Contacts of the helix formed by residues 153 - 172 (chain A) in PDB entry 2OY0
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 153 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A LYS* 4.4 1.3 - - - -
151A SER* 3.1 5.1 + - - +
152A SER* 1.3 79.9 + - - +
154A ALA* 1.3 61.0 + - - +
155A GLU* 3.3 13.7 + - - +
156A VAL* 3.2 31.5 + - - +
157A GLU* 3.2 28.6 + - - +
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Residues in contact with ALA 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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10A GLU* 5.3 4.5 - - + +
13A LYS* 4.4 10.9 - - + +
152A SER 4.2 1.2 + - - -
153A SER* 1.3 72.1 + - - +
155A GLU* 1.3 67.2 + - - +
156A VAL 3.0 1.6 - - - -
157A GLU* 3.7 7.9 - - - +
158A GLU* 2.8 26.0 + - - +
187A TYR* 3.7 24.0 - - + +
188A MET* 3.9 22.6 - - + +
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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
----------------------------------------------------------
153A SER* 3.3 9.0 + - - +
154A ALA* 1.3 78.6 - - - +
156A VAL* 1.3 66.1 + - + +
158A GLU* 3.4 8.7 + - - +
159A HIS* 3.3 20.2 + - + +
188A MET* 4.2 14.8 - - + +
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Residues in contact with VAL 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A SER* 3.9 15.3 - - - +
153A SER* 3.2 30.7 - - - +
154A ALA 3.0 0.2 - - - -
155A GLU* 1.3 80.5 - - + +
157A GLU* 1.3 63.9 + - - +
159A HIS* 3.4 6.2 + - + +
160A ARG* 3.1 52.8 + - + +
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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
----------------------------------------------------------
12A TRP* 5.1 4.3 - - - -
13A LYS* 3.8 12.1 + - - +
149A GLU 5.4 0.2 - - - +
150A SER* 3.8 5.4 - - - -
151A SER* 3.5 32.8 + - - +
153A SER 3.2 15.2 + - - +
154A ALA* 3.1 6.3 + - - +
156A VAL* 1.3 73.6 - - - +
158A GLU* 1.3 63.3 + - - +
159A HIS 3.0 1.2 + - - -
160A ARG* 3.3 3.3 + - - +
161A THR* 2.7 32.5 + - - -
184A LEU* 3.7 36.6 - - + +
185A CYS* 3.5 18.4 - - + +
187A TYR* 3.7 19.1 + - - -
217A HIS* 6.0 0.3 - - - +
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Residues in contact with GLU 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 ALA 2.8 12.5 + - - +
155A GLU* 3.5 13.3 - - - +
157A GLU* 1.3 77.5 - - - +
159A HIS* 1.3 54.7 + - - +
161A THR* 3.7 1.9 - - - -
162A ILE* 3.1 27.5 + - - +
185A CYS* 4.0 4.1 - - - +
188A MET* 3.1 43.0 - - + +
189A PRO* 3.5 5.4 - - - +
190A LYS* 2.7 57.9 + - + +
191A VAL* 3.8 12.6 - - + +
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Residues in contact with HIS 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* 3.3 9.8 + - + +
156A VAL* 3.6 10.1 - - + +
157A GLU 3.0 0.6 - - - -
158A GLU* 1.3 75.8 - - - +
160A ARG* 1.3 59.1 + - + +
161A THR 2.7 15.6 + - - -
162A ILE* 2.9 20.1 + - + -
163A ARG* 2.9 39.6 + - + +
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Residues in contact with ARG 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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133A PHE* 5.0 0.9 - - - -
148A GLY* 5.8 0.8 - - - -
149A GLU* 2.6 73.4 + - + +
150A SER 3.7 7.6 + - - -
151A SER* 4.0 10.8 + - - -
156A VAL* 3.1 39.8 + - + +
157A GLU* 4.0 2.9 - - - +
159A HIS* 1.3 80.2 - - + +
161A THR* 1.3 57.1 + - - +
163A ARG* 3.7 8.4 - - - +
164A VAL* 3.0 29.3 + - - +
184A LEU* 4.5 11.4 - - + -
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Residues in contact with THR 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 GLU 2.7 20.2 + - - -
158A GLU 3.7 4.5 - - - -
159A HIS 2.7 4.9 + - - -
160A ARG* 1.3 71.5 - - - +
162A ILE* 1.3 67.9 + - - +
163A ARG 2.9 1.3 - - - -
164A VAL* 2.8 9.4 + - + +
165A LEU* 2.8 29.9 + - + +
183A VAL* 3.8 27.4 - - + -
184A LEU* 3.5 12.7 - - - +
185A CYS 3.2 20.5 + - - +
191A VAL* 3.6 22.0 - - + -
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Residues in contact with ILE 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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158A GLU 3.1 17.6 + - - +
159A HIS* 2.9 14.7 + - + +
161A THR* 1.3 75.9 - - - +
163A ARG* 1.3 65.8 + - - +
165A LEU* 3.7 6.1 - - + +
166A GLU* 3.0 40.4 + - + +
190A LYS* 3.2 52.3 - - + +
191A VAL* 3.9 5.8 - - + +
194A LYS* 3.7 22.9 - - + -
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Residues in contact with ARG 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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133A PHE* 4.3 17.6 - - + -
159A HIS* 2.9 39.4 + - - +
160A ARG* 3.7 11.0 - - - +
161A THR 2.9 0.6 + - - -
162A ILE* 1.3 81.7 - - - +
