Contacts of the strand formed by residues 124 - 133 (chain C) in PDB entry 3BRW
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 GLN 124 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120C VAL* 3.5 5.6 - - - -
121C ILE 3.0 37.3 + - - +
123C ASP* 1.3 85.3 + - - +
125C GLU* 1.3 70.7 + - - +
126C HIS* 3.6 31.7 - - - +
143C PRO* 4.1 10.0 - - - +
144C ILE 6.0 0.2 + - - -
145C SER* 5.8 5.9 + - - +
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Residues in contact with GLU 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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176B LYS* 2.9 23.0 + - - -
118C TYR* 2.6 38.2 + - + +
119C ASP 3.8 2.0 - - - -
120C VAL* 4.3 10.1 - - + -
123C ASP 3.7 6.0 + - - +
124C GLN* 1.3 81.0 + - - +
126C HIS* 1.3 61.2 + - - +
143C PRO* 3.5 8.3 - - - +
144C ILE* 3.0 43.0 + - + +
145C SER 3.0 24.2 - - - +
146C CYS* 4.4 9.2 - - - -
148C THR 5.5 2.0 - - - +
150C PHE* 5.4 0.2 - - - -
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Residues in contact with HIS 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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118C TYR* 3.5 22.7 - - - -
119C ASP* 3.1 20.9 + - + +
121C ILE* 4.0 26.0 - - + +
124C GLN* 3.6 45.1 - - + +
125C GLU* 1.3 74.2 - - - +
127C LEU* 1.3 66.5 + - - +
141C VAL* 4.1 21.5 - - + +
142C ILE 3.7 6.5 - - - -
143C PRO* 4.0 17.5 - - + +
144C ILE* 4.1 3.4 - - - +
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Residues in contact with LEU 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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175B PRO* 5.7 0.7 - - + -
116C LEU* 5.8 0.4 - - + -
117C LYS 3.6 13.5 - - - +
118C TYR* 4.1 18.6 - - + +
119C ASP* 5.0 0.4 - - - +
126C HIS* 1.3 83.0 - - - +
128C ARG* 1.3 63.2 + - - +
129C LEU* 3.7 11.3 + - + +
140C ASP 3.6 0.5 - - - +
141C VAL* 3.5 3.4 - - - +
142C ILE* 3.1 52.4 + - + +
144C ILE* 4.7 15.3 - - + -
150C PHE* 4.2 15.3 - - + -
151C PRO* 4.9 8.3 - - + -
156C MET* 3.5 44.6 - - + -
159C LEU* 5.2 1.1 - - + -
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Residues in contact with ARG 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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89C ILE* 4.3 0.7 - - - -
93C HIS* 3.4 54.6 + - - +
94C PHE* 3.5 31.7 - - + -
116C LEU* 3.6 0.2 - - - -
117C LYS* 3.0 50.7 + - + +
119C ASP* 5.6 4.8 + - + +
126C HIS* 5.4 0.2 - - - +
127C LEU* 1.3 70.3 - - - +
129C LEU* 1.3 65.0 + - - +
139C HIS* 3.1 31.8 + - + +
140C ASP 3.5 4.5 - - - +
141C VAL* 3.4 30.6 - - + +
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Residues in contact with LEU 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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94C PHE* 4.5 0.7 - - - -
114C PHE* 4.1 6.3 - - + -
115C SER 3.7 2.5 - - - -
116C LEU* 4.1 6.5 - - + -
127C LEU* 3.8 13.9 - - + +
128C ARG* 1.3 82.1 - - - +
130C LEU* 1.3 65.5 + - - +
138C TYR 4.4 0.9 - - - -
139C HIS* 3.4 23.2 - - - -
140C ASP 2.8 20.2 + - - +
142C ILE* 3.7 26.5 - - + -
156C MET* 3.1 62.4 - - + +
160C VAL* 3.8 26.7 - - + -
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Residues in contact with LEU 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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86C THR* 4.9 4.9 - - + +
89C ILE* 4.4 12.3 - - + -
90C TYR* 3.8 25.8 - - + +
94C PHE* 3.8 21.5 - - + -
113C VAL 4.0 1.7 - - - +
114C PHE* 3.3 4.2 - - - -
115C SER* 2.8 40.4 + - - +
129C LEU* 1.3 82.1 - - - +
131C LEU* 1.3 61.1 + - - +
132C ARG* 3.6 28.0 + - - +
137C THR* 4.5 11.9 - - - +
138C TYR 3.3 6.1 - - - +
139C HIS* 3.8 29.2 - - + -
185C ASP* 4.2 2.9 - - - +
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Residues in contact with LEU 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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112C LEU* 3.8 21.5 - - + -
113C VAL 4.0 0.9 - - - +
114C PHE* 3.7 20.8 - - + -
130C LEU* 1.3 75.9 - - - +
132C ARG* 1.3 74.6 + - - +
133C THR* 3.9 4.9 - - - +
137C THR* 3.2 4.0 + - - -
138C TYR* 2.7 49.2 + - + +
157C ALA* 3.9 22.9 - - + +
160C VAL* 4.0 14.3 - - + +
161C CYS* 4.3 15.5 - - + -
164C VAL* 3.7 22.4 - - + -
169C PHE* 4.4 7.4 - - + -
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Residues in contact with ARG 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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90C TYR* 3.9 1.2 - - - -
101C ASN* 4.6 0.2 + - - -
111C HIS 3.9 0.9 - - - +
112C LEU* 3.5 9.0 - - - +
113C VAL* 3.0 55.7 + - + +
115C SER* 2.6 42.6 + - - +
130C LEU* 3.6 20.1 + - - +
131C LEU* 1.3 76.3 - - - +
133C THR* 1.3 60.2 + - - +
136C ARG 3.9 3.1 - - - -
137C THR* 3.4 25.4 - - - +
181C ILE* 3.6 21.9 - - - +
184C PHE* 3.4 24.0 - - + -
185C ASP* 2.9 42.0 + - - -
390C ARG* 4.1 4.7 - - - +
394C LEU* 4.1 7.0 - - + +
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Residues in contact with THR 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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109C LEU* 3.7 29.6 + - + +
111C HIS 4.2 0.2 - - - -
112C LEU* 4.0 17.9 - - - -
131C LEU* 3.9 3.5 - - + +
132C ARG* 1.3 74.8 - - - +
134C LYS* 1.3 73.4 + - - +
135C CYS* 3.0 12.0 + - + +
136C ARG* 2.8 37.6 + - + +
138C TYR* 3.3 35.4 - - + +
390C ARG* 3.4 10.0 + - - -
394C LEU* 3.6 6.3 - - - +
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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