Contacts of the strand formed by residues 127 - 141 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82B SER 5.4 3.6 - - - -
83B MET* 4.1 31.2 - - + -
112B ARG* 3.7 8.0 + - - -
123B LEU* 3.5 23.6 - - + -
124B ALA 3.2 9.0 + - - +
125B THR 3.6 0.9 - - - -
126B ASN* 1.3 94.2 - - + +
128B ASN* 1.3 63.2 + - - +
129B LYS 4.2 5.8 - - - +
198B ILE* 3.4 18.1 - - + +
239B LEU* 3.8 35.4 - - + -
240B SER* 3.5 28.5 - - - +
241B ASP 3.6 3.4 - - - -
242B PRO* 3.9 22.4 - - + -
243B THR* 4.0 7.6 - - - +
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Residues in contact with ASN 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156A ASN* 3.2 22.7 - - - +
157A ASP* 3.6 6.4 - - - +
158A ASP* 3.1 32.3 + - - +
161A ASP* 5.2 5.1 + - - -
112B ARG* 5.6 2.8 - - - +
127B PHE* 1.3 75.7 + - - +
129B LYS* 1.3 61.1 + - + +
197B PHE* 3.3 12.3 - - + -
198B ILE* 2.8 27.5 + - - +
200B ASP* 4.7 5.7 + - - -
241B ASP* 2.7 33.9 + - - +
243B THR* 3.5 26.9 + - - +
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Residues in contact with LYS 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A ASP* 3.7 11.5 + - - -
192A ASP* 4.9 14.3 + - - +
127B PHE* 3.6 1.2 - - - +
128B ASN* 1.3 84.3 - - - +
130B TYR* 1.3 66.2 + - - +
195B THR* 4.2 17.5 - - + +
196B ARG 3.3 12.8 - - - +
197B PHE* 3.7 31.3 - - + -
198B ILE* 3.8 9.8 - - - +
239B LEU* 3.6 3.6 - - - +
240B SER* 3.0 39.7 + - - +
241B ASP* 3.4 25.5 - - + +
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Residues in contact with TYR 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B VAL 4.4 1.2 + - - -
110B SER* 4.7 1.2 - - - -
111B PRO* 3.8 30.9 - - + +
129B LYS* 1.3 78.1 - - - +
131B ARG* 1.3 64.4 + - - +
132B ILE* 4.2 29.4 - - + -
194B LYS 4.3 0.5 - - - +
195B THR* 3.6 3.7 - - - -
196B ARG* 2.9 57.2 + - + +
197B PHE 3.3 20.6 - - - -
198B ILE* 3.5 17.9 - - + -
209B VAL 2.9 19.3 + - - -
210B ASP* 3.7 0.7 - - - -
211B PHE* 3.3 26.7 + + + +
237B ILE* 4.6 5.2 - - + -
238B VAL 3.2 9.6 - - - +
239B LEU* 3.9 16.2 - - + -
240B SER* 4.9 0.7 - - - -
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Residues in contact with ARG 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B TYR* 1.3 78.1 - - - +
132B ILE* 1.3 71.7 + - - +
133B THR* 3.6 13.9 + - - -
192B ASP 5.1 0.2 - - - +
193B GLY* 3.2 22.3 + - - +
194B LYS 3.4 16.8 - - - +
195B THR* 3.0 26.9 + - + +
237B ILE* 3.4 1.3 - - - -
238B VAL* 2.7 61.9 + - + +
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Residues in contact with ILE 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B VAL* 4.2 12.6 - - + -
111B PRO* 6.0 1.1 - - + -
117B PHE* 5.4 4.9 - - + -
130B TYR* 4.2 17.6 - - + -
131B ARG* 1.3 78.1 + - - +
133B THR* 1.3 61.2 + - - +
134B ALA 3.6 26.7 - - - +
135B LEU* 4.0 16.6 - - + -
191B VAL* 3.0 30.7 - - + +
192B ASP 4.2 3.8 + - - +
194B LYS 4.7 2.4 + - - -
211B PHE* 3.6 43.0 - - + -
236B THR 3.9 4.5 - - - +
237B ILE* 3.8 21.5 - - + -
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Residues in contact with THR 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B THR* 5.9 0.4 - - - +
131B ARG* 3.6 15.3 + - - -
132B ILE* 1.3 74.5 - - - +
134B ALA* 1.3 67.0 + - + +
191B VAL* 3.7 16.9 - - - +
236B THR* 2.8 33.0 + - + -
237B ILE* 5.1 0.4 - - - -
238B VAL* 4.2 15.8 - - - +
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Residues in contact with ALA 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B ILE* 3.6 5.4 - - - +
