Contacts of the strand formed by residues 139 - 153 (chain A) in PDB entry 1AOC
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 ARG 139 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131A SER* 4.3 16.8 - - - +
132A ASN 3.7 9.0 - - - +
133A SER* 4.6 0.9 - - - +
134A CYS* 3.2 7.2 - - - -
138A GLY* 1.3 74.6 - - - +
140A CYS* 1.3 67.5 + - - +
141A THR* 3.2 17.7 + - - +
173A ARG 2.5 37.8 + - - +
175A PHE* 3.0 70.7 + - + +
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Residues in contact with CYS 140 (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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88A CYS* 2.0 51.8 - - - -
89A PRO* 5.2 1.1 - - - -
127A CYS* 4.1 0.6 - - - -
130A GLY 3.6 18.7 - - - +
131A SER* 2.9 27.2 + - - -
132A ASN* 3.0 34.6 + - - +
134A CYS* 3.5 13.9 - - - -
139A ARG* 1.3 71.9 - - - +
141A THR* 1.3 58.8 + - - +
170A CYS* 3.7 8.5 - - - -
171A PRO 3.9 0.2 - - - -
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Residues in contact with THR 141 (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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127A CYS* 3.5 5.6 - - - -
131A SER* 4.6 2.2 - - - +
139A ARG* 3.2 21.0 + - - +
140A CYS* 1.3 74.6 + - - +
142A GLN* 1.3 69.3 + - - +
170A CYS* 3.2 4.7 - - - -
171A PRO* 2.9 41.6 + - + +
173A ARG* 3.8 14.5 - - + +
175A PHE 3.8 17.4 + - - +
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Residues in contact with GLN 142 (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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125A HIS 3.0 18.3 + - - -
126A LYS* 3.0 30.0 - - - +
127A CYS* 3.1 16.5 + - - +
131A SER* 5.3 1.8 + - - -
141A THR* 1.3 81.6 - - - +
143A GLN* 1.3 72.9 + - - +
144A ARG* 3.6 40.2 + - - +
167A CYS* 3.6 23.1 - - - +
169A GLY 2.7 25.4 + - - -
171A PRO* 5.3 0.2 - - - -
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Residues in contact with GLN 143 (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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75A CYS* 3.7 23.9 - - - +
80A PRO* 6.2 2.4 - - - +
84A PHE* 3.2 28.2 - - - -
141A THR 3.4 1.0 + - - -
142A GLN* 1.3 92.8 + - - +
144A ARG* 1.3 73.6 + - - +
168A CYS* 3.2 12.3 + - - -
169A GLY 2.9 8.0 + - - +
171A PRO* 3.7 17.3 - - + +
173A ARG* 2.9 27.4 + - - +
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Residues in contact with ARG 144 (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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6A PRO* 3.7 41.2 - - - +
7A ILE 5.0 1.0 - - - +
8A CYS* 3.6 32.3 - - - +
11A ASP* 5.6 1.6 + - - -
142A GLN* 3.6 37.7 + - - +
143A GLN* 1.3 89.0 - - - +
145A SER* 1.3 68.5 + - - +
165A ARG* 4.4 15.0 - - + +
166A THR 3.1 9.2 - - - +
167A CYS* 4.2 1.3 - - - -
168A CYS* 3.8 4.7 - - - -
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Residues in contact with SER 145 (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 PHE* 3.4 51.5 - - - +
79A PRO* 4.7 5.5 + - - +
144A ARG* 1.3 76.8 - - - +
146A VAL* 1.3 71.7 + - - +
165A ARG* 3.3 10.0 - - - +
166A THR* 2.9 28.0 + - - -
168A CYS* 4.3 6.1 - - - -
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Residues in contact with VAL 146 (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 PHE* 4.1 10.2 - - - -
103A VAL* 3.8 19.5 - - + -
145A SER* 1.3 86.3 + - - +
147A VAL* 1.3 71.0 + - - +
148A ARG* 5.3 3.1 - - + -
163A SER* 3.8 29.4 - - - +
164A PHE 3.2 10.5 - - - +
165A ARG* 4.3 10.8 - - + +
166A THR* 4.6 0.2 - - - -
