Contacts of the helix formed by residues 150 - 162 (chain B) in PDB entry 1D2G
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 GLN 150 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145B ASP* 3.6 19.7 - - - +
148B GLY 5.1 1.1 - - - +
149B ASP* 1.3 68.4 - - - +
151B SER* 1.3 55.8 + - - -
152B GLU 3.3 3.1 - - - +
153B HIS* 3.1 32.9 + - + +
154B ARG* 2.9 47.1 + - - +
243B TYR* 3.0 30.4 + - - +
245B HIS* 4.2 3.1 + - - -
249B SER* 4.5 12.0 + - - -
253B LEU* 3.5 21.6 - - + +
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Residues in contact with SER 151 (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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147B LYS* 3.7 18.6 + - - +
149B ASP* 2.5 42.5 + - - -
150B GLN* 1.3 69.6 - - - +
152B GLU* 1.3 62.7 + - - +
154B ARG* 3.1 15.0 + - - +
155B LEU* 2.8 29.4 + - - +
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Residues in contact with GLU 152 (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 LEU* 3.6 23.6 - - + +
143B LEU* 3.9 11.8 - - + +
144B PRO 4.0 7.1 - - - +
145B ASP* 4.1 3.7 - - - +
146B SER* 3.2 39.6 + - - -
147B LYS* 3.8 14.9 + - + +
149B ASP 4.3 0.6 + - - -
150B GLN 3.3 0.6 - - - -
151B SER* 1.3 83.4 + - - +
153B HIS* 1.3 69.4 + - + +
155B LEU* 3.3 8.7 + - + -
156B ALA* 3.0 27.2 + - - +
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Residues in contact with HIS 153 (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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140B PHE* 3.6 15.2 - + + -
143B LEU* 3.0 35.5 - - + +
144B PRO 3.0 23.0 + - - -
145B ASP* 3.9 7.0 - - + +
150B GLN* 3.1 46.5 + - + +
152B GLU* 1.3 78.5 - - - +
154B ARG* 1.3 56.4 + - - +
157B LEU* 3.1 34.8 + - - +
243B TYR* 3.5 25.8 - + - -
245B HIS* 3.6 17.2 + + - -
253B LEU* 4.1 11.4 - - + -
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Residues in contact with ARG 154 (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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149B ASP* 4.8 5.3 - - - +
150B GLN* 2.9 46.2 + - - +
151B SER* 3.1 11.8 + - - +
153B HIS* 1.3 75.8 - - - +
155B LEU* 1.3 60.1 + - - +
157B LEU* 3.8 6.7 - - - +
158B LYS* 2.9 31.4 + - - +
252B GLU* 5.1 6.7 + - - -
253B LEU* 3.6 24.0 - - + +
256B GLU* 3.3 39.7 + - - +
257B ALA* 5.4 0.7 - - - +
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Residues in contact with LEU 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B LEU* 3.7 37.5 - - + +
151B SER 2.8 19.0 + - - +
152B GLU* 3.3 8.0 + - + +
154B ARG* 1.3 73.8 - - - +
156B ALA* 1.3 58.9 + - - +
158B LYS* 3.4 19.4 + - - +
159B ASN* 3.0 50.5 + - - +
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Residues in contact with ALA 156 (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 TRP* 3.5 34.3 - - + -
118B LEU* 3.7 9.2 - - + -
140B PHE* 4.0 8.7 - - + -
143B LEU* 4.0 12.3 - - + -
152B GLU 3.0 16.9 + - - +
153B HIS 3.9 3.1 - - - +
155B LEU* 1.3 75.7 - - - +
157B LEU* 1.3 59.2 + - - +
159B ASN* 3.2 1.9 + - - +
160B ILE* 2.9 37.5 + - - +
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Residues in contact with LEU 157 (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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140B PHE* 3.5 36.6 - - + -
153B HIS 3.1 22.2 + - - +
154B ARG* 3.8 6.1 - - - +
156B ALA* 1.3 77.3 - - - +
158B LYS* 1.3 57.0 + - - +
160B ILE* 3.6 7.4 + - + +
161B ALA* 3.1 29.5 + - - +
170B LEU* 5.7 4.0 - - + +
172B ILE* 4.2 16.6 - - + -
250B PHE* 4.9 7.2 - - + -
253B LEU* 3.8 39.9 - - + +
254B VAL* 4.3 21.8 - - + +
257B ALA* 3.5 12.3 - - + +
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Residues in contact with LYS 158 (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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154B ARG 2.9 18.1 + - - +
155B LEU* 3.6 18.5 - - + +
157B LEU* 1.3 75.8 - - - +
159B ASN* 1.3 78.5 + - - +
161B ALA* 3.4 2.9 + - - +
162B SER* 3.0 25.3 + - - -
257B ALA* 4.1 19.5 - - + +
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Residues in contact with ASN 159 (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 TRP 2.6 29.8 - - - +
118B LEU* 3.3 19.2 - - - +
119B THR* 3.6 1.7 + - - -
120B LEU* 3.8 16.3 + - + -
121B ASP* 4.2 21.3 - - - +
155B LEU* 3.0 31.4 + - - +
156B ALA 3.5 2.0 - - - +
158B LYS* 1.3 86.5 - - - +
160B ILE* 1.3 65.7 + - - +
162B SER* 2.9 24.0 + - - -
163B MET* 3.5 11.8 - - - +
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Residues in contact with ILE 160 (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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63B VAL* 4.3 11.2 - - + -
117B TRP* 3.8 41.5 - - + +
120B LEU* 4.1 13.2 - - + -
133B VAL* 3.9 13.7 - - + +
135B CYS* 4.9 1.3 - - + -
140B PHE* 4.3 18.4 - - + -
156B ALA 2.9 21.3 + - - +
157B LEU* 3.9 9.2 - - + +
159B ASN* 1.3 74.8 - - + +
161B ALA* 1.3 65.2 + - - +
163B MET* 3.1 19.1 + - - +
164B VAL* 4.0 5.5 - - - +
170B LEU* 3.7 28.3 - - + -
172B ILE* 4.9 8.5 - - + -
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Residues in contact with ALA 161 (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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157B LEU 3.1 19.5 + - - +
158B LYS 3.6 4.9 - - - +
159B ASN 3.3 0.2 - - - -
160B ILE* 1.3 77.5 - - - +
162B SER* 1.3 57.7 + - - +
163B MET 3.0 5.4 + - - -
164B VAL* 3.1 21.7 + - - +
170B LEU* 4.9 2.7 - - + +
257B ALA* 3.9 20.0 - - + +
258B PHE* 3.8 33.8 - - + -
290B LYS* 3.3 12.9 + - - +
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Residues in contact with SER 162 (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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121B ASP* 4.8 5.4 - - - +
126B ALA* 4.7 6.4 - - - +
129B GLY* 5.4 1.2 - - - -
158B LYS* 3.0 18.4 + - - -
159B ASN* 2.9 16.6 + - - -
160B ILE 3.2 0.2 - - - -
161B ALA* 1.3 75.9 - - - +
163B MET* 1.3 75.1 + - - +
164B VAL 3.3 5.2 - - - +
290B LYS* 3.9 10.6 + - - +
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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