 + - - -
145A ARG* 3.0 61.3 + - - +
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Residues in contact with LEU 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A ILE* 4.1 11.0 - - + -
97A LEU* 3.7 21.3 - - + +
98A TRP* 3.6 30.7 - - - +
99A ALA* 3.9 7.4 - - + -
110A LEU* 3.7 39.0 - - + +
111A GLU* 3.7 12.1 - - - +
112A ILE* 3.8 18.3 - - + +
138A ALA 3.0 17.1 + - - +
139A ALA* 3.6 6.5 - - - +
140A CYS 3.3 0.2 - - - -
141A GLU* 1.3 76.2 - - - +
143A LEU* 1.3 62.0 + - + +
145A ARG* 3.2 21.0 + - - +
146A LEU* 3.2 19.3 + - - +
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Residues in contact with LEU 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A ALA* 4.5 2.7 - - + -
84A VAL* 5.3 0.4 - - + -
86A ILE* 4.0 12.8 - - + -
112A ILE* 3.8 20.0 - - + -
117A LEU* 3.2 32.5 - - + -
123A VAL* 4.2 14.4 - - + -
125A VAL* 3.5 32.8 - - + -
139A ALA 3.0 16.8 + - - +
140A CYS 3.8 0.2 - - - +
142A LEU* 1.3 72.4 - - - +
144A GLY* 1.3 64.4 + - - +
146A LEU* 3.1 10.0 + - - +
148A ALA* 3.0 32.3 + - + +
150A VAL* 3.7 24.5 - - + -
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Residues in contact with GLY 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A CYS 2.9 17.3 + - - -
141A GLU* 3.8 2.2 - - - -
143A LEU* 1.3 75.4 - - - +
145A ARG* 1.3 57.8 + - - +
147A GLN* 2.9 21.5 + - - +
148A ALA 4.0 11.0 - - - -
150A VAL* 5.0 1.7 - - - +
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Residues in contact with ARG 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A LEU* 3.7 38.4 - - + +
98A TRP 2.9 29.3 + - - +
141A GLU* 3.0 48.4 + - + +
142A LEU* 3.6 13.7 - - - +
143A LEU 3.1 0.4 - - - -
144A GLY* 1.3 78.5 - - - +
146A LEU* 1.4 60.1 + - - +
147A GLN* 3.3 6.2 + - - +
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Residues in contact with LEU 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A LEU* 3.8 24.5 - - + -
112A ILE* 3.9 26.7 - - + -
113A GLN 3.7 18.2 - - - +
114A LYS* 3.4 20.6 - - + +
117A LEU* 4.0 36.6 - - + +
118A GLU 4.2 1.9 - - - -
119A PRO* 3.7 17.5 - - - +
142A LEU 3.2 10.8 + - - +
143A LEU* 3.1 11.0 + - - +
145A ARG* 1.4 77.6 - - - +
147A GLN* 1.3 71.5 + - - +
148A ALA 3.3 1.7 + - - +
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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