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Residues in contact with VAL 147 (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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9A LEU* 3.9 27.4 - - + -
63A TYR* 3.5 34.5 - - + +
78A PHE* 3.6 27.1 - - + -
122A VAL* 4.3 9.6 - - + -
146A VAL* 1.3 72.0 - - - +
148A ARG* 1.3 64.3 + - - +
149A LEU* 4.1 12.0 + - + -
162A GLU 3.7 0.5 - - - +
163A SER* 3.5 2.6 - - - -
164A PHE* 2.9 39.7 + - + +
166A THR* 3.8 13.0 - - + +
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Residues in contact with ARG 148 (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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59A GLU* 3.7 15.4 + - - -
60A CYS* 3.6 26.9 - - + +
63A TYR* 4.0 11.3 - - - -
146A VAL* 5.3 3.1 - - + -
147A VAL* 1.3 78.5 - - - +
149A LEU* 1.3 68.5 + - - +
161A CYS* 3.6 31.8 + - + +
162A GLU* 3.2 23.9 + - - +
163A SER* 3.2 26.2 + - - +
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Residues in contact with LEU 149 (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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9A LEU* 3.5 31.6 - - + -
60A CYS* 3.7 6.1 - - - +
63A TYR* 3.7 26.9 - - + -
97A PRO* 4.8 4.0 - - + -
110A ILE* 4.3 19.7 - - + -
120A GLN* 3.7 24.9 - - + +
122A VAL* 4.1 13.2 - - + -
147A VAL* 4.1 7.8 - - + -
148A ARG* 1.3 81.9 - - - +
150A VAL* 1.3 65.9 + - - +
151A THR* 3.4 5.4 + - - +
161A CYS* 3.5 1.0 - - - -
162A GLU 3.0 27.1 + - - -
164A PHE* 4.0 20.4 - - + -
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Residues in contact with VAL 150 (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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56A VAL* 4.1 13.9 - - + +
57A PHE* 4.3 13.5 - - + -
60A CYS* 3.5 19.7 - - - -
61A GLY* 3.6 25.8 - - - +
110A ILE* 3.8 4.9 - - - +
111A VAL* 3.1 25.6 + - + -
118A PHE* 4.3 7.0 - - + -
120A GLN* 3.0 31.9 - - - +
149A LEU* 1.3 71.2 - - - +
151A THR* 1.3 70.3 + - - +
159A PHE* 4.0 20.4 - - + -
160A LEU 3.6 4.0 - - - -
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Residues in contact with THR 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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108A ARG* 4.4 11.1 - - + -
109A VAL 3.1 15.3 - - - +
110A ILE* 4.7 1.6 - - + -
111A VAL* 3.6 5.0 - - - +
149A LEU 3.7 3.6 - - - +
150A VAL* 1.3 81.8 - - - +
152A TYR* 1.3 63.2 + - - +
159A PHE* 3.3 6.2 - - - -
160A LEU* 2.7 44.7 + - - +
162A GLU* 3.4 40.3 + - + +
164A PHE* 3.6 21.8 - - + -
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Residues in contact with TYR 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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26A ILE* 5.2 1.3 - - + -
29A LYS* 2.7 51.1 + - + +
30A ILE* 3.6 27.6 - - + -
33A ALA* 4.3 15.9 - - + +
108A ARG* 5.7 2.9 - - - -
109A VAL* 2.9 36.9 + - + +
111A VAL* 3.6 16.3 - - + +
151A THR* 1.3 76.3 - - - +
153A ASN* 1.3 72.0 + - - +
154A LEU* 3.5 28.2 + - + +
157A ASP* 3.7 28.4 + - - +
158A GLY* 3.9 6.1 - - - -
159A PHE* 4.0 16.4 - + - -
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Residues in contact with ASN 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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151A THR* 4.2 0.6 + - - -
152A TYR* 1.3 73.3 - - - +
154A LEU* 1.3 58.4 + - - +
155A GLU* 2.8 24.0 + - - +
156A LYS* 3.0 34.2 + - - +
157A ASP* 2.9 27.4 + - - -
158A GLY 2.7 23.2 + - - +
160A LEU* 5.6 9.5 - - + +
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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