Contacts of the strand formed by residues 84 - 95 (chain C) in PDB entry 3RBH
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 TRP 84 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148A PHE* 5.4 14.1 - + - -
80C GLN* 3.8 3.1 - - - +
81C TRP* 3.3 38.9 + - + +
83C ASP* 1.3 87.2 - - + +
85C SER* 1.3 65.0 + - - +
133C VAL* 4.6 15.9 - - + -
134C ASP 3.5 22.7 - - - -
135C TYR* 4.0 24.5 - - + -
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Residues in contact with SER 85 (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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78C PHE* 3.9 18.1 - - - -
79C GLY 3.1 20.2 - - - -
80C GLN* 4.4 10.2 + - - -
81C TRP* 3.7 4.9 - - - -
83C ASP 5.0 0.9 + - - -
84C TRP* 1.3 76.9 - - - +
86C ALA* 1.3 61.4 + - - +
132C TRP* 4.2 4.5 - - - -
133C VAL* 3.7 3.3 - - - +
134C ASP* 2.9 51.5 + - - +
147C ARG* 5.6 0.5 + - - -
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Residues in contact with ALA 86 (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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88A PHE* 5.0 20.4 - - + -
77C ALA 3.9 0.6 - - - +
78C PHE* 3.4 7.1 - - - -
79C GLY 3.3 26.1 + - - -
81C TRP* 3.9 12.8 - - + -
85C SER* 1.3 76.4 - - - +
87C TYR* 1.3 65.1 + - - +
132C TRP* 3.5 14.4 - - - +
133C VAL* 4.7 5.2 - - + -
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Residues in contact with TYR 87 (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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76C TRP* 3.6 37.6 - + + +
77C ALA 3.3 14.1 - - - -
78C PHE* 3.9 15.5 - + + -
86C ALA* 1.3 78.6 - - - +
88C PHE* 1.3 61.7 + - - +
89C MSE 3.6 31.2 - - + +
130C GLU* 4.1 20.4 - - + -
131C PHE* 3.3 5.0 - - - +
132C TRP* 3.1 74.5 + + + +
447C MSE 3.7 21.7 - - - -
448C SER* 6.1 2.5 - - - -
449C GLN* 3.7 13.7 + - - -
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Residues in contact with PHE 88 (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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42A PHE* 3.5 33.4 - + + -
77A ALA* 5.4 3.6 - - + -
75C PRO* 4.7 5.2 - - + -
76C TRP* 3.2 7.7 - - - +
77C ALA* 3.0 39.8 + - + +
87C TYR* 1.3 79.1 - - - +
89C MSE 1.3 61.3 + - - +
90C GLY* 3.3 30.7 - - - -
127C ALA 5.4 0.2 - - - -
128C ALA* 4.3 12.3 - - + -
130C GLU 3.5 13.7 - - - -
131C PHE* 3.9 10.8 - - + -
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Residues in contact with MSE 89 (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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45C ASP* 3.9 11.2 - - - +
74C ARG* 4.0 28.9 - - + +
75C PRO 3.5 9.4 - - - +
76C TRP* 3.9 20.2 - - + -
87C TYR* 3.6 28.5 - - + +
88C PHE* 1.3 79.6 - - - +
90C GLY* 1.3 71.9 + - - +
128C ALA* 3.9 1.4 - - - -
129C ARG* 3.0 41.6 + - + -
130C GLU* 2.9 30.3 + - + +
449C GLN* 3.8 27.4 - - + +
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Residues in contact with GLY 90 (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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74C ARG* 3.3 18.9 - - - +
75C PRO* 3.0 22.3 + - - -
88C PHE* 3.3 19.1 - - - -
89C MSE 1.3 82.2 - - - +
91C GLN* 1.3 63.7 + - - +
127C ALA 3.5 10.5 - - - -
129C ARG* 4.8 0.2 - - - -
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Residues in contact with GLN 91 (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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72C ASP* 2.7 33.2 + - - +
73C LEU 3.2 5.6 - - - -
74C ARG* 3.4 12.1 - - + +
75C PRO* 4.4 2.1 - - - +
90C GLY* 1.3 76.8 - - - +
92C ALA* 1.3 63.9 + - - +
93C VAL* 3.6 19.9 - - + +
101C THR* 4.0 4.6 + - - -
102C ASP* 5.7 0.2 - - - +
125C TYR* 4.0 12.4 + - + -
126C LEU* 3.3 8.0 - - - +
127C ALA* 2.9 46.7 + - + +
129C ARG* 3.0 43.4 + - + +
191C ARG* 6.1 0.2 - - - -
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Residues in contact with ALA 92 (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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71C ILE* 3.8 1.6 - - - +
72C ASP* 3.5 2.8 - - - -
73C LEU* 2.8 57.8 + - + +
91C GLN* 1.3 73.8 - - - +
93C VAL* 1.3 63.0 + - - +
125C TYR 3.6 4.3 - - - -
126C LEU* 3.7 18.6 - - + -
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Residues in contact with VAL 93 (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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71C ILE 3.5 7.4 - - - +
72C ASP* 3.7 12.8 - - - +
91C GLN* 3.6 30.1 - - + +
92C ALA* 1.3 79.4 - - - +
94C ALA* 1.3 69.5 + - - +
95C ALA* 4.6 5.4 - - + +
101C THR* 4.1 16.2 - - + +
123C LYS 4.4 4.9 - - - +
124C SER* 3.0 5.4 - - - -
125C TYR* 2.8 72.5 + - + +
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Residues in contact with ALA 94 (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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70C GLY* 3.3 0.7 - - - -
71C ILE* 2.9 41.6 + - + +
92C ALA 4.4 0.2 - - - -
93C VAL* 1.3 74.5 - - - +
95C ALA* 1.3 61.5 + - - +
123C LYS 3.5 0.7 - - - -
124C SER* 3.3 19.3 - - - +
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Residues in contact with ALA 95 (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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69C ILE 3.1 12.6 - - - +
70C GLY* 3.6 8.7 - - - -
93C VAL* 4.7 8.1 - - + -
94C ALA* 1.3 76.2 - - - +
96C THR* 1.3 63.7 + - - +
97C ASP 3.1 21.3 - - - +
99C ILE* 4.0 12.3 - - + -
123C LYS* 2.8 31.3 + - - +
124C SER* 4.3 0.5 + - - -
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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