133B THR* 1.3 85.3 - - + +
135B LEU* 1.3 64.0 + - - +
136B THR* 6.1 0.4 - - - +
191B VAL* 4.4 2.9 - - - -
234B GLN 4.5 0.2 - - - -
235B TYR* 3.3 4.5 - - - +
236B THR* 3.0 46.6 + - - +
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Residues in contact with LEU 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B VAL* 4.4 15.5 - - + -
117B PHE* 5.1 4.0 - - + -
132B ILE* 4.0 21.1 - - + -
134B ALA* 1.3 76.6 - - - +
136B THR* 1.3 68.5 + - - +
188B VAL* 3.8 1.4 - - - +
189B ILE* 2.9 61.1 + - + +
191B VAL* 4.6 3.5 - - + +
211B PHE* 4.2 21.5 - - + -
214B ILE* 5.7 0.4 - - + -
233B ILE* 3.8 25.1 - - + -
234B GLN 3.6 6.3 - - - +
235B TYR* 3.6 25.8 - - + -
237B ILE* 5.8 0.2 - - + -
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Residues in contact with THR 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B LEU* 1.3 79.4 + - - +
137B VAL* 1.3 74.9 + - - +
138B LYS* 3.9 5.3 + - + -
186B ASP* 3.9 22.0 - - + +
187B LEU 3.3 18.6 - - - +
188B VAL* 3.8 14.7 - - + +
232B PHE 3.9 0.2 - - - +
233B ILE* 3.7 3.8 - - - +
234B GLN* 2.9 53.1 + - - +
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Residues in contact with VAL 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B LEU* 4.5 10.3 - - + -
135B LEU* 5.6 0.4 - - + -
136B THR* 1.3 77.8 - - - +
138B LYS* 1.3 62.0 + - - +
153B LEU* 4.1 19.7 - - + +
185B LYS 4.1 0.9 - - - +
186B ASP* 3.5 1.9 - - - -
187B LEU* 2.8 45.3 + - + +
189B ILE* 3.9 15.7 - - + -
214B ILE* 3.9 31.4 - - + -
231B LEU* 4.2 21.3 - - + -
232B PHE 3.5 8.1 - - - +
233B ILE* 4.7 9.2 - - + +
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Residues in contact with LYS 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B THR* 5.0 4.7 - - + -
136B THR* 4.4 10.8 - - + +
137B VAL* 1.3 76.8 - - - +
139B TYR* 1.3 63.9 + - - +
140B SER* 3.7 2.4 + - - -
186B ASP* 3.2 34.2 + - - +
231B LEU* 3.2 7.0 - - - -
232B PHE* 2.8 53.5 + - + +
234B GLN* 3.4 39.7 + - + +
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Residues in contact with TYR 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94B VAL* 4.0 25.6 - - + -
137B VAL 4.1 0.8 + - - -
138B LYS* 1.3 72.2 - - - +
140B SER* 1.3 62.2 + - - +
141B PRO* 3.4 26.1 - - + +
151B VAL* 4.1 24.2 - - + +
153B LEU* 4.7 14.3 - - + +
179B THR* 3.8 13.2 - - + -
180B ALA 4.2 2.0 - - - -
181B ALA* 2.7 32.6 + - - -
183B THR 3.4 24.2 - - - -
184B ALA* 3.4 4.2 - - - +
185B LYS* 2.9 35.7 + - + +
186B ASP* 5.3 0.2 - - - +
228B VAL* 3.6 19.2 + - - +
229B GLY* 4.1 10.8 - - - -
230B GLU 3.8 6.3 - - - -
231B LEU* 4.3 6.5 - - + -
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Residues in contact with SER 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B LYS* 3.7 3.0 + - - -
139B TYR* 1.3 74.9 - - - +
141B PRO* 1.3 72.3 + - - +
142B ALA* 4.6 0.9 - - - +
184B ALA* 5.0 1.1 - - - -
229B GLY* 3.4 0.5 - - - -
230B GLU* 2.9 38.9 + - - +
232B PHE* 3.9 26.1 - - - -
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Residues in contact with PRO 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139B TYR* 3.4 25.5 - - + +
140B SER* 1.3 92.5 + - - +
142B ALA* 1.3 59.5 + - - +
143B CYS* 3.6 5.6 - - - +
181B ALA 3.4 23.6 - - - +
182B GLN* 3.8 16.8 - - - +
184B ALA* 3.6 32.3 - - + +
228B VAL 3.7 0.2 - - - +
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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