Contacts of the helix formed by residues 155 - 172 (chain A) in PDB entry 2O71
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 ASN 155 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152A HIS* 3.3 12.9 + - + +
153A PRO 3.6 1.2 + - - -
154A HIS* 1.3 81.0 + - - +
156A VAL* 1.3 63.1 + - - +
157A GLN* 3.1 17.1 + - - +
158A SER* 3.0 45.4 + - - +
159A GLN* 3.2 14.1 + - - +
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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
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131A TRP* 4.6 8.7 - - + +
154A HIS 4.3 0.2 - - - -
155A ASN* 1.3 73.1 + - - +
157A GLN* 1.3 63.5 + - - +
159A GLN* 2.9 37.8 + - - +
160A VAL* 3.0 23.9 + - + +
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Residues in contact with GLN 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A ASN* 4.5 10.5 + - - +
124A ALA* 3.3 38.9 - - - +
125A GLN* 2.9 35.0 + - - +
155A ASN* 3.1 12.0 + - - +
156A VAL* 1.3 80.5 - - - +
158A SER* 1.3 59.4 + - - +
160A VAL* 3.2 6.3 + - - +
161A VAL* 3.0 34.1 + - + +
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Residues in contact with SER 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A HIS* 3.4 34.3 + - - -
155A ASN* 3.0 31.8 + - - +
157A GLN* 1.3 77.4 - - - +
159A GLN* 1.3 57.0 + - - +
161A VAL* 3.9 7.1 - - - +
162A GLU* 3.0 30.3 + - - +
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Residues in contact with GLN 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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131A TRP* 4.1 17.5 - - + -
148A CYS* 3.6 31.6 - - - +
149A LYS* 3.5 34.3 - - - +
152A HIS* 2.9 24.5 - - + +
153A PRO* 4.6 5.0 - - - +
155A ASN 3.2 10.0 + - - +
156A VAL* 2.9 32.8 + - - +
158A SER* 1.3 77.7 - - - +
160A VAL* 1.3 56.7 + - - +
162A GLU* 3.3 3.9 + - - +
163A ALA* 3.0 27.1 + - - +
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Residues in contact with VAL 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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124A ALA* 3.6 29.8 - - + +
127A LEU* 4.7 2.0 - - + +
131A TRP* 3.6 47.8 - - + +
156A VAL* 3.0 20.7 + - + +
157A GLN* 3.7 7.0 - - - +
159A GLN* 1.3 73.9 - - - +
161A VAL* 1.3 66.0 + - - +
163A ALA* 3.2 6.7 + - - +
164A PHE* 3.1 44.7 + - + -
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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
----------------------------------------------------------
120A ILE* 3.9 15.0 - - + +
121A ASN* 3.6 39.3 - - - +
124A ALA* 3.8 17.3 - - + -
157A GLN* 3.0 25.2 + - + +
158A SER* 3.9 7.4 - - - +
160A VAL* 1.3 76.6 - - - +
162A GLU* 1.3 64.0 + - - +
164A PHE* 3.2 2.4 + - - -
165A ILE* 2.9 48.4 + - + +
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Residues in contact with GLU 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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147A ARG* 5.5 0.3 - - - +
148A CYS* 3.7 20.3 - - + -
151A ASN* 2.6 34.5 + - - +
152A HIS* 2.7 31.3 - - + +
158A SER 3.0 18.7 + - - +
159A GLN 3.6 4.5 - - - +
161A VAL* 1.3 77.3 - - - +
163A ALA* 1.3 56.1 + - - +
165A ILE* 3.2 11.8 + - - +
166A ARG* 2.9 62.0 + - + +
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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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131A TRP* 3.8 24.7 - - + -
135A VAL* 4.1 15.3 - - + -
140A LEU* 3.4 20.6 - - + +
145A ILE* 5.8 0.7 - - + -
148A CYS* 3.5 15.4 - - - -
159A GLN 3.0 12.9 + - - +
160A VAL 3.5 9.2 - - - +
161A VAL 3.2 0.2 - - - -
162A GLU* 1.3 77.1 - - - +
164A PHE* 1.3 57.5 + - - +
166A ARG* 3.2 2.9 + - - +
167A TRP* 3.0 22.6 + - - +
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Residues in contact with PHE 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A ILE* 3.7 32.3 - - + +
123A LEU* 3.9 16.4 - - + -
