Contacts of the helix formed by residues 151 - 171 (chain A) in PDB entry 4H3K
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 SER 151 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108A LEU* 5.3 3.3 - - - +
149A VAL* 4.1 5.3 + - - +
150A ILE* 1.3 77.4 - - - +
152A GLU* 1.3 60.7 + - - +
153A LEU* 3.8 9.7 + - - +
154A GLN* 3.0 26.4 + - - +
155A GLU* 3.0 26.0 + - - +
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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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151A SER* 1.3 74.1 - - - +
153A LEU* 1.3 56.2 - - - +
155A GLU* 3.4 21.2 + - - +
156A ALA* 2.9 28.4 + - - +
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Residues in contact with LEU 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A LEU* 3.6 31.5 - - + +
151A SER* 3.9 8.7 - - - +
152A GLU* 1.3 76.0 - - - +
154A GLN* 1.3 60.5 + - - +
156A ALA* 3.2 12.3 + - + +
157A CYS* 2.8 28.2 + - - +
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Residues in contact with GLN 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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105A GLU* 5.3 0.5 - - - +
108A LEU* 3.7 12.5 - - + +
143A TRP* 3.4 41.8 + - + -
144A MET* 3.5 22.9 - - - +
147A SER* 3.0 29.1 + - - -
149A VAL 3.8 15.4 - - - +
150A ILE* 3.8 13.1 - - + +
151A SER* 3.0 23.9 + - - +
153A LEU* 1.3 72.9 - - - +
155A GLU* 1.3 65.5 + - - +
157A CYS* 3.2 2.1 + - - +
158A TRP* 3.0 22.7 + - - +
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Residues in contact with GLU 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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144A MET* 4.6 2.5 - - - -
150A ILE* 3.7 21.6 - - + +
151A SER 3.0 15.4 + - - +
152A GLU* 3.5 30.9 + - - +
153A LEU 3.3 0.2 - - - -
154A GLN* 1.3 75.2 - - - +
156A ALA* 1.3 62.7 + - - +
158A TRP* 3.2 4.7 + - - +
159A ASP* 3.0 28.1 + - - +
222A TYR* 3.2 41.9 + - + +
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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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152A GLU 2.9 18.2 + - - +
153A LEU* 3.2 14.3 + - + +
155A GLU* 1.3 75.6 - - - +
157A CYS* 1.3 63.2 + - - +
159A ASP* 3.2 13.7 + - - +
160A MET* 3.0 27.4 + - - +
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Residues in contact with CYS 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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107A LEU* 3.7 51.1 - - - -
108A LEU* 3.7 16.8 - - + +
111A ILE* 4.2 8.7 - - + -
143A TRP* 4.0 13.0 - - + -
153A LEU* 2.8 17.0 + - - +
154A GLN* 3.2 10.1 + - - +
156A ALA* 1.3 72.3 - - - +
158A TRP* 1.3 61.4 + - - +
160A MET* 3.1 8.7 + - - +
161A VAL* 3.0 25.6 + - - +
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Residues in contact with TRP 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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137A TYR* 3.6 37.7 - + - -
140A ALA* 3.9 5.6 - - + -
141A LEU* 3.7 45.1 - - + -
143A TRP* 6.3 0.2 - - - -
144A MET* 3.5 42.7 - - + -
154A GLN 3.0 7.3 + - - -
155A GLU 3.7 5.4 - - - +
157A CYS* 1.3 74.6 - - - +
159A ASP* 1.3 61.7 + - - +
161A VAL* 3.1 25.5 + - + -
162A SER* 2.8 41.7 + - - -
222A TYR* 3.8 25.5 - + - -
223A ILE* 4.7 7.9 - - + +
228A LEU* 4.7 10.0 - - + +
231A GLU* 6.2 0.2 - - - -
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Residues in contact with ASP 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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155A GLU* 3.0 20.8 + - - +
156A ALA* 3.4 14.8 - - - +
158A TRP* 1.3 78.4 - - - +
160A MET* 1.3 60.0 + - - +
162A SER* 3.5 5.5 + - - -
163A ALA* 2.9 31.6 + - - +
222A TYR* 3.4 17.5 + - - -
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Residues in contact with MET 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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111A ILE* 3.9 32.3 - - + +
112A ALA* 5.3 13.0 - - + -
115A ASN* 4.5 16.3 + - + +
156A ALA* 3.0 14.6 + - - +
157A CYS* 3.2 10.3 - - - +
159A ASP* 1.3 76.3 - - - +
161A VAL* 1.3 56.6 + - - +
163A ALA* 3.3 5.3 + - - +
164A MET* 2.8 35.2 + - - +
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Residues in contact with VAL 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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107A LEU* 3.7 29.8 - - + -
111A ILE* 3.8 19.7 - - + -
133A MET* 4.0 11.5 - - + +
136A LEU 5.6 0.2 - - - -
137A TYR* 3.8 18.8 - - + -
140A ALA* 4.1 10.5 - - + -
157A CYS* 3.0 19.7 + - - +
