Contacts of the strand formed by residues 127 - 141 (chain A) in PDB entry 1OPO
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 PHE 127 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82A SER* 4.5 18.4 - - - -
83A MET 5.6 1.6 - - - -
112A ARG* 3.7 9.5 + - - -
123A LEU* 3.7 23.1 - - + -
124A ALA 3.5 4.4 + - - +
125A THR 3.7 0.6 - - - -
126A ASN* 1.3 92.7 - - + +
128A ASN* 1.3 63.3 + - - +
129A LYS 3.5 5.6 - - - +
198A ILE* 3.6 18.9 - - + +
239A LEU* 3.7 38.8 - - + -
240A SER* 3.3 32.5 - - - +
241A ASP 3.5 3.8 - - - -
242A PRO* 3.9 15.3 - - + -
243A THR* 4.0 7.5 - - - +
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Residues in contact with ASN 128 (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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112A ARG* 5.4 2.2 - - - +
127A PHE* 1.3 76.7 + - - +
129A LYS* 1.3 64.4 + - + +
197A PHE* 3.3 9.5 - - + -
198A ILE* 3.0 26.1 + - - +
200A ASP* 4.4 6.5 + - - -
241A ASP* 2.8 33.9 + - - +
243A THR* 3.6 25.1 + - - +
156C ASN* 3.3 24.4 + - - +
157C ASP* 3.8 4.6 - - - +
158C ASP* 3.0 31.4 + - - +
161C ASP* 4.5 5.3 + - - -
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Residues in contact with LYS 129 (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 PHE* 3.5 2.2 - - - +
128A ASN* 1.3 86.0 - - - +
130A TYR* 1.3 63.8 + - - +
195A THR* 4.2 16.6 - - + +
196A ARG 3.2 14.8 - - - +
197A PHE* 3.8 34.2 - - + -
198A ILE* 3.5 5.0 - - - +
239A LEU* 3.6 5.9 - - - +
240A SER* 2.9 43.9 + - - +
241A ASP* 3.5 23.4 + - + +
157C ASP* 3.7 11.6 + - - -
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Residues in contact with TYR 130 (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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109A VAL 4.3 0.3 + - - -
110A SER* 5.8 0.2 - - - -
111A PRO* 3.6 32.6 - - + +
129A LYS* 1.3 76.0 - - - +
131A ARG* 1.3 65.7 + - - +
132A ILE* 4.1 31.4 - - + -
195A THR* 3.5 3.4 - - - -
196A ARG* 2.8 71.7 + - + +
197A PHE 3.5 11.4 - - - -
198A ILE* 3.5 19.5 - - + -
209A VAL 2.7 29.2 + - - -
210A ASP* 3.8 0.5 - - - -
211A PHE* 3.2 24.8 + + + +
237A ILE* 4.5 4.9 - - + -
238A VAL 3.4 7.0 - - - -
239A LEU* 3.8 19.1 - - + -
240A SER* 4.5 0.6 + - - -
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Residues in contact with ARG 131 (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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130A TYR* 1.3 79.2 - - - +
132A ILE* 1.3 73.2 + - - +
133A THR* 4.0 17.2 - - - +
191A VAL* 5.7 0.2 - - - -
193A GLY* 3.5 25.4 + - - +
194A LYS 3.3 21.8 - - - +
195A THR* 3.3 22.4 + - + +
196A ARG* 5.8 0.2 - - - -
237A ILE* 4.4 0.7 - - - -
238A VAL* 2.8 57.8 + - + +
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Residues in contact with ILE 132 (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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109A VAL* 4.2 11.2 - - + -
111A PRO* 5.8 1.1 - - + -
117A PHE* 5.4 4.5 - - + -
130A TYR* 4.1 17.3 - - + -
131A ARG* 1.3 77.8 - - - +
133A THR* 1.3 63.4 + - - +
134A ALA 3.6 26.9 - - - +
135A LEU* 4.0 16.8 - - + -
191A VAL* 2.8 30.2 - - + +
192A ASP 4.1 1.2 + - - +
194A LYS 5.0 1.4 + - - -
211A PHE* 3.7 47.9 - - + -
236A THR 3.9 4.9 - - - +
237A ILE* 3.6 22.2 - - + -
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Residues in contact with THR 133 (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 ARG* 4.0 19.7 - - - +
132A ILE* 1.3 77.6 - - - +
134A ALA* 1.3 61.3 + - - +
191A VAL* 3.7 18.4 - - - +
236A THR* 2.8 31.9 + - - +
238A VAL* 3.7 28.0 - - + -
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Residues in contact with ALA 134 (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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132A ILE* 3.6 5.1 - - - +
133A THR* 1.3 82.8 - - - +