124A ALA* 5.4 0.2 - - - -
127A LEU* 3.6 33.7 - - + -
131A TRP* 4.5 2.7 - - + -
134A MET* 3.9 26.0 - - + -
135A VAL* 3.7 27.4 - - + -
138A LEU* 4.0 6.1 - - + -
160A VAL* 3.1 37.1 + - + -
163A ALA* 1.3 76.2 - - - +
165A ILE* 1.3 60.5 + - - +
167A TRP* 3.5 17.1 - + + -
168A ARG* 2.9 30.1 + - - +
180A LEU* 3.9 18.8 - - + -
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Residues in contact with ILE 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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117A ASP* 6.4 3.4 - - + -
120A ILE* 4.1 16.6 - - + -
161A VAL* 2.9 41.8 + - + +
162A GLU* 3.5 12.3 - - + +
164A PHE* 1.3 75.0 - - - +
166A ARG* 1.3 76.9 + - - +
168A ARG* 3.3 19.3 + - - +
169A GLN* 2.9 30.4 + - + +
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Residues in contact with ARG 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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140A LEU* 4.4 14.4 - - + -
144A ASP* 5.8 5.2 - - + -
148A CYS* 4.6 8.1 - - - -
151A ASN* 5.5 1.8 - - - +
162A GLU* 2.9 47.7 + - + +
163A ALA* 3.4 8.7 - - - +
165A ILE* 1.3 100.8 + - - +
167A TRP* 1.3 59.9 + - - +
169A GLN* 3.4 10.3 + - - +
170A ARG* 2.9 43.1 + - + +
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Residues in contact with TRP 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 PRO* 3.9 18.8 - - + -
135A VAL* 5.6 1.8 - - + -
138A LEU* 3.6 42.3 + - + +
140A LEU* 4.0 18.5 - - + +
163A ALA 3.0 13.2 + - - +
164A PHE* 3.5 33.9 - + + +
165A ILE 3.3 0.2 - - - -
166A ARG* 1.3 77.7 - - - +
168A ARG* 1.3 63.9 + - + +
171A PHE* 3.0 62.0 + + - +
175A ALA* 3.2 45.8 - - + +
176A THR 3.6 6.3 - - - -
179A SER* 3.7 19.1 - - - -
180A LEU* 3.5 27.8 - - + -
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Residues in contact with ARG 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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114A SER* 4.4 15.7 - - - +
115A PRO* 2.8 41.3 + - + -
116A SER* 3.4 21.0 + - - +
117A ASP* 3.6 9.3 - - - +
120A ILE* 3.8 16.5 - - + +
164A PHE 2.9 17.7 + - - +
165A ILE* 3.7 21.2 + - - +
167A TRP* 1.3 82.0 - - + +
169A GLN* 1.3 60.2 + - - +
172A GLY* 2.9 31.1 + - - +
175A ALA* 3.5 19.1 - - + +
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Residues in contact with GLN 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 ILE* 2.9 19.7 + - + +
166A ARG* 3.8 12.3 + - - +
168A ARG* 1.3 79.3 - - - +
170A ARG* 1.3 79.5 + - - +
172A GLY* 3.8 5.2 + - - -
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Residues in contact with ARG 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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139A GLY 3.6 20.6 + - - -
140A LEU* 3.8 10.8 - - - +
141A SER* 4.3 2.6 - - - +
144A ASP* 2.6 41.4 + - - -
166A ARG* 2.9 28.4 + - + +
167A TRP* 4.7 0.2 - - - -
169A GLN* 1.3 92.9 - - - +
171A PHE* 1.3 83.9 + - + +
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Residues in contact with PHE 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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138A LEU 3.5 22.0 - - - -
139A GLY* 4.0 24.2 - - - -
140A LEU* 4.7 1.8 - - + -
167A TRP* 3.0 45.4 + + - +
168A ARG 3.9 0.2 - - - -
170A ARG* 1.3 100.0 - - + +
172A GLY* 1.3 66.3 + - - +
173A LYS 3.1 1.0 + - - -
174A GLN* 2.9 39.3 + - + +
175A ALA* 3.9 14.1 - - + +
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Residues in contact with GLY 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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114A SER* 3.4 14.0 + - - -
168A ARG* 2.9 20.2 + - - +
169A GLN 3.8 4.5 + - - -
170A ARG 3.5 2.6 + - - -
171A PHE* 1.3 73.7 - - - +
173A LYS* 1.3 58.6 + - - -
175A ALA* 2.8 22.9 + - - +
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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