158A TRP* 3.5 33.0 - - + +
160A MET* 1.3 74.6 - - - +
162A SER* 1.3 60.1 + - - +
164A MET* 3.2 3.9 + - - +
165A ALA* 2.8 28.2 + - - +
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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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137A TYR* 4.7 5.3 - - - -
158A TRP* 2.8 40.1 + - - -
159A ASP* 3.8 5.8 - - - -
161A VAL* 1.3 76.6 - - - +
163A ALA* 1.3 56.2 + - - +
165A ALA* 3.3 9.4 + - - +
166A GLY* 2.9 23.9 + - - -
231A GLU* 4.1 15.6 + - - -
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Residues in contact with ALA 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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115A ASN* 5.3 0.2 - - - -
159A ASP 2.9 19.5 + - - +
160A MET* 3.9 5.8 - - - +
162A SER* 1.3 73.4 - - - +
164A MET* 1.3 60.0 + - - +
166A GLY* 3.3 2.5 + - - +
167A ASP* 2.9 35.6 + - - +
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Residues in contact with MET 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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111A ILE* 4.2 11.7 - - - -
114A LEU* 3.6 30.7 - - + +
115A ASN* 3.7 27.7 - - - +
118A LEU* 3.4 36.6 - - + -
129A ALA* 4.8 1.3 - - + +
133A MET* 3.3 44.4 - - + +
160A MET 2.8 20.7 + - - +
161A VAL* 3.5 5.4 - - - +
163A ALA* 1.3 69.2 - - - +
165A ALA* 1.3 66.2 + - - +
167A ASP* 3.2 9.9 + - - +
168A ILE* 3.0 28.3 + - - +
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Residues in contact with ALA 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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133A MET* 4.4 1.9 - - + +
137A TYR* 3.9 21.8 - - + -
161A VAL 2.8 13.8 + - - +
162A SER* 3.4 9.0 - - - +
164A MET* 1.3 76.3 - - - +
166A GLY* 1.3 62.2 + - - +
168A ILE* 3.2 4.4 + - - +
169A ILE* 3.0 28.2 + - - +
186A PHE* 3.6 33.1 - - + -
190A LEU* 5.0 6.5 - - + -
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Residues in contact with GLY 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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162A SER 2.9 14.5 + - - -
163A ALA* 3.3 4.7 + - - -
165A ALA* 1.3 75.8 - - - +
167A ASP* 1.3 62.4 + - - +
169A ILE* 3.3 16.1 + - - +
170A LEU* 3.1 28.9 + - - +
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Residues in contact with ASP 167 (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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115A ASN* 4.1 6.1 + - - -
118A LEU* 4.6 7.2 - - + -
119A ARG* 2.9 39.3 + - - +
163A ALA* 2.9 24.0 + - - +
164A MET* 3.2 14.5 + - - +
166A GLY* 1.3 73.5 - - - +
168A ILE* 1.3 62.7 + - - +
170A LEU* 3.2 20.0 + - - +
171A LEU* 3.1 26.5 + - + +
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Residues in contact with ILE 168 (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* 3.9 26.0 - - + -
130A ILE* 3.9 25.1 - - + -
133A MET* 3.6 37.9 - - + -
164A MET 3.0 20.0 + - - +
165A ALA 3.2 6.5 + - - +
167A ASP* 1.3 73.5 - - - +
169A ILE* 1.3 58.7 + - - +
171A LEU* 2.8 27.7 + - + +
183A ALA* 3.5 16.3 - - + +
186A PHE* 3.5 42.2 - - + -
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Residues in contact with ILE 169 (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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165A ALA 3.0 19.0 + - - +
166A GLY* 3.5 16.2 - - - +
168A ILE* 1.3 76.5 - - - +
170A LEU* 1.3 63.7 + - + +
172A LEU* 3.2 31.8 + - + +
173A ASP* 5.4 0.3 - - - +
186A PHE* 4.8 1.6 - - + -
187A VAL* 3.9 25.6 - - + -
190A LEU* 3.6 27.6 - - + -
231A GLU 5.8 0.7 - - - +
235A ALA* 4.4 13.0 - - + -
238A GLN* 4.6 25.1 - - + +
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Residues in contact with LEU 170 (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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166A GLY 3.1 20.7 + - - +
167A ASP* 3.2 22.6 + - - +
169A ILE* 1.3 78.8 - - + +
171A LEU* 1.3 59.5 + - + +
172A LEU 3.1 1.3 - - - -
173A ASP* 3.0 38.9 + - - +
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Residues in contact with LEU 171 (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* 4.4 17.5 - - + +
126A VAL* 4.7 6.5 - - + -
130A ILE* 3.9 25.4 - - + -
167A ASP* 3.1 18.6 + - + +
168A ILE* 2.8 19.2 + - + +
170A LEU* 1.3 75.3 - - - +
172A LEU* 1.3 64.3 + - - +
173A ASP 3.0 1.1 - - - -
174A SER* 2.9 28.0 + - - +
179A ILE* 3.8 22.4 - - + -
180A ARG* 3.6 9.9 - - - +
183A ALA* 3.9 9.0 - - + -
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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