Contacts of the helix formed by residues 150 - 163 (chain A) in PDB entry 1D2H
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145A ASP* 3.7 6.3 - - - +
148A GLY 5.1 0.4 - - - +
149A ASP* 1.3 77.5 - - - +
151A SER* 1.3 63.7 + - - +
152A GLU* 3.3 2.5 - - - -
153A HIS* 3.2 22.0 + - + +
154A ARG* 3.2 41.3 + - - +
243A TYR* 2.8 37.9 + - - +
245A HIS* 4.9 0.2 + - - -
249A SER* 4.3 21.1 + - - -
253A LEU* 4.7 16.2 - - + +
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Residues in contact with SER 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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147A LYS* 3.5 21.1 + - - +
149A ASP* 2.9 32.0 + - - -
150A GLN* 1.3 76.6 - - - +
152A GLU* 1.3 74.2 + - - +
154A ARG* 2.8 36.0 - - - +
155A LEU* 3.3 4.5 + - - +
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Residues in contact with GLU 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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118A LEU* 3.7 30.3 - - + +
143A LEU* 4.3 8.1 - - + +
144A PRO 4.2 9.6 - - - +
145A ASP* 5.1 2.0 - - - -
146A SER* 2.9 36.9 + - - +
147A LYS* 3.6 20.4 + - + +
149A ASP 5.4 1.8 - - - +
150A GLN 3.3 0.8 - - - -
151A SER* 1.3 87.9 + - - +
153A HIS* 1.3 72.9 + - - +
154A ARG 2.8 1.7 + - - -
155A LEU* 3.0 18.5 + - - +
156A ALA* 3.1 12.3 + - - +
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Residues in contact with HIS 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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140A PHE* 3.8 8.8 - + + -
143A LEU* 2.9 36.2 + - + +
144A PRO 3.8 17.0 - - - -
145A ASP* 3.8 8.3 - - + -
150A GLN* 3.2 22.3 + - + +
152A GLU* 1.3 76.0 - - - +
154A ARG* 1.3 63.4 + - - +
156A ALA* 3.5 8.7 - - - +
157A LEU* 3.0 24.9 + - - +
243A TYR* 3.1 31.7 - + - -
245A HIS* 2.9 30.0 + + - -
253A LEU* 4.0 17.5 - - + -
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Residues in contact with ARG 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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149A ASP* 5.5 0.8 + - - +
150A GLN* 3.2 40.2 + - - +
151A SER* 2.8 20.5 + - - +
152A GLU 2.8 1.2 + - - -
153A HIS* 1.3 76.0 - - - +
155A LEU* 1.3 57.1 + - + +
157A LEU* 3.6 2.5 - - - +
158A LYS* 2.6 44.2 + - + +
252A GLU* 5.7 0.4 + - - -
253A LEU* 4.4 18.3 - - - +
256A GLU* 2.9 36.9 + - - -
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Residues in contact with LEU 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 TRP 4.6 0.2 - - - -
118A LEU* 4.7 22.2 - - + +
151A SER 3.3 3.7 + - - +
152A GLU* 3.0 12.5 + - - +
154A ARG* 1.3 76.0 - - + +
156A ALA* 1.3 54.9 + - - +
158A LYS* 3.6 34.1 - - + +
159A ASN* 2.6 54.0 + - - +
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Residues in contact with ALA 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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117A TRP* 3.9 17.6 + - + +
118A LEU* 4.1 3.2 - - + +
140A PHE* 3.4 14.8 - - + -
143A LEU* 3.3 33.9 - - + -
152A GLU 3.1 7.1 + - - +
153A HIS 3.5 6.7 - - - +
154A ARG 3.1 0.2 + - - -
155A LEU* 1.3 83.2 - - - +
157A LEU* 1.3 59.7 + - - +
159A ASN* 3.5 2.9 - - - +
160A ILE* 2.7 30.9 + - - +
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Residues in contact with LEU 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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140A PHE* 3.4 30.3 - - + -
