Contacts of the helix formed by residues 151 - 166 (chain A) in PDB entry 1DM0
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 THR 151 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120A VAL* 3.6 2.9 - - - -
145A HIS* 4.5 8.1 - - + -
149A SER* 3.2 13.5 + - - -
150A LEU* 1.3 77.0 - - - +
152A GLN* 1.3 70.6 + - - +
153A SER* 3.1 13.0 + - - +
154A VAL* 3.0 33.9 + - + +
155A ALA* 2.9 23.9 + - - +
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Residues in contact with GLN 152 (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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120A VAL* 3.5 28.4 - - + +
121A ALA* 3.8 7.8 - - - +
122A GLY* 5.3 1.2 - - - -
151A THR* 1.3 77.9 + - - +
153A SER* 1.3 58.0 + - - +
155A ALA* 3.4 0.9 - - - +
156A ARG* 3.0 69.0 + - + +
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Residues in contact with SER 153 (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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141A ASP* 2.9 43.4 + - - +
151A THR* 3.1 12.8 + - - +
152A GLN* 1.3 79.7 - - - +
154A VAL* 1.3 64.2 + - - +
155A ALA 3.2 0.7 - - - -
156A ARG* 4.6 5.0 - - - +
157A ALA* 3.5 20.4 + - - +
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Residues in contact with VAL 154 (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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81A PHE* 3.6 22.9 - - + -
108A LEU* 5.0 3.8 - - + -
141A ASP 5.2 2.9 - - - +
142A LEU* 3.2 31.4 - - + -
145A HIS* 3.6 26.9 - - + +
149A SER 4.7 0.7 - - - +
150A LEU* 3.9 13.5 - - + -
151A THR* 3.0 31.1 + - + +
153A SER* 1.3 74.1 - - - +
155A ALA* 1.3 65.8 + - - +
157A ALA* 3.3 2.4 + - - +
158A MET* 3.0 31.2 + - + +
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Residues in contact with ALA 155 (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 LEU* 3.8 17.7 - - - +
120A VAL* 3.9 9.0 - - + -
121A ALA* 3.3 31.4 - - + +
150A LEU* 3.7 11.1 - - + +
151A THR 2.9 17.7 + - - +
152A GLN 3.4 2.7 - - - +
154A VAL* 1.3 78.5 - - - +
156A ARG* 1.4 63.6 + - - +
158A MET* 3.1 2.6 + - - +
159A LEU* 3.0 22.9 + - - +
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Residues in contact with ARG 156 (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 ALA* 2.6 37.3 + - + +
122A GLY* 4.0 5.9 + - - -
123A ILE* 3.6 28.3 - - + +
128A MET* 4.4 0.9 - - - +
138A SER* 5.6 0.2 - - - +
152A GLN* 3.0 44.5 + - - +
153A SER* 4.6 5.2 - - - +
154A VAL 3.6 0.2 - - - -
155A ALA* 1.4 75.1 - - - +
157A ALA* 1.3 56.2 + - - +
159A LEU* 3.6 8.5 - - - +
160A ARG* 2.9 45.4 + - - +
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Residues in contact with ALA 157 (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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138A SER* 3.6 42.0 - - - +
141A ASP* 5.2 1.1 - - + -
142A LEU* 4.0 12.8 - - + -
153A SER 3.5 17.6 + - - +
154A VAL 3.3 4.0 + - - +
155A ALA 3.2 0.2 - - - -
156A ARG* 1.3 76.9 - - - +
158A MET* 1.3 62.3 + - - +
159A LEU 3.4 0.2 - - - -
160A ARG* 3.6 2.2 + - - +
161A PHE* 3.1 33.8 + - - -
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Residues in contact with MET 158 (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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69A LEU* 4.0 17.0 - - + -
78A VAL* 3.6 31.4 - - + -
80A GLY 4.2 12.8 - - - -
81A PHE* 4.0 10.5 - - + -
92A PHE* 3.9 34.5 - - + -
117A LEU* 4.5 9.4 - - + -
142A LEU* 4.0 27.4 - - + -
150A LEU* 6.0 0.4 - - + -
154A VAL* 3.0 25.6 + - + +
155A ALA 3.7 3.1 - - - +
157A ALA* 1.3 75.2 - - - +
159A LEU* 1.3 60.1 + - - +
160A ARG 3.2 0.2 - - - -
161A PHE* 4.3 2.0 - - - +
162A VAL* 2.7 45.1 + - + +
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Residues in contact with LEU 159 (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 TYR* 3.5 33.1 - - + -
117A LEU* 4.0 23.0 - - + +
118A GLN* 4.2 11.4 - - + -
121A ALA* 4.3 10.1 - - + -
123A ILE* 3.5 34.1 - - + +
125A ARG* 4.2 9.2 - - + +
128A MET* 3.2 28.3 - - + -
