Contacts of the helix formed by residues 156 - 166 (chain B) in PDB entry 1H5Y
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 ALA 156 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132B ILE* 4.2 12.8 - - + +
134B ALA* 4.0 24.0 - - + -
141B TYR* 2.8 26.9 + - + +
143B VAL* 3.7 16.6 - - + -
154B LEU 3.6 2.4 + - - -
155B ASP* 1.3 71.2 + - - +
157B VAL* 1.3 57.9 + - - +
159B TRP* 3.5 1.8 + - - +
160B ALA* 3.0 28.8 + - - +
173B LEU* 5.2 0.2 - - + -
189B LEU* 4.5 8.3 - - + -
193B VAL* 4.4 7.0 - - + +
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Residues in contact with VAL 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B TYR* 5.7 5.6 - - + -
155B ASP* 2.7 21.1 + - - +
156B ALA* 1.3 73.9 - - + +
158B LYS* 1.3 62.4 + - + +
160B ALA* 3.3 6.8 + - - +
161B LYS* 3.2 33.9 + - - +
189B LEU* 6.1 0.2 - - + -
192B ARG* 3.9 37.0 - - + +
193B VAL* 4.4 8.7 - - + -
196B SER* 2.7 31.6 + - - +
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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
----------------------------------------------------------
155B ASP* 3.1 35.0 + - + +
157B VAL* 1.3 76.1 - - + +
159B TRP* 1.3 65.5 + - - +
161B LYS* 3.4 11.0 + - - +
162B GLU* 3.0 24.4 + - - +
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Residues in contact with TRP 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B ASN* 5.5 0.4 + - - +
109B ALA* 3.5 25.1 - - + -
110B VAL* 3.7 37.1 - - + +
113B PRO* 4.0 18.6 - - + -
116B VAL* 5.2 0.2 - - + -
130B VAL* 4.2 4.8 - - + +
131B ALA 5.2 1.8 + - - -
132B ILE* 3.7 32.2 - - + +
143B VAL* 4.0 24.2 - - + +
154B LEU* 4.3 20.2 - - + +
155B ASP 2.9 14.7 + - - +
156B ALA 3.8 3.4 - - - +
158B LYS* 1.3 77.0 - - - +
160B ALA* 1.3 58.4 + - - +
162B GLU* 3.1 36.0 + - + +
163B VAL* 2.8 53.1 + - + +
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Residues in contact with ALA 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B ILE* 4.0 8.9 - - + +
156B ALA 3.0 19.1 + - - +
157B VAL* 3.5 7.4 - - - +
159B TRP* 1.3 76.9 - - - +
161B LYS* 1.3 63.9 + - - +
163B VAL* 3.3 4.8 + - - +
164B GLU* 3.0 23.7 + - - +
171B ILE* 3.5 27.9 - - + +
193B VAL* 4.0 14.6 - - + -
196B SER* 4.9 1.6 - - - -
197B VAL* 3.6 11.3 - - + +
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Residues in contact with LYS 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157B VAL* 3.2 20.9 + - - +
158B LYS* 3.6 10.5 - - - +
160B ALA* 1.3 77.0 - - - +
162B GLU* 1.3 58.3 + - - +
164B GLU* 3.4 6.3 + - - +
165B GLU* 3.0 28.8 + - - +
196B SER* 3.2 46.2 + - - +
197B VAL* 3.7 8.0 - - - +
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Residues in contact with GLU 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B PRO* 3.8 17.0 - - - +
154B LEU* 6.1 1.0 - - - +
158B LYS 3.0 15.8 + - - +
159B TRP* 3.1 34.9 + - + +
161B LYS* 1.3 77.1 - - - +
163B VAL* 1.3 58.4 + - - +
165B GLU* 3.2 7.9 + - + +
166B LEU* 3.0 42.6 + - + +
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Residues in contact with VAL 163 (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 VAL* 3.8 7.9 - - + +
130B VAL* 3.8 33.0 - - + -
132B ILE* 4.8 1.8 - - + -
159B TRP* 2.8 61.7 + - + +
160B ALA* 3.4 15.7 - - - +
162B GLU* 1.3 70.3 - - - +
164B GLU* 1.3 65.4 + - - +
166B LEU* 3.3 10.0 + - + +
167B GLY 3.1 6.1 + - - -
168B ALA* 2.8 36.7 + - + +
171B ILE* 4.5 10.5 - - + -
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Residues in contact with GLU 164 (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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111A ARG* 5.2 0.5 - - - -
160B ALA 3.0 13.7 + - - +
161B LYS* 3.4 10.2 - - - +
163B VAL* 1.3 73.9 - - - +
165B GLU* 1.3 62.4 + - - +
167B GLY* 2.8 21.8 + - - -
168B ALA 3.9 10.1 + - - +
196B SER 4.2 2.8 - - - +
197B VAL* 3.5 24.7 - - + +
198B ARG* 2.8 34.1 + - - +
199B ILE* 3.1 30.1 + - + +
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Residues in contact with GLU 165 (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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161B LYS 3.0 17.9 + - - +
162B GLU* 3.7 7.2 - - + +
164B GLU* 1.3 77.5 + - - +
166B LEU* 1.3 62.8 + - + +
167B GLY* 3.4 1.2 + - - -
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Residues in contact with LEU 166 (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 PRO* 3.5 38.4 - - + +
114B GLN* 3.8 24.9 - - - +
116B VAL* 4.1 11.7 - - + -
117B ALA* 3.2 32.8 + - + +
120B ALA* 4.4 1.0 - - - +
162B GLU* 3.0 38.4 + - + +
163B VAL* 3.6 15.7 - - + +
164B GLU 3.1 0.4 - - - -
165B GLU* 1.3 81.4 - - + +
167B GLY* 1.3 54.9 + - - +
168B ALA 3.8 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
------------------------------------------------------------
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