Contacts of the helix formed by residues 131 - 143 (chain A) in PDB entry 1PZO
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 131 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73A LYS* 4.1 0.7 + - - -
105A TYR 3.8 4.7 - - - -
106A SER* 3.3 9.6 - - - -
107A PRO* 4.2 6.1 - - + -
108A VAL* 2.8 32.0 + - + +
109A THR* 2.8 35.4 + - - -
125A ALA* 3.0 27.3 + - + +
126A ALA* 3.9 4.6 + - - -
129A MET 3.1 3.3 - - - -
130A SER* 1.3 75.0 - - - +
132A ASN* 1.3 60.9 + - - +
133A THR 3.2 4.0 + - - -
134A ALA* 2.9 23.2 + - + +
135A ALA* 3.3 20.1 + - - +
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Residues in contact with ASN 132 (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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70A SER* 4.4 1.4 + - - -
73A LYS* 3.0 24.2 + - - +
103A VAL* 3.5 11.0 - - + -
104A GLU* 2.8 40.4 + - - +
105A TYR* 3.0 19.4 + - - +
130A SER 3.2 3.1 + - - +
131A ASP* 1.3 68.8 + - - +
133A THR* 1.3 68.3 + - - +
135A ALA* 3.3 4.8 + - - +
136A ASN* 3.1 23.4 + - - -
166A GLU* 3.1 30.1 + - + +
167A PRO* 4.7 2.8 - - - +
170A ASN* 5.1 2.6 - - - +
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Residues in contact with THR 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A TYR* 4.8 1.3 - - + -
101A ASP* 3.5 26.5 - - + +
102A LEU* 3.3 10.8 - - + -
103A VAL* 2.9 25.7 + - - +
106A SER* 2.5 23.5 + - - -
109A THR* 3.2 22.2 - - - +
131A ASP* 3.2 0.4 + - - -
132A ASN* 1.3 76.0 - - - +
134A ALA* 1.3 56.3 + - - +
136A ASN* 3.1 6.5 + - + +
137A LEU* 2.9 45.8 + - + +
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Residues in contact with ALA 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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109A THR* 3.6 16.5 - - + +
122A LEU* 3.6 35.5 - - + +
125A ALA* 3.9 3.8 - - + -
126A ALA* 4.1 1.8 - - - +
131A ASP* 2.9 30.0 + - + +
133A THR* 1.3 76.4 - - - +
135A ALA* 1.3 57.3 + - - +
137A LEU* 3.1 4.1 + - - +
138A LEU* 2.9 34.2 + - - +
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Residues in contact with ALA 135 (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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72A PHE* 3.9 17.3 - - + -
73A LYS* 3.6 33.2 - - + -
76A LEU* 3.5 16.0 - - + +
126A ALA* 4.4 1.5 - - + +
131A ASP 3.3 4.9 + - - +
132A ASN 3.6 8.3 - - - +
133A THR 3.2 0.4 - - - -
134A ALA* 1.3 80.2 - - - +
136A ASN* 1.3 52.0 + - - +
138A LEU* 3.4 3.2 + - - -
139A LEU* 2.7 38.8 + - - +
166A GLU* 4.4 3.1 - - + -
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Residues in contact with ASN 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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101A ASP 4.9 4.1 + - - +
103A VAL* 3.8 20.8 - - - +
132A ASN 3.1 11.6 + - - -
133A THR* 3.1 11.2 + - + +
135A ALA* 1.3 73.7 - - - +
137A LEU* 1.3 65.1 + - + +
139A LEU* 4.2 7.0 - - - +
140A THR* 3.0 20.6 + - - -
165A TRP* 3.3 29.2 - - + +
166A GLU* 2.9 51.2 + - - +
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Residues in contact with LEU 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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95A ILE* 4.4 13.8 - - + +
96A HIS 4.8 1.1 - - - +
97A TYR* 3.5 52.0 - - + -
101A ASP* 5.0 11.7 - - + -
109A THR* 4.6 1.1 - - + -
122A LEU* 4.1 28.5 - - + -
133A THR* 2.9 34.2 + - + +
134A ALA* 3.6 5.6 - - - +
136A ASN* 1.3 74.3 - - + +
138A LEU* 1.3 63.3 + - - +
140A THR* 3.1 16.1 + - - +
141A THR* 3.2 18.5 + - - +
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Residues in contact with LEU 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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76A LEU* 3.8 15.0 - - + -
77A CYS* 3.8 7.2 - - - -
80A VAL* 3.9 20.0 - - + -
119A VAL* 4.1 16.4 - - + -
122A LEU* 3.7 38.8 - - + +
123A CYS* 3.6 28.7 - - - -
126A ALA* 4.2 9.2 - - + -
134A ALA 2.9 20.3 + - - +
135A ALA 3.7 3.6 - - - +
137A LEU* 1.3 73.7 - - - +
139A LEU* 1.3 66.6 + - - +
141A THR* 2.8 28.4 + - + +
142A ILE* 3.4 9.2 + - - +
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Residues in contact with LEU 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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72A PHE* 4.1 13.7 - - + -
76A LEU* 3.9 21.5 - - + +
135A ALA 2.7 23.3 + - - +
136A ASN* 3.3 8.3 + - - +
138A LEU* 1.3 71.7 - - - +
140A THR* 1.3 58.2 + - - +
142A ILE* 3.3 11.6 + - + +
144A GLY 2.6 55.5 + - - +
145A PRO* 3.7 3.8 - - + -
148A LEU* 4.7 2.9 - - + -
162A LEU* 3.8 28.5 - - + -
164A ARG 4.5 0.4 - - - +
165A TRP* 3.5 41.3 - - + -
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Residues in contact with THR 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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136A ASN 3.0 7.9 + - - -
137A LEU* 3.4 13.5 - - - +
138A LEU 3.1 0.4 - - - -
139A LEU* 1.3 76.5 - - - +
141A THR* 1.3 63.8 + - + +
143A GLY* 3.1 14.2 + - - -
144A GLY 4.6 0.7 - - - +
165A TRP* 3.3 26.0 - - + -
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Residues in contact with THR 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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80A VAL* 4.2 6.4 - - - +
83A ARG* 3.4 23.3 + - - -
89A GLU* 3.8 18.5 + - - +
93A ARG* 3.8 19.4 + - - +
95A ILE* 4.4 18.6 - - + -
119A VAL* 5.2 1.2 - - + +
137A LEU 3.2 17.0 - - - +
138A LEU* 2.8 24.4 + - + +
140A THR* 1.3 75.1 - - - +
142A ILE* 1.3 66.5 + - - +
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Residues in contact with ILE 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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76A LEU* 3.9 16.2 - - + -
79A ALA* 4.1 12.8 - - + -
80A VAL* 3.6 37.2 - - + +
83A ARG* 3.7 29.7 + - - +
138A LEU 3.8 4.9 - - - +
139A LEU* 3.3 17.0 - - + +
141A THR* 1.3 80.8 + - - +
143A GLY* 1.3 57.3 + - - +
144A GLY 4.0 5.6 - - - +
147A GLU* 3.2 19.8 - - - +
148A LEU* 3.8 40.4 - - + +
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Residues in contact with GLY 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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140A THR* 3.1 12.5 + - - -
141A THR 3.4 1.0 + - - -
142A ILE* 1.3 78.5 - - - +
144A GLY* 1.3 63.9 + - - +
146A LYS* 4.6 4.2 + - - +
147A GLU* 3.8 19.5 + - - +
165A TRP* 5.5 0.2 - - - -
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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
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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