135A LEU* 1.3 64.0 + - - +
136A THR* 5.2 3.1 - - + -
191A VAL* 4.4 3.6 - - - -
234A GLN 4.5 0.2 - - - -
235A TYR* 3.3 3.4 - - - -
236A THR* 2.9 50.4 + - - +
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Residues in contact with LEU 135 (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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109A VAL* 4.4 19.1 - - + -
117A PHE* 5.0 5.6 - - + -
132A ILE* 4.0 14.4 - - + -
134A ALA* 1.3 76.4 - - - +
136A THR* 1.3 69.5 + - - +
137A VAL* 5.5 1.6 - - + -
155A PHE* 5.5 0.2 - - + -
188A VAL* 4.4 0.5 - - - +
189A ILE* 3.0 47.7 + - + +
191A VAL* 4.6 5.5 - - + +
211A PHE* 3.8 31.0 - - + -
214A ILE* 5.5 3.8 - - + -
233A ILE* 3.3 36.3 - - + -
234A GLN 3.4 8.7 - - - +
235A TYR* 3.7 10.5 - - + -
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Residues in contact with THR 136 (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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134A ALA* 5.2 3.4 - - + -
135A LEU* 1.3 85.6 - - - +
137A VAL* 1.3 66.6 + - - +
138A LYS* 4.0 10.2 + - - -
186A ASP* 4.7 6.6 + - - +
187A LEU 3.2 12.7 + - - -
188A VAL* 3.8 21.8 - - + -
189A ILE* 4.3 1.1 - - - +
233A ILE* 3.8 1.7 - - - +
234A GLN* 2.8 58.3 + - + +
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Residues in contact with VAL 137 (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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91A LEU* 4.9 8.5 - - + -
135A LEU* 5.5 1.6 - - + -
136A THR* 1.3 76.1 - - - +
138A LYS* 1.3 62.0 + - - +
139A TYR 4.1 0.3 + - - -
153A LEU* 4.0 21.9 - - + +
185A LYS 4.3 0.2 - - - +
186A ASP* 3.5 0.7 - - - -
187A LEU* 2.7 47.7 + - + +
189A ILE* 4.5 15.0 - - + -
214A ILE* 3.8 34.1 - - + -
231A LEU* 4.5 17.5 - - + -
232A PHE 3.5 10.8 - - - +
233A ILE* 4.6 11.4 - - + +
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Residues in contact with LYS 138 (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 THR* 4.7 9.9 - - + -
136A THR* 4.4 12.1 - - - +
137A VAL* 1.3 76.2 - - - +
139A TYR* 1.3 60.7 + - - +
140A SER* 3.9 1.9 + - - -
185A LYS 3.7 0.2 - - - -
186A ASP* 2.8 43.2 + - - +
231A LEU* 3.2 6.1 - - - +
232A PHE* 2.7 56.0 + - + +
234A GLN* 3.5 31.2 + - + +
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Residues in contact with TYR 139 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94A VAL* 4.2 19.5 - - + -
137A VAL 4.1 0.4 + - - -
138A LYS* 1.3 73.9 - - - +
140A SER* 1.3 62.5 + - - +
141A PRO* 3.6 21.5 - - + -
151A VAL* 4.2 22.6 - - + +
153A LEU* 4.5 15.9 - - + +
179A THR* 4.1 13.0 - - + -
180A ALA 4.1 5.4 - - - -
181A ALA* 2.7 29.6 + - - +
183A THR 3.6 19.3 - - - -
184A ALA* 3.5 9.0 - - - +
185A LYS* 2.9 29.3 + - + +
186A ASP* 4.9 1.0 - - - +
228A VAL* 3.7 17.8 + - - +
229A GLY* 4.1 17.5 - - - -
230A GLU 3.7 9.2 - - - -
231A LEU* 4.1 6.1 - - + -
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Residues in contact with SER 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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138A LYS* 3.9 1.8 + - - -
139A TYR* 1.3 77.3 - - - +
141A PRO* 1.3 72.2 + - - +
142A ALA* 4.8 0.3 - - - +
184A ALA* 4.7 1.6 - - - -
229A GLY* 3.3 1.0 - - - -
230A GLU* 2.9 42.3 + - - +
232A PHE* 4.0 24.2 - - - -
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Residues in contact with PRO 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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139A TYR* 3.6 19.0 - - + +
140A SER* 1.3 94.9 + - - +
142A ALA* 1.3 62.3 + - - +
143A CYS 4.5 3.6 - - - +
181A ALA 3.4 15.3 - - - +
182A GLN* 3.5 25.1 - - - +
183A THR 3.6 0.7 - - - -
184A ALA* 3.5 31.6 - - + +
228A VAL 3.7 6.7 - - - +
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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