Contacts of the helix formed by residues 112 - 123 (chain B) in PDB entry 1DIZ
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 112 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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77B LYS* 4.5 8.4 + - - +
110B CYS* 3.5 6.4 - - - +
111B VAL* 1.3 89.5 - - + +
113B ALA* 1.3 63.7 + - - +
114B PHE* 3.2 12.7 + - - +
115B GLU* 2.8 37.7 + - + +
116B GLN* 3.0 20.1 + - - +
155B PHE* 5.4 0.7 - - - -
196B MET* 3.0 33.1 - - - +
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Residues in contact with ALA 113 (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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110B CYS* 3.9 11.3 - - - -
112B ASP* 1.3 71.3 + - - +
114B PHE* 1.3 64.8 + - - +
116B GLN* 3.3 2.4 + - - -
117B GLY* 3.0 17.8 + - - -
194B LEU* 4.5 0.6 - - - +
195B PRO 4.1 0.4 - - - +
196B MET* 3.5 48.8 + - + +
223B PHE* 3.1 29.1 - - + -
227B GLY 4.1 7.9 - - - +
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Residues in contact with PHE 114 (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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112B ASP* 3.2 17.2 + - - +
113B ALA* 1.3 78.2 - - - +
115B GLU* 1.3 65.7 + - + +
117B GLY* 3.2 1.9 + - - -
118B VAL* 3.1 30.5 + - + +
155B PHE* 4.8 0.4 - + - -
156B PRO 3.5 23.8 - - - -
157B THR 3.9 0.7 - - - -
158B PRO* 3.3 43.1 - - + -
161B LEU* 3.4 26.9 - - + -
182B LEU 4.8 0.4 - - - -
185B LEU* 3.7 26.0 - - + -
186B ALA* 3.6 22.4 - - + -
189B ALA* 4.0 19.5 - - + -
194B LEU* 4.1 8.5 - - + -
196B MET* 3.5 8.5 - - + +
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Residues in contact with GLU 115 (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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27B VAL* 5.5 0.2 - - - +
37B ARG* 2.9 42.7 + - - -
110B CYS* 6.5 0.4 - - - -
111B VAL* 4.1 12.6 + - - +
112B ASP* 2.8 26.9 + - - +
114B PHE* 1.3 77.9 - - - +
116B GLN* 1.3 62.4 + - - +
118B VAL* 3.4 4.9 - - - +
119B ARG* 3.2 43.9 + - - +
155B PHE* 3.2 49.5 - - + +
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Residues in contact with GLN 116 (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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110B CYS* 3.6 26.8 - - + +
112B ASP 3.0 11.9 + - - +
113B ALA 3.7 7.9 - - - +
114B PHE 3.2 0.2 - - - -
115B GLU* 1.3 75.8 - - - +
117B GLY* 1.3 60.4 + - - +
119B ARG* 3.3 20.4 + - - +
120B ALA* 2.8 29.8 + - - +
222B TYR* 4.3 9.5 - - - -
223B PHE* 4.2 7.0 - - + -
226B ARG* 3.7 44.5 + - + +
227B GLY* 3.6 28.5 - - - +
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Residues in contact with GLY 117 (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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113B ALA 3.0 10.7 + - - -
114B PHE 3.2 3.7 + - - -
116B GLN* 1.3 72.5 - - - +
118B VAL* 1.3 66.6 + - - +
120B ALA* 3.0 5.2 + - - +
121B ILE* 2.9 26.9 + - - +
185B LEU* 3.7 19.5 - - - -
219B THR* 6.4 0.2 - - - -
223B PHE* 3.5 22.1 - - - -
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Residues in contact with VAL 118 (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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114B PHE* 3.1 42.9 + - + +
115B GLU 3.4 7.6 - - - +
117B GLY* 1.3 76.9 - - - +
119B ARG* 1.3 63.7 + - + +
121B ILE* 3.1 4.2 + - - +
122B LEU* 3.0 42.1 + - + +
135B THR* 5.2 0.2 - - + -
138B VAL* 5.1 5.4 - - + -
155B PHE* 3.7 26.9 - - + -
161B LEU* 3.9 13.0 - - + -
182B LEU* 3.9 20.8 - - + +
185B LEU* 3.6 3.7 - - + +
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Residues in contact with ARG 119 (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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22B ARG* 3.2 31.1 + - - +
24B VAL* 3.3 17.1 - - - +
27B VAL* 5.8 1.2 - - - +
28B GLU* 2.6 35.6 + - - -
37B ARG* 4.7 1.6 - - - +
115B GLU* 3.2 38.4 + - - +
116B GLN* 3.5 30.5 - - - +
118B VAL* 1.3 81.4 - - - +
120B ALA* 1.3 56.6 + - - +
122B LEU* 3.4 6.1 + - - +
123B GLY* 2.9 27.0 + - - -
131B ALA* 5.6 0.5 - - - +
135B THR* 4.4 20.8 + - + +
155B PHE* 4.7 3.9 - - + -
222B TYR* 5.3 2.8 - - + -
226B ARG* 5.0 9.1 - - - +
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Residues in contact with ALA 120 (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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116B GLN* 2.8 19.4 + - - +
117B GLY* 3.0 13.0 + - - +
119B ARG* 1.3 72.4 - - - +
121B ILE* 1.3 62.3 + - - +
123B GLY* 3.3 5.7 + - - -
124B GLN* 3.8 0.9 - - - +
218B TRP* 3.2 24.8 - - + -
219B THR* 4.0 24.8 - - + +
222B TYR* 4.1 28.7 - - + -
223B PHE* 4.6 8.1 - - + -
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Residues in contact with ILE 121 (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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117B GLY 2.9 15.7 + - - +
118B VAL 3.4 7.2 - - - +
120B ALA* 1.3 73.1 - - - +
122B LEU* 1.3 58.8 + - - +
123B GLY 2.9 9.1 + - - -
124B GLN* 3.1 35.7 + - - +
178B ARG* 3.6 34.0 - - + +
181B ALA* 3.7 31.4 - - + +
182B LEU* 3.4 29.2 - - + -
185B LEU* 4.4 12.8 - - + -
214B GLY 5.0 0.2 - - - +
215B ILE* 4.5 13.2 - - + -
219B THR* 4.4 13.2 - - + -
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Residues in contact with LEU 122 (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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118B VAL* 3.0 36.3 + - + +
119B ARG 3.6 3.6 - - - +
121B ILE* 1.3 75.1 - - - +
123B GLY* 1.3 58.7 + - - +
124B GLN 3.4 1.9 - - - +
126B VAL* 3.9 8.0 - - - +
131B ALA* 3.3 20.3 - - - +
134B LEU* 4.0 26.7 - - + +
135B THR* 3.1 46.2 - - - +
138B VAL* 4.1 8.7 - - + -
174B MET* 3.7 33.4 - - + -
178B ARG* 4.8 6.7 - - + +
182B LEU* 3.9 12.3 - - + -
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Residues in contact with GLY 123 (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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119B ARG 2.9 16.5 + - - -
120B ALA 3.3 4.9 + - - -
121B ILE 2.9 1.2 - - - -
122B LEU* 1.3 78.1 - - - +
124B GLN* 1.3 67.6 + - - +
126B VAL 3.6 6.9 - - - +
131B ALA* 4.0 11.8 - - - +
218B TRP* 4.0 10.1 - - - -
222B TYR* 6.1 1.1 - - - -
8C NRI 3.4 22.4 - - - -
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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