Contacts of the strand formed by residues 113 - 120 (chain C) in PDB entry 3OP5
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 TYR 113 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84C LEU* 3.2 24.0 - - + +
87C TYR* 3.6 42.0 - - + +
88C GLN* 3.7 25.3 + - + -
91C ALA 4.2 9.9 + - - +
92C LYS* 6.3 3.4 - - + -
93C PRO* 4.5 18.5 - - + +
111C PRO 3.9 1.6 + - - -
112C LYS* 1.3 71.5 - - - +
114C TRP* 1.3 61.8 + - - +
115C GLY* 3.5 29.0 - - - -
116C SER* 3.1 25.7 + - - -
129C MET* 4.4 2.9 - - + -
131C MET* 3.7 23.3 - - + -
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Residues in contact with TRP 114 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31C ASP* 4.7 2.3 - - - +
37C TRP* 3.9 27.0 - + + -
56C MET* 6.4 1.3 - - + -
67C PRO* 5.2 6.1 - - + -
68C CYS* 3.8 20.0 - - - -
112C LYS* 3.6 13.1 + - + +
113C TYR* 1.3 76.2 - - - +
115C GLY* 1.3 58.6 + - - +
130C ILE* 3.0 23.3 + - + +
131C MET* 3.4 26.8 - - - -
132C ASP* 2.8 33.1 + - - +
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Residues in contact with GLY 115 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31C ASP* 4.2 12.8 - - - -
113C TYR* 3.5 18.7 - - - -
114C TRP* 1.3 81.2 - - - +
116C SER* 1.3 59.1 + - - -
129C MET* 3.5 2.4 - - - -
130C ILE* 2.7 41.3 + - - +
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Residues in contact with SER 116 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31C ASP* 3.1 4.4 - - - +
32C MET* 2.9 39.3 + - - +
84C LEU* 3.6 28.9 - - - +
88C GLN* 4.9 1.4 + - - -
113C TYR* 3.1 19.6 + - - -
115C GLY* 1.3 73.3 - - - -
117C GLY* 1.3 58.3 + - - +
128C PHE* 3.4 24.0 - - - -
129C MET* 4.0 4.3 - - - -
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Residues in contact with GLY 117 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31C ASP* 4.4 1.3 - - - -
32C MET* 4.1 18.6 - - - -
116C SER* 1.3 78.0 + - - +
118C LEU* 1.3 64.6 + - - +
127C ARG* 3.6 4.5 - - - +
128C PHE* 2.9 43.5 + - - +
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Residues in contact with LEU 118 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C THR 4.3 6.5 + - - +
32C MET* 5.5 3.7 - - - -
117C GLY* 1.3 77.0 - - - +
119C HIS* 1.3 62.5 + - - +
120C ASP* 5.7 2.5 - - - +
125C SER* 4.2 19.1 - - - +
126C TYR 3.4 4.7 - - - +
127C ARG* 3.7 30.1 - - + +
128C PHE* 3.5 9.2 - - - -
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Residues in contact with HIS 119 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C PHE* 3.8 35.0 - + + -
27C GLU* 3.1 30.2 + - + -
28C ILE 3.7 22.7 - - - -
29C ILE* 3.5 22.5 - - + +
30C THR 4.9 1.2 + - - -
118C LEU* 1.3 75.7 + - - +
120C ASP* 1.3 77.0 + - - +
121C LYS* 5.0 1.6 - - + -
126C TYR* 2.8 42.3 + - - +
128C PHE* 4.1 11.2 - - + -
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Residues in contact with ASP 120 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C GLU* 5.5 0.2 - - - +
118C LEU* 5.7 2.3 - - - +
119C HIS* 1.3 86.6 + - - +
121C LYS* 1.3 60.0 + - - +
122C ASN 4.4 2.5 - - - +
124C LYS 3.4 6.3 - - - +
125C SER* 3.5 29.5 + - - -
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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