Contacts of the helix formed by residues 117 - 132 (chain C) in PDB entry 2BHT
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 117 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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203B GLY 4.0 10.7 + - - +
205B SER* 3.5 14.5 - - - +
234B GLN* 2.5 32.8 + - - -
113C VAL* 3.0 29.6 - - + +
114C THR* 3.2 25.0 + - - +
116C GLU* 1.3 80.4 - - + +
118C GLY* 1.3 56.8 + - - +
120C GLU* 3.5 9.0 + - - +
121C GLY* 2.6 42.1 + - - -
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Residues in contact with GLY 118 (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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92C PRO* 3.7 22.0 - - - -
94C ASN* 5.8 0.2 - - - -
113C VAL* 3.7 2.6 - - - +
114C THR 3.5 7.9 + - - -
115C LYS 3.9 7.8 + - - -
116C GLU 3.4 1.8 - - - -
117C GLN* 1.3 73.6 - - - +
119C MET* 1.3 52.2 + - - -
120C GLU* 3.0 10.3 - - - -
122C ALA* 2.5 36.4 + - - +
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Residues in contact with MET 119 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C ALA* 4.2 5.6 - - + -
68C THR* 3.4 31.4 - - - +
69C SER* 2.9 29.8 - - - +
92C PRO* 3.7 15.3 - - + -
95C MET* 4.5 3.8 - - + -
118C GLY* 1.3 69.9 - - - -
120C GLU* 1.3 62.6 + - - +
122C ALA* 3.7 7.6 - - - -
123C ARG* 3.1 24.4 + - - +
141C PHE* 3.3 39.0 - - + -
210C ARG* 4.0 19.3 - - - +
212C TRP* 3.6 21.9 - - + -
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Residues in contact with GLU 120 (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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116C GLU 5.3 0.5 - - - +
117C GLN 3.6 10.2 - - - +
118C GLY* 4.1 2.6 - - - -
119C MET* 1.3 88.9 + - - +
121C GLY* 1.3 58.3 + - - +
122C ALA 3.3 0.4 - - - -
123C ARG 3.7 1.1 + - - +
124C ASP* 2.3 39.0 + - - +
210C ARG* 4.4 8.7 - - - +
212C TRP* 3.8 12.5 - - + -
213C PRO* 3.6 25.6 - - + +
216C TYR* 3.4 47.5 - - + +
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Residues in contact with GLY 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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90C LEU* 4.7 0.2 - - - +
113C VAL* 4.8 2.9 - - - -
117C GLN* 2.6 43.2 + - - -
118C GLY 3.6 0.4 - - - -
120C GLU* 1.3 70.0 - - - +
122C ALA* 1.3 64.5 + - - +
124C ASP* 3.1 14.2 + - - +
125C LEU* 3.2 15.8 + - - +
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Residues in contact with ALA 122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C ALA* 3.7 15.4 - - + +
90C LEU* 3.1 40.8 - - + +
92C PRO* 4.6 7.2 - - + -
113C VAL* 4.1 14.5 - - + +
118C GLY 2.5 22.2 + - - +
119C MET* 3.7 13.0 - - + -
121C GLY* 1.3 72.8 - - - +
123C ARG* 1.3 61.9 + - - +
126C ALA* 3.4 10.6 + - - +
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Residues in contact with ARG 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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67C ALA* 3.8 10.1 - - + -
119C MET* 3.1 17.9 + - + +
120C GLU* 4.0 5.8 - - - +
121C GLY 3.2 0.6 - - - -
122C ALA* 1.3 80.4 - - - +
124C ASP* 1.3 66.8 + - - +
126C ALA* 3.5 4.2 + - - +
127C LEU* 3.5 18.9 + - - +
137C LEU* 5.6 1.4 - - - +
139C ASP* 5.0 3.8 - - - -
141C PHE* 3.0 59.7 - - + +
142C ASN* 4.7 7.7 - - - +
212C TRP* 3.0 48.8 - - - +
216C TYR* 2.7 41.4 + - + +
217C LEU 5.1 0.2 + - - -
218C PRO* 4.3 5.3 - - - +
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Residues in contact with ASP 124 (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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120C GLU 2.3 26.3 - - - +
121C GLY* 3.1 6.8 + - - +
123C ARG* 1.3 79.9 - - - +
