Contacts of the helix formed by residues 116 - 131 (chain C) in PDB entry 2BP1
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 LYS 116 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114C SER* 2.7 34.9 + - - +
115C LEU* 1.3 73.5 - - - +
117C PRO* 1.4 76.1 - - + +
118C ASP* 3.4 4.9 - - + +
119C SER* 3.0 15.4 + - - +
120C VAL* 3.0 9.8 + - - +
147C GLY 3.8 12.5 + - - -
148C THR* 2.6 31.7 + - + +
149C PRO* 5.6 0.6 - - + +
152C GLU* 3.9 16.8 - - - +
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Residues in contact with PRO 117 (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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115C LEU 3.8 2.0 - - - +
116C LYS* 1.4 85.6 - - + +
118C ASP* 1.3 64.5 + - - +
120C VAL* 3.2 3.1 + - + +
121C ARG* 3.0 25.7 + - - +
152C GLU* 3.8 39.9 - - + +
156C ALA* 3.7 24.6 - - + +
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Residues in contact with ASP 118 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116C LYS* 3.2 4.0 + - + +
117C PRO* 1.3 79.2 - - - +
119C SER* 1.3 57.5 + - - +
121C ARG* 3.6 7.8 + - - +
122C SER* 2.9 30.8 + - - -
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Residues in contact with SER 119 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113C LYS* 3.6 11.2 - - - +
114C SER* 2.8 39.6 + - - -
116C LYS* 3.0 11.1 + - - +
118C ASP* 1.3 76.6 - - - +
120C VAL* 1.3 59.8 + - - +
122C SER* 3.8 5.5 - - - -
123C GLN* 2.9 46.1 + - - +
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Residues in contact with VAL 120 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107C ALA* 4.6 7.6 - - + -
115C LEU* 3.5 43.5 - - + +
116C LYS 3.0 11.0 + - - +
117C PRO* 3.7 6.3 - - + +
119C SER* 1.3 75.5 - - - +
121C ARG* 1.3 62.4 + - - +
123C GLN* 4.0 2.0 - - - +
124C LEU* 3.1 23.0 + - - +
139C PHE* 3.7 30.6 - - + -
141C LEU* 4.8 1.6 - - + -
153C THR* 4.1 11.4 - - + -
156C ALA* 4.5 8.5 - - + -
157C CYS* 4.4 11.2 - - - -
160C LEU* 3.7 14.1 - - + -
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Residues in contact with ARG 121 (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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195A THR* 5.3 5.1 - - - +
117C PRO 3.0 16.4 + - - +
118C ASP* 3.7 7.9 - - - +
120C VAL* 1.3 76.8 - - - +
122C SER* 1.3 59.1 + - - +
124C LEU* 3.2 1.3 + - - +
125C GLU* 2.8 65.8 + - - +
159C ARG* 3.7 18.8 - - - +
160C LEU* 3.6 31.1 - - + +
163C GLU* 3.1 40.6 + - - -
165C LYS* 3.6 0.4 - - - +
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Residues in contact with SER 122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76C PHE* 5.2 0.4 - - - -
118C ASP 2.9 20.4 + - - -
119C SER* 3.8 6.7 - - - -
120C VAL 3.4 0.2 - - - -
121C ARG* 1.3 78.2 - - - +
123C GLN* 1.3 62.7 + - - +
125C GLU* 3.7 6.1 + - - +
126C THR* 3.0 32.4 + - - -
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Residues in contact with GLN 123 (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 PHE* 3.6 39.5 - - + -
106C LYS 5.4 0.2 - - - +
107C ALA* 3.3 19.5 - - + +
108C ASN* 2.7 47.9 + - - +
113C LYS* 3.4 22.7 - - + +
114C SER 3.7 2.2 + - - -
115C LEU* 4.5 1.4 - - - +
119C SER* 2.9 39.1 + - - +
120C VAL 4.0 0.2 - - - +
122C SER* 1.3 76.2 - - - +
124C LEU* 1.3 56.9 + - - +
126C THR 3.3 1.2 + - - -
127C SER* 3.0 32.0 + - - -
139C PHE* 5.5 0.2 - - - -
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Residues in contact with LEU 124 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105C THR* 4.4 8.3 - - + -
