Contacts of the strand formed by residues 124 - 135 (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 SER 124 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93C VAL 3.0 7.9 - - - -
94C ALA* 3.3 25.3 - - - +
95C ALA 4.3 0.5 + - - -
122C ASP* 3.2 17.1 - - - +
123C LYS* 1.3 81.9 + - - +
125C TYR* 1.3 69.5 + - - +
192C THR* 4.7 0.7 + - - -
193C ASP* 4.6 0.3 - - - +
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Residues in contact with TYR 125 (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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91C GLN* 4.0 14.6 + - + -
93C VAL* 2.8 71.2 + - + +
99C ILE 6.0 1.6 - - - -
101C THR* 4.1 7.4 + - - -
122C ASP 4.4 8.7 - - - -
124C SER* 1.3 79.4 - - - +
126C LEU* 1.3 78.5 + - - +
127C ALA* 4.2 14.1 - - + -
191C ARG* 3.3 39.7 + - + -
192C THR* 3.3 13.5 - - - +
193C ASP* 3.7 28.9 - - + +
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Residues in contact with LEU 126 (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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91C GLN 3.3 4.7 - - - +
92C ALA* 3.7 25.4 - - + -
125C TYR* 1.3 86.9 - - - +
127C ALA* 1.3 62.9 + - - +
190C TYR 3.9 0.2 - - - +
191C ARG* 3.3 3.3 - - - -
192C THR* 2.8 50.6 + - + +
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Residues in contact with ALA 127 (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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88C PHE* 5.4 0.2 - - - -
90C GLY* 3.5 3.6 - - - -
91C GLN* 2.9 54.2 + - + +
125C TYR* 4.2 5.2 - - + -
126C LEU* 1.3 77.7 - - - +
128C ALA* 1.3 63.6 + - - +
129C ARG* 3.9 1.6 - - + +
189C GLU 4.9 1.1 - - - +
190C TYR 3.0 12.8 - - - +
191C ARG* 3.5 19.1 - - + -
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Residues in contact with ALA 128 (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* 3.6 41.3 - - + -
88C PHE* 4.3 9.6 - - + -
89C MSE 4.0 4.7 - - - -
90C GLY* 4.5 2.0 - - - -
127C ALA* 1.3 73.3 - - - +
129C ARG* 1.3 64.4 + - - +
130C GLU 3.6 0.4 - - - -
131C PHE* 3.7 13.1 - - + -
150C ARG* 3.4 10.7 + - - -
189C GLU 4.7 1.0 - - - +
190C TYR* 3.1 22.6 + - + +
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Residues in contact with ARG 129 (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* 3.8 38.0 - - - +
89C MSE 3.0 25.8 + - + +
90C GLY 4.3 0.7 - - - -
91C GLN* 3.0 60.1 + - + +
102C ASP* 4.1 11.1 - - - +
104C LEU* 3.7 21.6 - - - +
127C ALA* 3.9 1.8 - - + -
128C ALA* 1.3 73.9 - - - +
130C GLU* 1.3 68.9 + - + +
150C ARG* 2.6 35.4 + - - +
164C ASN* 3.4 30.2 - - - +
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Residues in contact with GLU 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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87C TYR* 4.1 28.6 - - + -
88C PHE* 3.5 3.3 - - - -
89C MSE 2.9 39.4 + - + +
129C ARG* 1.3 88.6 - - + +
131C PHE* 1.3 69.4 + - - +
132C TRP* 3.2 21.3 + - - +
147C ARG* 5.5 0.9 + - - -
150C ARG 3.5 8.7 - - - +
151C GLN* 3.7 1.3 - - - -
152C ARG* 3.4 18.2 + - - +
164C ASN* 3.8 24.6 + - - +
448C SER* 3.9 21.0 - - - -
449C GLN* 4.7 3.3 - - - +
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Residues in contact with PHE 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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41A ASN* 6.2 0.4 - - + -
42A PHE* 3.3 36.6 - + + -
77A ALA* 5.2 8.3 - - + -
78A PHE 6.2 0.2 - - - -
79A GLY* 6.6 0.2 - - - -
87C TYR 3.3 8.7 - - - +
88C PHE* 3.9 15.0 - - + -
128C ALA* 3.7 17.5 - - + -
130C GLU* 1.3 80.1 - - - +
132C TRP* 1.3 60.6 + - - +
149C GLY* 3.5 4.8 - - - -
150C ARG* 2.9 66.0 + - + -
166C GLU* 5.2 2.7 - - + -
190C TYR* 3.8 29.6 - + - -
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Residues in contact with TRP 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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78C PHE* 4.5 13.9 - + - -
85C SER* 4.2 6.7 - - - -
86C ALA* 3.5 9.0 - - - +
87C TYR* 3.1 69.5 + + + +
130C GLU* 3.2 19.7 + - + -
131C PHE* 1.3 76.4 - - - +
133C VAL* 1.3 57.4 + - - +
134C ASP* 3.5 27.6 - - + -
147C ARG* 3.4 54.6 - - + +
148C PHE 3.0 23.3 - - - +
149C GLY* 4.2 1.6 - - - -
150C ARG 3.1 23.6 - - - +
151C GLN* 3.7 11.2 - - + +
447C MSE 5.4 7.6 - - + -
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Residues in contact with VAL 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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84C TRP* 4.6 17.7 - - + -
85C SER 3.7 8.1 - - - +
86C ALA* 4.5 4.5 - - + +
132C TRP* 1.3 75.7 - - - +
134C ASP* 1.3 60.2 + - - +
146C LEU 4.1 0.5 - - - +
147C ARG* 3.7 1.0 - - - +
148C PHE* 2.9 42.5 + - + +
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Residues in contact with ASP 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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83C ASP 4.2 0.7 - - - +
84C TRP* 3.5 11.4 - - - -
85C SER* 2.9 48.2 + - - +
132C TRP* 3.5 13.9 - - + -
133C VAL* 1.3 75.6 - - - +
135C TYR* 1.3 65.4 + - - +
136C ALA* 4.2 4.5 + - - +
145C HIS* 2.8 42.0 + - - +
146C LEU 3.3 11.0 - - - +
147C ARG* 2.9 21.9 + - - +
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Residues in contact with TYR 135 (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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83C ASP 4.3 2.0 - - - -
84C TRP* 4.0 31.2 - - + -
134C ASP* 1.3 77.6 + - - +
136C ALA* 1.3 60.7 + - - +
137C GLY 3.5 4.1 + - - +
138C LEU* 5.1 6.6 + - + +
144C GLU* 4.8 2.1 - - - +
145C HIS* 3.5 0.9 - - - -
146C LEU* 2.9 45.0 + - + +
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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