Contacts of the helix formed by residues 117 - 131 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113A VAL* 3.3 17.8 - - + +
114A THR* 2.7 36.2 + - - +
115A LYS 3.1 0.6 - - - -
116A GLU* 1.3 79.7 - - - +
118A GLY* 1.3 65.8 + - - +
119A MET 3.6 0.2 + - - -
120A GLU* 3.7 6.9 + - - +
121A GLY* 3.1 27.3 + - - -
203D GLY 4.3 13.7 + - - -
205D SER* 3.4 29.2 - - - +
234D GLN* 3.1 23.8 + - - +
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Residues in contact with GLY 118 (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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92A PRO* 3.8 17.7 - - - -
94A ASN* 5.4 0.4 - - - -
113A VAL* 3.7 6.8 - - - +
114A THR 2.6 18.7 + - - -
115A LYS* 2.9 16.0 + - - -
117A GLN* 1.3 78.3 - - - +
119A MET* 1.3 62.5 + - - -
120A GLU* 5.2 0.9 - - - -
122A ALA* 3.2 14.6 + - - +
210A ARG* 5.4 3.1 - - - -
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Residues in contact with MET 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A ALA* 4.0 8.3 - - + +
68A THR* 3.2 48.0 - - - +
69A SER* 3.6 15.7 - - - +
92A PRO* 3.8 17.9 - - + +
95A MET* 6.1 0.7 - - - +
117A GLN 3.6 0.2 + - - -
118A GLY* 1.3 72.3 - - - -
120A GLU* 1.3 66.4 + - - +
122A ALA* 3.2 5.0 + - - +
123A ARG* 3.1 24.9 + - - +
141A PHE* 4.0 18.2 - - + -
210A ARG* 3.8 33.5 - - - +
212A TRP* 3.5 24.2 - - + -
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Residues in contact with GLU 120 (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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117A GLN 4.3 4.9 - - - +
118A GLY* 3.3 0.7 - - - -
119A MET* 1.3 80.0 + - - +
121A GLY* 1.3 57.8 + - - +
123A ARG* 3.2 8.1 + - - +
124A ASP* 2.9 31.4 + - - -
210A ARG* 3.6 11.9 + - - -
212A TRP* 3.2 17.8 - - + -
213A PRO* 2.8 34.9 - - + +
216A TYR* 3.3 53.4 - - + +
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Residues in contact with GLY 121 (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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113A VAL* 4.8 5.6 - - - +
117A GLN* 3.1 29.9 + - - -
118A GLY 3.9 0.7 - - - -
120A GLU* 1.3 78.4 - - - +
122A ALA* 1.3 56.0 + - - +
124A ASP* 3.7 11.3 - - - +
125A LEU* 3.0 29.5 + - - +
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Residues in contact with ALA 122 (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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67A ALA* 3.1 26.1 - - + +
90A LEU* 3.2 28.2 - - + +
91A MET 4.6 0.4 - - - +
92A PRO* 4.7 4.7 - - + -
113A VAL* 4.3 13.6 - - + +
118A GLY 3.2 12.5 + - - +
119A MET* 3.2 13.5 + - - +
121A GLY* 1.3 74.5 - - - +
123A ARG* 1.3 60.5 + - - +
125A LEU* 4.4 1.1 - - - -
126A ALA* 2.8 22.7 + - - +
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Residues in contact with ARG 123 (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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67A ALA* 4.0 7.2 - - + -
119A MET 3.1 17.6 + - - +
120A GLU* 3.4 7.4 - - - +
122A ALA* 1.3 75.4 - - - +
124A ASP* 1.3 65.9 + - - +
126A ALA* 3.0 5.7 + - - +
127A LEU* 2.9 23.8 + - - +
137A LEU* 5.4 0.5 - - - +
139A ASP* 5.3 0.4 + - - -
141A PHE* 3.5 63.3 - - + +
142A ASN* 4.1 17.0 + - - +
212A TRP* 3.5 24.0 - - - -
216A TYR* 2.8 62.7 + - + +
217A LEU 4.7 0.6 + - - -
218A PRO* 4.5 2.8 - - - +