155A ALA 3.0 12.2 + - - +
156A ARG* 3.6 6.3 - - - +
158A MET* 1.3 78.6 - - - +
160A ARG* 1.3 63.3 + - - +
162A VAL* 4.1 3.2 - - - +
163A THR* 3.0 25.4 + - - +
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Residues in contact with ARG 160 (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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123A ILE* 4.6 7.5 - - - +
128A MET* 4.2 18.5 - - + +
129A GLN* 3.4 29.3 + - - +
130A ILE* 4.3 17.5 - - + +
134A SER* 4.0 24.5 - - - -
135A LEU* 4.6 11.2 - - + +
137A THR* 5.9 1.8 - - - +
138A SER* 3.5 26.2 + - - +
156A ARG* 2.9 42.7 + - - +
157A ALA* 3.6 4.7 + - - +
158A MET 3.2 0.4 - - - -
159A LEU* 1.3 78.6 - - - +
161A PHE* 1.3 61.5 + - + +
163A THR* 3.4 6.2 + - - +
164A VAL* 3.4 26.0 + - - +
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Residues in contact with PHE 161 (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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7A PHE* 4.4 8.3 - + - -
54A VAL* 3.7 19.7 - - + -
57A ILE* 4.7 5.2 - - + -
67A LEU* 3.7 29.2 - - + -
69A LEU* 4.1 28.6 - - + +
135A LEU* 3.9 36.6 - - + -
138A SER* 4.2 8.1 - - - -
139A TYR* 4.0 24.7 - - + -
142A LEU* 4.3 11.2 - - + -
157A ALA 3.1 28.2 + - - +
158A MET* 4.5 3.4 - - - +
160A ARG* 1.3 71.8 - - - +
162A VAL* 1.3 67.6 + - - +
163A THR 3.0 2.0 - - - -
164A VAL* 4.2 9.9 - - + -
165A THR* 3.0 30.9 + - - -
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Residues in contact with VAL 162 (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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69A LEU* 6.2 0.2 - - - -
78A VAL* 3.8 36.8 - - + +
92A PHE* 5.5 2.5 - - + -
114A TYR* 3.3 30.3 - - + +
117A LEU* 5.2 7.4 - - + -
158A MET* 2.7 31.8 + - + +
159A LEU* 4.1 3.1 - - - +
161A PHE* 1.3 77.9 - - - +
163A THR* 1.3 57.5 + - - +
165A THR* 4.7 0.9 - - - -
166A ALA* 3.0 33.8 + - + +
167A GLU* 3.2 7.8 + - + +
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Residues in contact with THR 163 (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 TYR* 4.3 6.8 + - - -
125A ARG* 5.0 4.7 + - - -
128A MET* 4.9 4.3 - - - -
130A ILE* 3.8 23.8 - - + -
159A LEU* 3.0 18.3 + - - +
160A ARG* 3.5 5.2 - - - -
161A PHE 3.0 0.8 - - - -
162A VAL* 1.3 79.6 - - - +
164A VAL* 1.3 60.1 + - + +
167A GLU* 3.2 17.0 - - + +
168A ALA* 3.0 26.9 + - - +
174A ILE* 4.0 6.2 - - + +
190A TYR* 4.6 9.2 - - + -
192A MET* 4.5 27.0 - - + +
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Residues in contact with VAL 164 (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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5A LEU* 4.6 1.0 - - - +
7A PHE* 3.6 28.5 - - + -
13A TYR* 2.6 36.2 + - - +
17A LEU* 4.5 2.3 - - - +
130A ILE* 4.2 15.9 - - + -
135A LEU* 4.9 4.7 - - + -
160A ARG 3.4 17.4 + - - +
161A PHE* 4.0 13.2 - - + +
163A THR* 1.3 77.8 - - + +
165A THR* 1.3 62.3 + - - +
168A ALA* 3.4 6.8 - - - +
174A ILE* 5.5 1.3 - - - -
178A PHE* 3.7 40.4 - - + -
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Residues in contact with THR 165 (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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5A LEU* 3.8 20.5 - - + +
17A LEU* 4.2 5.0 - - + +
52A VAL* 4.9 13.9 - - + +
69A LEU* 3.7 23.0 - - + +
71A VAL* 4.7 16.6 - - + -
78A VAL* 4.9 3.1 - - + -
161A PHE* 3.0 19.8 + - - +
162A VAL* 4.6 1.1 - - - -
164A VAL* 1.3 79.8 - - - +
166A ALA* 1.3 67.4 + - + +
169A LEU* 2.9 38.5 + - + +
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Residues in contact with ALA 166 (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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71A VAL* 5.4 2.0 - - + -
76A LEU* 3.6 30.9 - - + +
78A VAL* 4.3 14.6 - - + -
162A VAL* 3.0 15.0 + - + +
165A THR* 1.3 78.9 - - + +
167A GLU* 1.3 72.0 + - - +
169A LEU* 3.5 8.7 - - + +
170A ARG* 3.0 35.2 + - - +
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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