Contacts of the strand formed by residues 129 - 134 (chain C) in PDB entry 3ORH
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 129 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63C ARG* 3.6 19.5 - - + +
65C LEU* 3.7 23.6 - - + -
87C TRP* 3.5 57.2 - + - -
124C LEU* 4.1 22.0 - - + -
125C PRO* 4.2 1.8 - - + -
127C GLY 3.7 0.6 - - - -
128C HIS* 1.3 98.8 - + + +
130C ASP* 1.3 62.4 + - - +
131C GLY 3.9 10.5 - - - +
132C ILE* 4.3 9.0 - - + -
159C LEU* 3.0 34.4 + - + +
160C LEU* 3.4 7.2 - - - +
161C LYS* 2.9 29.2 + - - -
164C GLY* 4.5 0.3 - - - -
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Residues in contact with ASP 130 (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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57C ALA 4.8 0.2 - - - -
60C LYS* 3.9 27.2 - - + +
61C GLY 3.4 19.5 - - - +
62C GLY* 3.5 9.5 - - - -
63C ARG* 2.8 30.9 + - - +
129C PHE* 1.3 73.6 - - - +
131C GLY* 1.3 57.1 + - - +
160C LEU* 4.3 0.2 - - - -
161C LYS* 3.3 39.2 + - - +
164C GLY* 3.3 9.0 - - - -
165C VAL 2.9 22.1 + - - -
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Residues in contact with GLY 131 (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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57C ALA 3.3 22.9 + - - -
63C ARG 3.3 4.8 + - - +
64C VAL* 3.3 5.2 - - - +
65C LEU 2.9 24.6 + - - -
129C PHE* 3.4 3.2 - - - +
130C ASP* 1.3 82.7 - - - +
132C ILE* 1.3 66.2 + - - +
160C LEU* 4.2 0.9 - - - -
165C VAL* 3.2 10.5 - - - -
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Residues in contact with ILE 132 (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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57C ALA* 3.8 5.0 - - - +
65C LEU* 3.3 26.9 - - + +
67C VAL* 4.9 0.4 - - + -
129C PHE* 4.3 3.8 - - + -
131C GLY* 1.3 78.6 - - - +
133C LEU* 1.3 67.6 + - - +
134C TYR* 4.4 0.4 - - + +
151C PHE* 3.9 28.3 - - + -
156C ALA* 3.7 35.7 - - + +
159C LEU* 3.9 18.8 - - + -
160C LEU* 3.8 17.3 - - + +
165C VAL 2.9 9.0 + - - +
166C LEU* 3.9 13.7 - - + -
167C THR* 3.0 31.6 + - - +
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Residues in contact with LEU 133 (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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53C LEU* 3.8 16.2 - - + +
54C ALA* 3.7 34.3 - - - +
57C ALA* 3.8 10.5 - - + +
64C VAL* 5.4 1.3 - - + -
65C LEU 2.8 12.6 + - - +
66C GLU* 3.4 17.8 - - + +
67C VAL* 2.8 32.1 + - - +
68C GLY 6.1 0.4 - - - +
74C ALA* 3.8 22.2 - - + -
78C VAL* 4.4 7.4 - - + -
132C ILE* 1.3 74.1 - - - +
134C TYR* 1.3 57.8 + - - +
135C ASP* 3.9 24.7 - - + +
167C THR* 3.5 15.9 - - + +
168C TYR* 5.5 0.4 - - - -
4002C SAH 5.1 0.2 - - - +
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Residues in contact with TYR 134 (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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67C VAL* 3.9 14.4 - - + -
117C TRP* 2.9 40.5 + + - -
132C ILE* 4.1 1.5 - - + -
133C LEU* 1.3 71.2 - - - +
135C ASP* 1.3 61.3 + - - +
136C THR* 2.9 18.5 + - + -
147C HIS* 2.8 41.8 + + - -
148C GLN* 3.7 27.6 - - + -
151C PHE* 3.4 45.1 - + + -
152C ILE* 4.7 2.5 - - + -
166C LEU* 4.9 0.2 - - + -
167C THR 3.0 9.6 + - - +
168C TYR* 3.1 35.0 - - + +
169C CYS 3.2 10.1 + - - -
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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