Contacts of the strand formed by residues 156 - 163 (chain F) in PDB entry 1OP8
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 156 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16F ILE* 3.5 16.7 + - + +
19F GLY 2.9 23.2 + - - -
20F ASN 3.4 8.1 - - - +
21F GLU* 3.9 13.7 - - + +
22F VAL* 4.3 2.0 - - - +
139F ALA* 2.9 3.8 - - - +
140F GLY 2.8 37.9 + - - +
142F GLY 5.4 0.4 - - - -
144F THR* 3.8 21.5 - - - +
146F ASN* 6.1 1.0 - - - +
152F SER* 3.4 18.6 + - - +
154F THR* 3.4 16.0 + - - +
155F LEU* 1.3 76.6 - - - +
157F GLU* 1.3 61.7 + - - +
1001F SO4 2.7 35.4 + - - -
1019F SO4 3.1 24.3 + - - -
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Residues in contact with GLU 157 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16F ILE* 3.9 4.5 - - - -
19F GLY* 3.5 0.5 - - - -
20F ASN* 3.0 28.8 + - - +
22F VAL* 3.5 14.7 - - + +
27F ARG* 2.8 41.0 + - - -
29F TYR* 4.2 3.5 + - - -
137F GLN* 2.6 41.7 + - + +
138F VAL* 3.3 20.4 - - - +
139F ALA* 3.8 11.0 + - + +
156F ARG* 1.3 76.7 - - - +
158F VAL* 1.3 66.7 + - - +
159F ASN* 4.4 3.8 + - - +
200F LEU* 6.0 0.2 - - - +
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Residues in contact with VAL 158 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16F ILE* 3.4 27.3 - - + +
17F ILE 3.8 4.9 - - - +
18F GLY 3.2 28.7 - - - +
19F GLY* 3.7 4.3 - - - -
137F GLN* 3.3 3.6 - - - -
138F VAL* 3.0 36.1 + - + +
157F GLU* 1.3 74.8 - - - +
159F ASN* 1.3 77.9 + - - +
160F ILE* 4.0 8.9 + - + +
188F ARG* 3.9 11.4 - - + +
189F ASP 3.6 23.1 - - - +
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Residues in contact with ASN 159 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136F CYS 3.6 5.2 + - - +
137F GLN* 4.0 25.1 - - - +
157F GLU* 4.9 3.4 + - - +
158F VAL* 1.3 87.5 - - - +
160F ILE* 1.3 68.7 + - - +
188F ARG* 3.4 28.1 + - + +
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Residues in contact with ILE 160 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135F MET* 3.5 5.4 - - - +
136F CYS* 2.9 41.8 + - + +
138F VAL* 3.5 29.4 - - + -
158F VAL* 4.2 11.7 - - + +
159F ASN* 1.3 85.3 - - - +
161F THR* 1.3 67.1 + - - +
183F ALA* 3.9 13.5 - - + -
184F GLY* 3.5 14.4 - - - +
188F ARG* 3.3 34.8 - - + +
189F ASP* 4.3 1.1 - - - +
199F LEU* 3.9 9.6 - - + -
228F TYR* 3.6 15.5 - - - +
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Residues in contact with THR 161 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133F GLY* 3.3 38.6 - - - +
134F THR 3.3 4.0 - - - +
135F MET* 4.8 5.4 - - + +
136F CYS* 4.9 0.9 - - - +
160F ILE* 1.3 79.8 + - - +
162F ILE* 1.3 70.2 + - - +
163F ILE* 3.3 7.2 + - - +
183F ALA* 3.3 5.5 - - - -
184F GLY 3.2 28.2 + - - +
185F SER* 6.0 0.9 - - - -
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Residues in contact with ILE 162 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130F VAL* 3.4 47.8 - - + +
131F LYS 3.6 13.5 - - - +
132F PRO* 3.5 9.3 - - + +
133F GLY* 2.8 26.2 + - - -
134F THR 3.0 11.9 + - - +
136F CYS* 3.6 19.3 - - - -
161F THR* 1.3 73.6 - - - +
163F ILE* 1.3 69.0 + - - +
164F ASP 3.9 0.3 + - - -
181F VAL* 4.2 18.6 - - + -
182F CYS 3.3 16.4 - - - +
183F ALA* 3.8 12.8 - - + -
199F LEU* 4.4 4.7 - - + -
201F CYS* 4.3 2.9 - - - -
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Residues in contact with ILE 163 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161F THR* 3.6 7.6 - - - +
162F ILE* 1.3 79.1 - - - +
164F ASP* 1.3 77.1 + - - +
165F ARG 3.1 2.8 + - - -
167F VAL* 3.8 23.3 - - + -
168F CYS* 4.4 1.1 - - - +
171F HIS* 5.0 7.4 - - - +
182F CYS* 3.0 34.2 + - + +
183F ALA* 3.9 3.1 - - - +
184F GLY 3.7 18.8 - - - +
185F SER* 4.0 15.3 - - - +
186F LEU* 5.1 15.3 - - + +
225F PRO* 3.4 33.2 - - + -
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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