Contacts of the strand formed by residues 124 - 135 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93A VAL 3.0 8.7 - - - -
94A ALA* 3.5 20.0 - - - +
95A ALA 4.6 0.5 + - - -
122A ASP* 3.5 18.3 - - - +
123A LYS* 1.3 84.5 + - - +
125A TYR* 1.3 65.7 + - - +
192A THR* 4.7 0.5 + - - -
193A ASP* 4.6 0.3 - - - +
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Residues in contact with TYR 125 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91A GLN* 4.0 14.7 + - + -
92A ALA* 3.6 0.3 - - - -
93A VAL* 3.0 68.7 + - + +
101A THR* 4.2 6.4 + - - -
122A ASP 4.4 8.5 - - - -
123A LYS 5.2 0.4 - - - -
124A SER* 1.3 78.7 - - - +
126A LEU* 1.3 80.9 + - - +
127A ALA* 4.1 14.4 - - + -
191A ARG* 3.4 40.0 + - + -
192A THR* 3.3 14.1 - - - +
193A ASP* 3.7 28.0 - - + +
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Residues in contact with LEU 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A GLN 3.2 4.7 - - - +
92A ALA* 3.8 23.3 - - + -
125A TYR* 1.3 85.7 - - - +
127A ALA* 1.3 61.5 - - - +
191A ARG* 3.3 3.5 - - - -
192A THR* 2.9 50.7 + - + +
42C PHE* 3.4 40.2 - - + -
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Residues in contact with ALA 127 (chain A).
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* 5.2 0.5 - - - -
90A GLY* 3.4 3.6 - - - -
91A GLN* 2.8 52.4 + - + +
125A TYR* 4.1 4.9 - - + -
126A LEU* 1.3 79.0 - - - +
128A ALA* 1.3 64.4 + - - +
129A ARG* 3.9 1.3 - - + -
189A GLU 5.0 0.7 - - - +
190A TYR 3.1 13.0 - - - +
191A ARG* 3.5 18.6 - - + -
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Residues in contact with ALA 128 (chain A).
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* 4.1 18.6 - - + -
89A MSE 3.9 4.3 - - - -
90A GLY* 4.4 1.3 - - - -
127A ALA* 1.3 73.3 - - - +
129A ARG* 1.3 64.2 + - - +
130A GLU 3.6 0.2 - - - -
131A PHE* 3.8 27.4 - - + -
150A ARG* 3.4 10.6 + - - -
189A GLU 4.7 0.9 - - - +
190A TYR* 3.1 27.4 + - + +
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Residues in contact with ARG 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A ARG* 3.7 33.6 - - - +
89A MSE 2.9 26.6 + - + +
90A GLY 4.3 0.7 - - - -
91A GLN* 3.0 60.9 + - + +
102A ASP* 3.5 30.7 + - - +
104A LEU* 4.7 6.7 - - - +
127A ALA* 4.9 1.6 - - + -
128A ALA* 1.3 73.5 - - - +
130A GLU* 1.3 67.9 + - + +
150A ARG* 2.7 35.1 + - - +
152A ARG* 6.2 0.2 - - - +
164A ASN* 3.5 30.8 - - - +
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Residues in contact with GLU 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A TYR* 4.0 28.2 + - + -
88A PHE* 3.3 2.9 - - - -
89A MSE 2.8 40.8 + - + +
129A ARG* 1.3 88.7 - - + +
131A PHE* 1.3 70.2 + - - +
132A TRP* 3.2 20.2 + - - +
147A ARG* 5.5 1.4 + - - -
150A ARG 3.5 9.6 - - - +
151A GLN* 4.4 1.1 - - - -
152A ARG* 3.5 15.0 + - - +
164A ASN* 3.8 24.9 + - - +
448A SER* 2.8 29.0 + - - -
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Residues in contact with PHE 131 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87A TYR 3.1 8.3 - - - +
88A PHE* 3.8 18.2 - + + -
128A ALA* 3.8 29.6 - - + -
130A GLU* 1.3 79.9 - - - +
132A TRP* 1.3 60.0 + - - +
149A GLY* 3.5 3.9 - - - -
150A ARG* 2.9 70.2 + - + -
166A GLU* 5.2 2.9 - - + -
190A TYR* 3.8 32.5 - + - -
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Residues in contact with TRP 132 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78A PHE* 4.3 15.3 - + - -
85A SER* 4.1 6.7 - - - -
86A ALA* 3.2 11.0 - - - +
87A TYR* 2.9 71.3 + + + +
130A GLU* 3.2 20.4 + - - -
131A PHE* 1.3 75.7 - - - +
133A VAL* 1.3 60.5 - - - +
134A ASP* 3.6 29.4 - - + -
147A ARG* 3.5 49.5 - - + +
148A PHE 3.0 23.8 - - - +
149A GLY* 4.1 1.1 - - - -
150A ARG 3.1 23.6 - - - +
151A GLN* 3.7 10.3 - - + +
447A MSE 5.4 7.2 - - + -
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Residues in contact with VAL 133 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81A TRP* 5.7 0.4 - - + -
84A TRP* 4.6 20.0 - - + -
85A SER 3.4 5.2 - - - +
86A ALA* 4.2 14.6 - - + -
132A TRP* 1.3 78.7 - - - +
134A ASP* 1.3 60.1 + - - +
146A LEU 4.0 0.5 - - - +
147A ARG* 3.6 2.3 - - - +
148A PHE* 2.8 58.1 + - + +
148C PHE* 4.9 11.4 - - + -
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Residues in contact with ASP 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A ASP 3.6 0.7 - - - +
84A TRP* 3.3 11.0 - - - -
85A SER* 2.7 52.1 + - - +
132A TRP* 3.6 13.5 - - + -
133A VAL* 1.3 74.7 - - - +
135A TYR* 1.3 65.8 + - - +
136A ALA* 4.2 4.0 + - - +
145A HIS* 2.9 41.3 + - - +
146A LEU 3.3 6.4 - - - +
147A ARG* 2.9 27.0 + - - +
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Residues in contact with TYR 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A ASP* 3.3 24.2 + - + -
84A TRP* 3.5 48.7 - + + -
134A ASP* 1.3 75.7 + - - +
136A ALA* 1.3 59.5 + - - +
137A GLY* 3.4 18.4 + - - -
138A LEU* 3.4 44.7 - - + +
144A GLU* 4.9 1.9 - - - +
145A HIS* 3.6 0.7 - - - -
146A LEU* 2.9 43.1 + - + +
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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