153A HIS 3.0 13.4 + - - +
154A ARG* 3.7 2.9 - - - +
156A ALA* 1.3 76.4 - - - +
158A LYS* 1.3 66.2 + - - +
160A ILE* 2.9 18.7 + - + +
161A ALA 3.0 11.6 + - - -
170A LEU* 5.8 1.6 - - + -
172A ILE* 3.2 34.3 - - + -
250A PHE* 3.9 15.0 - - + -
253A LEU* 4.1 26.5 - - + +
254A VAL* 4.2 23.1 - - + +
257A ALA* 3.7 14.7 - - + +
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Residues in contact with LYS 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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154A ARG* 2.6 25.6 + - + +
155A LEU* 3.3 34.2 - - + +
157A LEU* 1.3 74.5 - - - +
159A ASN* 1.3 72.3 + - - +
161A ALA* 3.6 4.0 + - - +
162A SER* 3.5 17.3 + - - -
257A ALA* 3.7 21.7 - - + +
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Residues in contact with ASN 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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117A TRP 3.2 20.9 - - - +
118A LEU 4.2 6.9 - - - +
119A THR* 4.2 1.9 + - - -
120A LEU* 4.0 13.5 - - + +
121A ASP* 4.2 27.2 + - - +
155A LEU* 2.6 37.2 + - - +
156A ALA 3.5 3.8 - - - +
158A LYS* 1.3 84.6 - - - +
160A ILE* 1.3 65.1 + - - +
162A SER* 3.3 21.2 + - - -
163A MET* 3.6 10.6 + - - +
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Residues in contact with ILE 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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63A VAL* 4.2 14.4 - - + -
117A TRP* 3.8 23.3 - - + -
120A LEU* 3.9 18.4 - - + -
133A VAL* 3.9 9.7 - - + +
135A CYS* 5.4 1.8 - - + -
140A PHE* 4.1 14.4 - - + -
156A ALA 2.7 37.7 + - - +
157A LEU* 2.9 18.6 + - + +
159A ASN* 1.3 73.1 - - - +
161A ALA* 1.3 62.5 + - - +
163A MET* 3.0 19.8 + - - +
164A VAL* 3.9 4.3 - - - +
170A LEU* 3.8 33.9 - - + -
172A ILE* 4.8 9.0 - - + -
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Residues in contact with ALA 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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157A LEU 3.0 10.3 + - - +
158A LYS 3.8 8.7 - - - +
160A ILE* 1.3 73.5 - - - +
162A SER* 1.3 53.8 + - - +
163A MET 2.7 4.2 + - - -
164A VAL* 2.6 39.7 + - - +
170A LEU* 4.9 0.6 - - + +
257A ALA* 4.0 19.1 - - + +
258A PHE* 3.3 40.8 - - + -
290A LYS* 3.8 6.0 + - - +
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Residues in contact with SER 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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121A ASP* 6.0 2.5 - - - +
126A ALA* 5.3 1.4 - - - +
129A GLY* 4.7 6.1 - - - -
158A LYS 3.5 9.5 + - - -
159A ASN* 3.3 18.2 + - - -
161A ALA* 1.3 78.0 - - - +
163A MET* 1.3 61.9 + - - +
164A VAL 3.0 7.1 + - - +
290A LYS* 4.0 15.7 + - - +
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Residues in contact with MET 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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61A LEU* 3.0 29.2 - - + -
120A LEU* 3.5 37.7 - - + +
121A ASP* 4.5 5.8 - - - -
124A VAL* 2.8 44.9 - - + +
126A ALA* 4.1 9.9 - - + +
129A GLY* 4.4 1.1 - - - -
130A PHE* 3.0 33.5 + - - -
133A VAL* 3.1 25.6 - - + +
159A ASN 3.8 4.3 - - - +
160A ILE 3.0 11.8 + - - +
161A ALA 2.7 5.5 + - - -
162A SER* 1.3 78.9 - - - +
164A VAL* 1.3 54.9 + - - -
165A ARG 4.0 0.2 - - - -
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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