Contacts of the helix formed by residues 113 - 125 (chain A) in PDB entry 1Z6Z
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 113 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106A LYS* 6.2 1.1 - - - +
110A ASP 4.7 1.0 + - - +
111A LEU* 3.5 2.2 - - - +
112A SER* 1.3 76.9 + - - +
114A SER* 1.3 58.2 + - - +
115A THR* 3.2 13.3 + - - +
116A GLN* 2.9 41.2 + - + +
117A VAL* 3.0 32.0 + - + +
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Residues in contact with SER 114 (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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112A SER 3.3 5.6 + - - -
113A ASP* 1.3 69.3 + - - +
115A THR* 1.3 61.4 + - - +
117A VAL* 3.3 1.0 + - - -
118A ASN* 2.8 35.7 + - - -
70B GLU* 2.6 37.3 + - - -
73B LEU* 3.6 25.4 - - - -
74B GLN* 3.7 9.6 + - - +
126B THR* 3.7 10.4 - - - +
130B CYS* 3.9 11.7 - - - -
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Residues in contact with THR 115 (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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113A ASP* 3.2 10.3 + - - +
114A SER* 1.3 75.5 - - - +
116A GLN* 1.3 60.7 + - - +
118A ASN* 3.4 7.0 + - - +
119A ASN* 2.9 43.1 + - - +
70B GLU* 3.9 28.5 - - + +
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Residues in contact with GLN 116 (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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103A ASP* 4.7 19.4 + - - +
106A LYS* 4.2 21.9 + - - +
111A LEU* 4.6 16.3 - - - +
113A ASP* 2.9 33.8 + - - +
115A THR* 1.3 78.1 + - - +
117A VAL* 1.3 60.6 + - - +
119A ASN* 3.6 10.3 + - + +
120A TYR* 3.1 24.4 + - - +
166A LEU* 4.9 6.2 - - - +
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Residues in contact with VAL 117 (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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111A LEU* 4.6 15.7 - - + +
113A ASP 3.0 23.2 + - - +
114A SER 3.7 4.0 - - - +
115A THR 3.2 0.2 - - - -
116A GLN* 1.3 78.2 - - - +
118A ASN* 1.3 64.0 + - - +
120A TYR* 3.1 17.0 + - - +
121A TRP* 3.2 41.0 + - + +
166A LEU* 4.1 14.8 - - + -
126B THR* 3.6 17.0 - - + +
129B LEU* 3.9 27.6 - - + -
130B CYS* 4.6 7.0 - - - -
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Residues in contact with ASN 118 (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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114A SER 2.8 25.2 + - - +
115A THR* 3.8 6.8 - - - +
117A VAL* 1.3 73.1 - - - +
119A ASN* 1.3 60.1 + - - +
121A TRP* 3.3 9.5 + - - +
122A ALA* 3.0 28.2 + - - +
70B GLU* 3.4 20.6 + - - +
118B ASN* 4.9 3.5 - - - +
122B ALA* 3.5 24.6 + - - +
126B THR* 2.7 31.9 + - - +
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Residues in contact with ASN 119 (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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68A GLY* 4.9 9.9 - - - +
115A THR* 2.9 34.3 + - - +
116A GLN* 3.7 8.7 - - - +
118A ASN* 1.3 76.1 - - - +
120A TYR* 1.3 66.4 + - - +
122A ALA* 3.4 9.1 + - - +
123A LEU* 3.2 23.6 + - - +
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Residues in contact with TYR 120 (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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100A SER* 2.6 34.6 + - - -
101A LEU 3.8 0.3 + - - -
102A GLY* 3.7 24.9 - - - -
116A GLN 3.1 14.1 + - - +
117A VAL 3.1 10.6 + - - +
119A ASN* 1.3 77.5 - - - +
121A TRP* 1.3 79.0 + + - +
123A LEU* 5.1 1.1 - - - -
124A ASN* 3.0 62.2 + - + +
166A LEU* 3.3 49.4 - - + -
167A TYR* 3.4 22.5 + - - -
170A GLY* 4.8 3.2 - - - -
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Residues in contact with TRP 121 (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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117A VAL* 3.2 26.3 + - + +
118A ASN* 3.8 9.0 - - - +
120A TYR* 1.3 84.9 - + - +
122A ALA* 1.3 61.2 + - - +
125A LEU* 2.8 47.3 + - + +
126A THR* 3.0 10.0 + - - -
166A LEU* 3.7 41.3 - - + -
169A ALA* 3.9 20.2 - - + -
170A GLY* 4.0 12.8 - - - -
118B ASN* 5.4 0.2 - - - +
121B TRP* 3.8 34.1 - - + -
125B LEU* 3.7 30.9 - - + +
126B THR* 2.9 28.3 + - - -
129B LEU* 4.4 7.4 - - + -
177B LEU* 4.7 5.2 - - + -
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Residues in contact with ALA 122 (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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67A LEU 3.7 5.5 - - - +
68A GLY 3.7 18.6 - - - +
73A LEU* 6.0 0.3 - - - +
118A ASN 3.0 17.5 + - - +
119A ASN* 3.6 10.1 - - - +
120A TYR 3.3 0.2 - - - -
121A TRP* 1.3 76.7 - - - +
123A LEU* 1.3 56.6 + - - +
126A THR* 3.5 4.0 - - - -
127A SER* 3.1 29.6 + - - -
118B ASN* 3.6 30.0 + - - +
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Residues in contact with LEU 123 (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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67A LEU* 4.0 19.1 - - + -
68A GLY* 4.0 8.9 - - - +
98A ALA* 5.0 11.8 - - + +
99A GLY* 5.1 3.4 - - - +
100A SER* 3.4 35.7 - - - +
119A ASN 3.2 12.4 + - - +
120A TYR* 4.0 0.9 - - - +
122A ALA* 1.3 80.1 - - - +
124A ASN* 1.3 70.7 + - - +
125A LEU 3.7 0.2 + - - -
127A SER* 2.6 24.2 + - - +
128A MET 4.5 0.2 + - - -
174A ARG* 5.0 1.7 + - - -
801A NAP 3.5 50.5 - - + +
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Residues in contact with ASN 124 (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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98A ALA 4.7 1.1 - - - +
99A GLY* 3.3 10.0 - - - -
100A SER* 2.9 47.9 + - - +
120A TYR* 3.0 53.9 + - + +
123A LEU* 1.3 84.4 - - - +
125A LEU* 1.3 64.0 + - + +
128A MET* 3.7 1.4 - - - +
167A TYR* 6.0 0.2 - - - -
170A GLY* 5.4 2.9 - - - -
171A LYS* 5.6 2.3 + - - -
174A ARG* 2.8 44.9 + - - +
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Residues in contact with LEU 125 (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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121A TRP* 2.8 44.0 + - + +
124A ASN* 1.3 80.5 - - + +
126A THR* 1.3 65.0 + - - +
127A SER 3.4 1.3 - - - -
128A MET* 3.3 8.4 - - - +
129A LEU* 3.0 24.9 + - - +
170A GLY* 3.4 30.5 - - - +
173A ALA* 3.5 20.6 - - + -
174A ARG* 3.8 7.9 - - + +
177A LEU* 4.6 5.6 - - + +
121B TRP* 3.6 43.1 - - + +
125B LEU* 3.9 10.1 - - + -
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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