Contacts of the helix formed by residues 147 - 160 (chain A) in PDB entry 1D5R
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 LYS 147 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140A LEU* 3.8 6.9 - - - +
145A PHE* 4.3 0.3 - - - +
146A LEU* 1.3 89.0 - - + +
148A ALA* 1.3 68.1 + - - +
149A GLN* 4.5 4.0 - - + +
150A GLU* 2.9 50.0 + - + +
151A ALA 3.3 3.8 + - - -
179A SER* 4.6 1.3 - - - -
183A LYS* 5.8 5.8 - - - +
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Residues in contact with ALA 148 (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 LEU* 4.0 14.4 - - - +
147A LYS* 1.3 71.0 - - - +
149A GLN* 1.3 62.9 + - - +
151A ALA* 3.1 3.6 + - - +
152A LEU* 2.8 31.8 + - - +
175A VAL* 4.2 9.6 - - + +
176A TYR* 3.6 52.9 - - + +
179A SER* 4.1 9.0 + - - -
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Residues in contact with GLN 149 (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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147A LYS* 3.3 4.7 - - + +
148A ALA* 1.3 78.1 - - - +
150A GLU* 1.3 60.1 + - + +
152A LEU* 3.9 5.6 - - - -
153A ASP* 3.0 50.3 + - - +
172A ARG* 4.4 11.3 - - - +
176A TYR* 3.4 26.0 + - + +
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Residues in contact with GLU 150 (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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145A PHE* 3.5 25.4 - - + +
146A LEU* 3.3 25.3 + - - +
147A LYS* 2.9 42.6 + - + +
149A GLN* 1.3 76.4 - - + +
151A ALA* 1.3 63.1 + - - +
153A ASP* 4.0 4.6 - - - +
154A PHE* 3.1 23.6 + - - +
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Residues in contact with ALA 151 (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 CYS* 3.3 39.8 - - + +
139A LEU* 4.3 12.8 - - + +
140A LEU* 4.3 10.8 - - + -
145A PHE* 4.1 13.8 - - + -
147A LYS 3.3 5.7 + - - +
148A ALA 3.1 7.9 + - - +
150A GLU* 1.3 77.5 - - - +
152A LEU* 1.3 65.8 + - + +
154A PHE* 3.3 4.0 + - - +
155A TYR 3.0 19.8 + - - -
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Residues in contact with LEU 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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136A CYS* 3.9 12.8 - - + -
148A ALA 2.8 29.9 + - - +
149A GLN* 4.0 3.8 - - - +
151A ALA* 1.3 78.2 - - - +
153A ASP* 1.3 62.1 + - - +
155A TYR* 3.5 3.8 + - - +
156A GLY* 3.2 18.7 + - - -
166A VAL* 4.9 14.3 + - + -
172A ARG* 3.3 58.2 + - + +
175A VAL* 3.3 35.9 - - + -
176A TYR* 3.7 23.6 - - + -
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Residues in contact with ASP 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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149A GLN* 3.0 38.1 + - - +
150A GLU* 4.0 4.2 - - - +
152A LEU* 1.3 77.0 - - - +
154A PHE* 1.3 65.5 + - - +
156A GLY* 3.4 2.0 + - - +
157A GLU* 3.0 44.4 + - + +
172A ARG* 4.4 7.3 + - - -
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Residues in contact with PHE 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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28A ILE* 4.0 18.4 - - + -
29A TYR* 3.2 46.9 - + - -
139A LEU* 4.1 10.3 - - + -
145A PHE* 3.3 28.0 - + + -
150A GLU 3.1 19.3 + - - +
151A ALA 3.4 4.7 - - - +
153A ASP* 1.3 79.3 - - - +
155A TYR* 1.3 65.2 + - - +
157A GLU* 3.2 6.9 + - + +
158A VAL* 3.0 43.8 + - + +
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Residues in contact with TYR 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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28A ILE* 3.2 39.0 - - + -
34A ALA* 4.2 5.1 - - + +
127A GLY 3.3 18.7 + - - -
128A LYS* 2.9 23.1 + - - -
131A THR* 3.9 4.9 - - - +
132A GLY* 3.3 34.0 + - - -
135A ILE* 4.3 6.3 - - + -
136A CYS* 3.5 22.4 - - - -
139A LEU* 5.5 2.5 - - + -
151A ALA 3.0 4.1 + - - +
152A LEU 3.8 2.2 - - - +
154A PHE* 1.3 83.1 - - - +
156A GLY* 1.3 56.8 + - - +
158A VAL* 4.1 2.4 - - - +
159A ARG* 2.6 59.6 + - + +
165A GLY* 4.1 18.4 - - - -
166A VAL* 4.1 12.8 - - + -
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Residues in contact with GLY 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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152A LEU 3.2 12.3 + - - -
153A ASP* 3.8 3.6 - - - -
154A PHE 3.2 0.2 - - - -
155A TYR* 1.3 79.6 - - - +
157A GLU* 1.3 56.5 + - - +
159A ARG* 4.9 0.2 - - - -
160A THR* 2.5 43.4 + - - +
163A LYS* 3.9 9.8 - - - -
165A GLY* 4.0 21.3 - - - -
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Residues in contact with GLU 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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14A ARG* 2.5 37.6 + - + +
153A ASP* 3.0 32.4 + - + +
154A PHE* 3.8 5.9 + - - +
156A GLY* 1.3 74.7 - - - +
158A VAL* 1.3 59.3 + - + +
160A THR 3.2 2.4 - - - +
163A LYS* 3.8 34.4 - - + +
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Residues in contact with VAL 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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14A ARG* 4.6 2.0 - - - +
15A ARG* 2.8 64.4 - - - +
26A THR* 3.5 1.9 - - + +
27A TYR 3.9 10.8 - - - +
28A ILE* 4.1 17.5 - - + +
154A PHE* 3.0 44.3 + - + +
155A TYR* 4.1 2.5 - - - +
157A GLU* 1.3 80.7 - - + +
159A ARG* 1.3 60.7 + - - +
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Residues in contact with ARG 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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15A ARG 4.2 0.4 - - - -
16A TYR* 3.6 26.9 + - - -
24A ASP* 3.1 32.2 + - - -
25A LEU* 3.7 4.4 - - - +
26A THR* 2.8 41.8 + - - +
28A ILE* 5.0 3.1 - - + -
34A ALA* 3.6 23.6 + - - +
35A MET 4.5 1.4 - - - -
126A ALA 3.1 14.8 + - - -
127A GLY* 2.9 30.4 + - - +
128A LYS* 5.7 0.9 - - - -
155A TYR* 2.6 57.7 + - + +
158A VAL* 1.3 76.1 - - - +
160A THR* 1.3 68.4 + - + +
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Residues in contact with THR 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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14A ARG 2.8 20.6 + - - -
15A ARG 3.5 6.7 - - - -
16A TYR* 3.5 13.2 - - + -
128A LYS* 5.5 6.5 - - + -
156A GLY 2.5 29.2 + - - +
157A GLU* 3.2 5.2 - - - +
159A ARG* 1.3 86.7 - - + +
161A ARG* 1.3 61.8 + - - +
162A ASP* 3.5 11.6 + - - +
163A LYS* 3.3 2.8 + - - +
164A LYS 3.0 40.1 + - - +
165A GLY* 4.4 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