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Residues in contact with ASP 124 (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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120A GLU 2.9 14.0 + - - +
121A GLY* 3.7 10.8 - - - +
123A ARG* 1.3 73.6 - - - +
125A LEU* 1.3 56.1 + - - +
127A LEU* 3.1 16.5 + - - +
128A GLU* 2.8 39.3 + - - +
216A TYR* 2.3 40.5 + - - -
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Residues in contact with LEU 125 (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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90A LEU* 3.3 21.1 - - + -
111A ILE* 4.3 10.5 - - + -
113A VAL* 3.9 21.1 - - + -
121A GLY 3.0 18.2 + - - +
122A ALA* 4.4 0.4 - - - -
124A ASP* 1.3 73.2 - - - +
126A ALA* 1.3 65.7 + - - +
128A GLU* 3.4 12.5 + - + -
129A MET* 3.2 34.2 + - + +
132A ARG* 4.7 10.5 - - - +
234D GLN* 6.0 1.6 - - - +
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Residues in contact with ALA 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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65A ILE* 4.3 11.2 - - + +
67A ALA* 4.1 10.3 - - + +
90A LEU* 3.1 11.7 - - + +
122A ALA 2.8 21.1 + - - +
123A ARG* 3.0 9.2 + - - +
125A LEU* 1.3 78.1 - - - +
127A LEU* 1.3 63.7 + - - +
129A MET* 3.5 2.6 + - - +
130A ALA* 3.5 19.1 + - - +
137A LEU* 3.6 29.3 - - + +
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Residues in contact with LEU 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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123A ARG 2.9 12.5 + - - +
124A ASP* 3.1 10.7 + - - +
126A ALA* 1.3 77.0 - - - +
128A GLU* 1.3 69.6 + - - +
130A ALA* 3.4 3.1 + - + +
131A ASN* 3.1 49.6 + - + +
137A LEU* 3.9 19.5 - - + +
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Residues in contact with GLU 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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124A ASP* 2.8 30.4 + - - +
125A LEU* 3.6 17.9 - - + +
126A ALA 3.2 0.2 - - - -
127A LEU* 1.3 79.6 - - - +
129A MET* 1.3 63.8 + - - +
131A ASN* 2.9 7.6 + - - -
132A ARG* 2.8 47.5 + - + +
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Residues in contact with MET 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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65A ILE* 3.3 42.8 - - + -
88A LYS* 4.8 11.7 - - + -
90A LEU* 3.4 25.6 - - + -
111A ILE* 5.2 12.3 - - + -
125A LEU* 3.2 27.5 + - + +
126A ALA 3.8 2.5 - - - +
128A GLU* 1.3 78.3 - - - +
130A ALA* 1.3 61.0 + - - +
132A ARG* 3.1 28.9 + - - +
133A GLY 3.2 0.5 + - - -
134A GLU* 2.9 50.7 + - - +
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Residues in contact with ALA 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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65A ILE* 3.9 5.8 - - + +
126A ALA 3.5 3.9 + - - +
127A LEU* 3.4 8.6 + - + +
128A GLU 3.2 0.4 - - - -
129A MET* 1.3 74.7 - - - +
131A ASN* 1.3 63.2 + - - +
132A ARG 3.0 4.7 - - - -
133A GLY* 3.0 18.9 + - - -
134A GLU 4.3 0.4 - - - +
135A GLY 3.4 25.4 - - - +
136A LYS* 4.8 0.2 - - - -
137A LEU* 3.9 31.0 - - + +
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Residues in contact with ASN 131 (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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127A LEU* 3.1 44.0 + - + +
128A GLU* 2.9 8.5 + - - +
130A ALA* 1.3 77.9 - - - +
132A ARG* 1.3 59.9 + - - +
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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