125C LEU* 1.3 60.3 + - - +
127C LEU* 3.5 8.6 + - - +
128C GLU* 3.1 24.2 + - - +
216C TYR* 2.5 32.5 + - - -
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Residues in contact with LEU 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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233B HIS* 6.0 5.8 - - + +
90C LEU* 3.5 24.9 - - + -
111C ILE* 4.4 13.5 - - + -
113C VAL* 5.0 5.2 - - + -
121C GLY 3.2 12.7 + - - +
124C ASP* 1.3 76.4 - - - +
126C ALA* 1.3 55.6 + - - +
127C LEU 3.2 0.4 - - - -
128C GLU* 3.8 30.7 - - - +
129C MET* 2.6 64.2 + - + +
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Residues in contact with ALA 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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65C ILE* 3.6 13.3 - - + +
66C GLU 4.4 2.0 - - - -
67C ALA* 4.3 13.7 - - + +
90C LEU* 4.1 20.6 - - + +
122C ALA 3.4 16.4 + - - +
123C ARG* 3.7 6.7 - - - +
124C ASP 3.3 0.6 - - - -
125C LEU* 1.3 80.3 - - - +
127C LEU* 1.3 56.3 + - - +
129C MET* 4.4 3.1 - - - -
130C ALA* 3.0 25.3 + - - +
137C LEU* 4.2 20.5 - - + +
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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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123C ARG 3.5 10.6 + - - +
124C ASP* 3.9 9.2 - - - +
125C LEU 3.2 0.2 - - - -
126C ALA* 1.3 75.6 - - - +
128C GLU* 1.3 61.5 + - - +
129C MET 3.3 0.2 - - - -
130C ALA* 4.0 6.3 - - + -
131C ASN* 2.8 51.3 + - - +
137C LEU* 4.3 23.0 - - + +
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Residues in contact with GLU 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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233B HIS* 5.4 8.0 + - - -
124C ASP 3.1 15.2 + - - +
125C LEU* 3.1 31.6 + - + +
127C LEU* 1.3 76.2 - - - +
129C MET* 1.3 64.4 + - + +
131C ASN* 3.3 9.6 + - - +
132C ARG* 3.2 39.4 + - - +
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Residues in contact with MET 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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296B HIS 4.7 0.7 - - - +
65C ILE* 3.9 14.6 - - + -
88C LYS* 3.7 17.5 - - + -
90C LEU* 3.7 17.3 - - - -
111C ILE* 3.7 13.0 - - + -
125C LEU* 2.6 60.5 + - + +
126C ALA* 3.8 4.7 - - - +
128C GLU* 1.3 74.7 - - + +
130C ALA* 1.3 58.9 + - - +
132C ARG* 3.3 19.4 + - - +
134C GLU* 2.9 64.8 + - + +
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Residues in contact with ALA 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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65C ILE* 3.5 15.2 - - + +
126C ALA 3.0 19.9 + - - +
127C LEU* 3.6 14.1 - - + +
128C GLU 3.2 0.2 - - - -
129C MET* 1.3 76.0 - - - +
131C ASN* 1.3 59.0 + - - +
133C GLY* 2.9 19.9 + - - -
135C GLY 3.8 13.3 - - - +
137C LEU* 4.1 17.3 - - + +
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Residues in contact with ASN 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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127C LEU* 2.8 47.4 + - - +
128C GLU* 3.7 9.3 - - - +
129C MET 3.3 0.2 - - - -
130C ALA* 1.3 76.5 - - - +
132C ARG* 1.3 60.2 + - + +
133C GLY 3.2 2.0 + - - -
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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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235B ARG* 5.4 8.5 - - - +
128C GLU* 3.2 31.6 + - + +
129C MET* 3.7 15.0 + - - +
130C ALA 3.1 0.6 - - - -
131C ASN* 1.3 78.5 - - + +
133C GLY* 1.3 60.6 + - - +
134C GLU* 3.3 23.8 + - + +
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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