120C VAL 3.1 17.9 + - - +
121C ARG* 3.8 4.3 - - - +
123C GLN* 1.3 77.4 - - - +
125C GLU* 1.3 57.0 + - + +
127C SER* 3.2 4.0 + - - -
128C LEU* 2.9 45.3 + - + +
136C VAL* 4.2 14.8 - - + -
139C PHE* 3.7 36.0 - - + -
160C LEU* 4.3 13.5 - - + -
165C LYS* 3.7 26.9 - - + +
166C PHE* 3.8 23.1 - - + -
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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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121C ARG* 2.8 52.1 + - + +
122C SER* 4.2 4.8 - - - +
124C LEU* 1.3 73.7 - - + +
126C THR* 1.3 61.9 + - - +
128C LEU* 3.4 13.3 + - + +
129C LYS* 3.2 21.0 + - - +
160C LEU* 5.7 0.7 - - + -
165C LYS* 3.0 33.2 + - - +
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Residues in contact with THR 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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76C PHE* 3.7 12.4 - - + -
122C SER* 3.0 24.8 + - - -
123C GLN 3.7 4.0 - - - -
125C GLU* 1.3 73.6 - - - +
127C SER* 1.3 59.7 + - - +
129C LYS* 3.3 6.4 + - - +
130C ARG* 3.0 62.6 + - + +
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Residues in contact with SER 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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76C PHE* 3.9 10.0 - - - +
84C GLU* 2.5 38.2 + - - -
105C THR* 3.8 22.3 + - - +
106C LYS 5.0 0.3 + - - -
123C GLN 3.0 16.2 + - - -
124C LEU* 3.4 10.0 - - - -
126C THR* 1.3 76.5 - - - +
128C LEU* 1.3 58.2 + - - +
130C ARG* 3.3 0.9 + - - +
131C LEU* 2.9 39.0 + - - +
136C VAL* 5.7 0.2 - - - -
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Residues in contact with LEU 128 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124C LEU* 2.9 26.6 + - + +
125C GLU* 3.6 12.6 - - + +
127C SER* 1.3 77.8 - - - +
129C LYS* 1.3 56.7 + - - +
131C LEU* 3.7 2.4 + - - -
132C GLN* 3.0 21.0 + - - -
133C CYS* 3.1 33.7 + - - +
134C PRO* 3.9 9.0 - - + +
135C GLN* 3.7 17.5 - - - +
136C VAL* 3.7 29.4 - - + +
165C LYS* 3.9 38.8 - - + +
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Residues in contact with LYS 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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125C GLU 3.2 13.1 + - - +
126C THR* 3.8 8.3 - - - +
128C LEU* 1.3 77.4 - - - +
130C ARG* 1.3 62.2 + - + +
132C GLN* 3.1 19.8 + - - +
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Residues in contact with ARG 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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76C PHE* 3.1 44.5 + - - -
80C ASP 4.2 5.9 + - - -
81C GLY* 3.4 28.6 + - - +
84C GLU* 2.9 51.3 + - + +
85C THR* 3.7 24.9 + - - +
88C GLY* 3.4 13.7 - - - -
126C THR* 3.0 39.1 + - + +
127C SER 3.7 3.1 - - - +
129C LYS* 1.3 77.0 - - + +
131C LEU* 1.3 60.8 + - - +
132C GLN* 3.1 5.8 + - - +
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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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74C THR* 4.4 4.9 - - + -
84C GLU* 3.5 38.1 - - + +
87C LEU* 3.9 17.0 - - + -
88C GLY* 3.4 15.0 - - - +
94C LEU* 3.9 14.0 - - + +
103C ILE* 4.1 26.7 - - + -
105C THR* 4.7 2.5 - - - -
127C SER* 2.9 30.0 + - - +
128C LEU 4.2 0.2 - - - +
130C ARG* 1.3 72.2 - - - +
132C GLN* 1.3 71.0 + - - +
133C CYS* 3.9 17.5 - - - +
136C VAL* 4.0 26.2 - - + -
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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