164A VAL* 1.3 57.1 + - - +
166A GLU* 3.1 33.1 + - - +
167A MET* 2.9 27.0 + - - +
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Residues in contact with VAL 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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133A PHE* 3.7 27.8 - - + -
145A CYS* 4.4 14.8 - - - -
147A ILE* 4.4 26.2 - - + +
148A GLY* 5.2 2.9 - - - +
160A ARG 3.0 18.8 - - - +
161A THR* 2.8 10.2 + - + +
163A ARG* 1.3 72.0 - - - +
165A LEU* 1.3 59.4 + - + +
167A MET* 2.9 14.9 + - + +
168A VAL* 2.7 34.7 + - + +
181A VAL* 4.9 8.1 - - + -
182A LYS 4.8 9.2 - - - +
184A LEU* 6.6 0.2 - - + -
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Residues in contact with LEU 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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161A THR* 2.8 27.3 + - + +
162A ILE* 3.7 8.3 - - + +
164A VAL* 1.3 77.0 - - + +
166A GLU* 1.3 57.1 + - - +
168A VAL* 3.8 7.8 - - + +
169A GLU* 3.0 29.6 + - - +
181A VAL* 5.2 7.9 - - + -
182A LYS 5.8 1.1 - - - +
183A VAL* 4.8 13.2 - - + -
191A VAL* 4.2 23.1 - - + -
194A LYS* 3.7 42.1 - - + -
195A MET* 4.4 20.2 - - - -
198A LEU* 4.1 13.3 - - + +
221A TRP* 4.8 10.5 - - + -
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Residues in contact with GLU 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 ILE* 3.0 35.8 + - + +
163A ARG* 3.1 43.8 + - - +
165A LEU* 1.3 75.0 - - - +
167A MET* 1.3 65.3 + - - +
168A VAL 3.5 0.2 + - - -
169A GLU* 3.9 5.7 + - - +
170A ASP* 3.8 18.2 + - - +
194A LYS* 4.1 21.0 + - - +
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Residues in contact with MET 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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80A LEU* 3.2 20.9 - - + -
132A VAL* 3.1 42.6 - - + +
133A PHE* 3.5 38.8 - - + -
145A CYS* 4.1 8.1 - - - -
147A ILE* 3.8 16.8 - - + -
163A ARG 2.9 12.1 + - - +
164A VAL* 2.9 13.9 + - + +
166A GLU* 1.3 78.1 - - - +
168A VAL* 1.3 54.3 + - + +
170A ASP* 3.9 5.4 + - - +
171A TRP* 2.7 39.4 + - - +
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Residues in contact with VAL 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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80A LEU* 5.1 4.5 - - + -
143A LEU* 4.5 9.2 - - + -
145A CYS* 4.3 16.6 - - + -
164A VAL* 2.7 15.3 + - + +
165A LEU* 3.8 9.4 - - + +
167A MET* 1.3 75.5 - - - +
169A GLU* 1.3 55.1 + - + +
170A ASP 2.7 5.0 + - - -
171A TRP* 2.7 29.3 + - + +
172A LEU* 2.7 35.0 - - + +
181A VAL* 3.9 33.7 - - + -
198A LEU* 5.2 0.4 - - + -
221A TRP* 4.0 24.2 - - + -
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Residues in contact with GLU 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 LEU 3.0 13.7 + - - +
166A GLU* 3.9 6.4 + - - +
168A VAL* 1.3 84.5 - - + +
170A ASP* 1.3 60.7 + - - +
172A LEU* 3.4 19.6 + - - +
194A LYS* 3.9 11.4 + - - -
198A LEU* 3.8 23.1 - - + +
201A ARG* 2.5 41.0 + - - -
202A TYR* 3.6 27.5 + - + +
221A TRP* 6.3 0.2 - - - -
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Residues in contact with ASP 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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137A SER* 3.6 24.3 + - - -
166A GLU 3.8 11.3 + - - +
167A MET* 4.0 10.1 - - - +
168A VAL 2.7 5.7 + - - -
169A GLU* 1.3 73.6 - - - +
171A TRP* 1.3 61.9 + - + +
172A LEU* 3.1 7.9 + - - -
173A HIS* 4.7 8.0 + - - +
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Residues in contact with TRP 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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78A ILE* 4.3 14.8 - - + -
80A LEU* 4.3 16.2 - - + -
103A TYR* 4.6 9.2 - + - -
132A VAL* 4.7 4.9 - - + +
135A ARG* 3.4 35.5 + - + -
136A PRO 3.7 13.2 - - - -
137A SER* 3.8 17.4 + - - +
138A GLU* 3.3 47.6 - - + -
140A CYS* 5.7 0.4 - - - -
143A LEU* 3.6 30.7 - - + -
167A MET* 2.7 45.6 + - - +
168A VAL* 2.7 12.5 + - - +
170A ASP* 1.3 77.6 + - + +
172A LEU* 1.3 58.4 + - + +
173A HIS* 3.0 6.6 + - - +
174A ARG* 2.5 31.4 + - - -
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Residues in contact with LEU 172 (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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143A LEU* 5.3 9.0 - - + -
168A VAL* 2.7 56.8 + - + +
169A GLU* 3.6 12.7 - - - +
170A ASP 3.1 2.4 - - - +
171A TRP* 1.3 76.4 - - + +
173A HIS* 1.3 66.1 + - - +
174A ARG* 3.8 17.3 - - + +
179A PHE* 4.3 31.0 - - + -
181A VAL* 5.8 2.5 - - + -
202A TYR* 3.1 51.2 + - + -
221A TRP* 5.2 6.3 - - + -
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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