Contacts of the helix formed by residues 113 - 125 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106D LYS* 5.5 7.2 - - - +
110D ASP 4.7 0.2 + - - -
111D LEU* 3.6 1.8 - - - +
112D SER* 1.3 76.4 + - - +
114D SER* 1.3 58.2 + - - +
115D THR* 3.2 12.4 + - - +
116D GLN* 2.9 42.2 + - + +
117D VAL* 3.0 31.5 + - - +
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Residues in contact with SER 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70C GLU* 2.7 36.9 + - - -
73C LEU* 3.7 23.1 - - - -
74C GLN* 3.7 9.0 + - - +
77C LEU* 6.0 0.2 - - - -
126C THR* 3.7 11.1 - - - +
130C CYS* 3.8 12.6 - - - -
112D SER 3.3 5.6 + - - -
113D ASP* 1.3 70.6 + - - +
115D THR* 1.3 61.2 + - - +
117D VAL* 3.3 0.6 + - - -
118D ASN* 2.8 36.1 + - - -
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Residues in contact with THR 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70C GLU* 3.9 27.8 - - + +
113D ASP* 3.2 9.8 + - - +
114D SER* 1.3 73.6 - - - +
116D GLN* 1.3 62.4 + - - +
118D ASN* 3.4 8.0 + - - +
119D ASN* 2.9 43.2 + - - +
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Residues in contact with GLN 116 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103D ASP* 4.7 22.7 + - - +
106D LYS* 4.6 18.6 - - - +
111D LEU* 4.6 13.3 - - - +
113D ASP* 2.9 34.0 + - - +
115D THR* 1.3 77.9 + - - +
117D VAL* 1.3 60.7 + - - +
119D ASN* 3.5 10.2 + - - +
120D TYR* 3.2 24.9 + - - +
166D LEU* 5.0 7.0 - - + +
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Residues in contact with VAL 117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126C THR* 3.7 16.8 - - + +
129C LEU* 3.9 29.8 - - + -
130C CYS* 4.6 6.5 - - - -
111D LEU* 4.7 15.3 - - + +
113D ASP* 3.0 23.5 + - + +
114D SER 3.7 3.8 - - - +
115D THR 3.2 0.2 - - - -
116D GLN* 1.3 77.5 - - - +
118D ASN* 1.3 64.7 + - - +
120D TYR* 3.1 17.0 + - - +
121D TRP* 3.2 35.4 + - + +
166D LEU* 4.1 16.8 - - + -
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Residues in contact with ASN 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70C GLU* 3.4 21.0 + - - +
118C ASN* 4.8 3.6 - - - +
121C TRP* 5.4 0.2 - - - +
122C ALA* 3.5 25.3 + - - +
126C THR* 2.6 31.1 + - - +
114D SER 2.8 25.9 + - - +
115D THR* 3.8 7.2 - - - +
117D VAL* 1.3 71.8 - - - +
119D ASN* 1.3 60.6 + - - +
121D TRP* 3.4 8.5 + - - +
122D ALA* 3.1 26.7 + - - +
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Residues in contact with ASN 119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68D GLY* 4.8 9.5 - - - +
115D THR* 2.9 30.5 + - - +
116D GLN* 3.7 9.4 - - - +
117D VAL 3.3 0.2 - - - -
118D ASN* 1.3 75.3 - - - +
120D TYR* 1.3 65.8 + - - +
122D ALA* 3.4 8.2 + - - +
123D LEU* 3.2 23.2 + - - +
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Residues in contact with TYR 120 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100D SER* 2.6 34.2 + - - -
101D LEU 3.8 0.3 + - - -
102D GLY* 3.7 24.7 - - - -
116D GLN 3.2 12.5 + - - +
117D VAL 3.1 11.3 + - - +
119D ASN* 1.3 78.3 - - - +
121D TRP* 1.3 75.1 + + - +
123D LEU* 3.5 1.1 + - - -
124D ASN* 3.0 66.3 + - + +
166D LEU* 3.3 47.1 - - + -
167D TYR* 3.3 23.9 + - - -
170D GLY* 4.7 3.9 - - - -
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Residues in contact with TRP 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121C TRP* 3.8 35.2 - - + -
125C LEU* 3.6 30.9 - - + +
126C THR* 3.0 28.0 + - - +
129C LEU* 4.5 7.2 - - + -
177C LEU* 4.7 5.8 - - + -
117D VAL* 3.2 25.6 + - + +
118D ASN* 3.4 7.6 + - - +
120D TYR* 1.3 84.8 - + - +
122D ALA* 1.3 61.4 + - - +
125D LEU* 2.6 47.4 + - + +
126D THR* 3.0 8.6 + - - -
166D LEU* 3.7 31.2 - - + -
169D ALA* 3.9 20.6 - - + -
170D GLY* 3.9 22.4 - - - -
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Residues in contact with ALA 122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118C ASN* 3.4 31.3 + - - +
67D LEU 3.8 4.8 - - - +
68D GLY 3.6 19.3 - - - +
73D LEU* 6.0 0.2 - - - +
118D ASN 3.1 16.1 + - - +
119D ASN* 3.6 9.9 - - - +
120D TYR 3.3 0.2 - - - -
121D TRP* 1.3 75.0 - - - +
123D LEU* 1.3 57.2 + - - +
126D THR* 3.5 3.9 - - - -
127D SER* 3.1 30.1 + - - -
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Residues in contact with LEU 123 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67D LEU* 4.1 18.2 - - + -
68D GLY* 4.0 8.9 - - - +
98D ALA* 5.0 11.8 - - + +
99D GLY* 5.0 3.4 - - - +
100D SER* 3.4 35.7 - - - +
119D ASN 3.2 12.6 + - - +
120D TYR* 3.9 3.1 - - + +
122D ALA* 1.3 79.6 - - - +
124D ASN* 1.3 68.6 + - - +
127D SER* 2.7 23.5 + - - +
128D MET* 4.5 0.5 + - - +
174D ARG* 5.1 1.7 + - - -
804D NAP 3.5 50.5 - - + +
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Residues in contact with ASN 124 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98D ALA 5.5 0.2 - - - -
99D GLY* 3.3 9.5 - - - -
100D SER* 2.9 48.6 + - - +
120D TYR* 3.0 56.6 + - + +
123D LEU* 1.3 83.8 - - - +
125D LEU* 1.3 64.4 + - + +
128D MET* 3.6 1.7 - - - +
167D TYR* 5.8 0.3 - - - -
170D GLY* 5.3 2.7 - - - -
171D LYS* 5.6 2.9 + - - -
174D ARG* 2.8 44.0 + - - +
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Residues in contact with LEU 125 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121C TRP* 3.6 42.0 - - + +
125C LEU* 3.9 10.1 - - + -
121D TRP* 2.6 45.8 + - + +
124D ASN* 1.3 80.8 - - + +
126D THR* 1.3 64.9 + - - +
127D SER 3.4 1.3 - - - -
128D MET* 3.3 8.0 - - - +
129D LEU* 3.0 25.1 + - - +
170D GLY* 3.4 29.2 - - - +
173D ALA* 3.5 21.5 - - + -
174D ARG* 3.9 8.7 - - + +
177D LEU* 4.7 5.2 - - + +
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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