Contacts of the helix formed by residues 117 - 134 (chain A) in PDB entry 2BU6
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 ASP 117 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79A TRP* 4.4 10.7 - - + -
113A ASN 5.7 0.2 - - - +
114A ARG 5.1 1.2 + - - -
115A HIS 3.2 1.0 - - - -
116A ASN* 1.3 85.8 - - - +
118A VAL* 1.3 64.1 + - - +
119A VAL 3.3 2.5 - - - -
120A PRO* 3.2 19.0 - - + +
121A THR* 2.9 30.9 + - - +
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Residues in contact with VAL 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A VAL* 4.6 4.5 - - + -
79A TRP* 3.9 17.9 - - + -
80A TYR* 4.4 2.9 - - + +
115A HIS* 2.9 52.1 + - + +
116A ASN 3.4 1.2 - - - -
117A ASP* 1.3 78.0 - - - +
119A VAL* 1.3 58.7 + - - +
121A THR* 3.7 1.1 - - - -
122A MET* 2.9 32.3 + - + +
150A PHE* 3.5 37.7 - - + -
151A TYR* 4.8 1.1 - - + -
154A ARG* 3.6 21.1 - - - +
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Residues in contact with VAL 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A ASN 5.7 1.1 - - - +
118A VAL* 1.3 77.6 - - - +
120A PRO* 1.3 73.0 - - + +
123A ALA* 2.8 21.0 + - - +
151A TYR* 3.5 28.4 + - + +
154A ARG* 3.6 25.3 - - - +
320A TYR* 4.0 14.4 - - + -
324A ILE* 3.8 30.1 - - + -
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Residues in contact with PRO 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A ASN 4.9 1.8 - - - +
117A ASP* 3.2 30.7 - - + +
119A VAL* 1.3 97.0 - - + +
121A THR* 1.3 55.3 + - - +
123A ALA* 3.1 10.4 + - + +
124A GLN* 2.9 28.8 + - - +
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Residues in contact with THR 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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72A SER* 3.5 21.2 - - - +
75A LEU* 4.1 19.0 - - + +
76A VAL* 3.5 28.0 - - + -
79A TRP* 3.8 12.3 - - + -
117A ASP* 2.9 23.9 + - - +
118A VAL 3.7 3.4 - - - -
120A PRO* 1.3 79.5 - - - +
122A MET* 1.3 61.2 + - - +
124A GLN* 3.2 24.3 - - + +
125A GLY 3.5 4.0 + - - -
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Residues in contact with MET 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A ILE* 6.3 0.7 - - + -
72A SER* 5.1 1.8 - - - -
73A VAL* 4.6 23.6 - - + -
76A VAL* 3.6 31.4 - - + -
118A VAL* 2.9 25.0 + - + +
121A THR* 1.3 74.9 - - - +
123A ALA* 1.3 65.6 + - - +
125A GLY* 3.0 12.7 + - - +
126A VAL* 3.2 16.2 + - - +
146A PHE* 3.7 33.0 - - + -
147A LEU* 3.9 12.1 - - + -
150A PHE* 3.8 24.0 - - + -
151A TYR* 3.4 17.5 - - + +
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Residues in contact with ALA 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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119A VAL 2.8 11.2 + - - +
120A PRO* 3.3 14.1 - - + +
122A MET* 1.3 76.0 - - - +
124A GLN* 1.3 62.8 + - - +
126A VAL* 3.0 14.7 + - - +
127A LEU* 3.1 13.2 + - - +
151A TYR* 4.2 0.8 + - - -
302A THR* 4.2 6.2 - - + +
320A TYR* 3.2 40.8 + - + +
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Residues in contact with GLN 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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71A PRO* 6.2 1.8 - - - +
72A SER* 4.9 6.8 - - - +
120A PRO 2.9 11.1 + - - +
121A THR* 3.2 19.0 + - - +
122A MET 3.1 0.2 - - - -
123A ALA* 1.3 77.6 - - - +
125A GLY* 1.3 55.8 + - - +
127A LEU* 3.3 9.4 + - + +
128A GLU* 2.9 45.5 + - + +
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Residues in contact with GLY 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A THR* 5.2 3.8 - - - +
72A SER* 3.4 24.1 + - - -
73A VAL* 5.7 2.5 - - - -
121A THR 3.5 3.8 + - - -
122A MET 3.0 9.5 + - - -
124A GLN* 1.3 76.6 - - - +
126A VAL* 1.3 59.3 + - - +
128A GLU* 3.5 9.4 - - - +
129A TYR* 2.9 28.4 + - - +
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Residues in contact with VAL 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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122A MET 3.2 13.4 + - - +
123A ALA* 3.0 9.5 + - - +
125A GLY* 1.3 76.8 - - - +
127A LEU* 1.3 57.6 + - - +
129A TYR* 3.2 7.6 + - - +
130A LYS* 2.9 30.7 + - + +
143A ILE* 4.4 12.8 - - + -
147A LEU* 3.8 26.9 - - + -
298A TYR 4.1 0.7 - - - +
299A MET* 3.8 26.0 - - + +
302A THR* 3.7 21.1 - - - +
320A TYR* 3.5 15.0 - - - +
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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 ALA 3.1 5.7 + - - +
124A GLN* 3.3 11.0 + - + +
126A VAL* 1.3 78.3 - - - +
128A GLU* 1.3 64.4 + - - +
130A LYS* 3.3 22.6 + - + -
131A ASP* 3.2 38.9 + - - +
302A THR* 4.0 17.2 - - + +
303A ALA 4.0 19.3 - - - +
304A PRO* 4.0 30.3 - - + -
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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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70A THR* 3.4 33.9 - - + +
71A PRO* 3.9 15.2 - - - +
72A SER* 4.2 7.1 + - - -
124A GLN* 2.9 37.0 + - + +
125A GLY* 3.5 11.9 - - - +
127A LEU* 1.3 76.7 - - - +
129A TYR* 1.3 58.8 + - - +
131A ASP* 3.4 4.0 + - - +
132A THR* 2.8 39.5 + - - +
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Residues in contact with TYR 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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66A ARG* 2.6 33.8 + - - -
67A VAL* 4.0 27.1 - - + -
70A THR* 6.1 1.3 - - - +
125A GLY 2.9 13.8 + - - +
126A VAL* 3.2 11.2 + - - +
128A GLU* 1.3 77.1 - - - +
130A LYS* 1.3 59.0 + - - +
132A THR* 3.0 4.4 + - - -
133A TYR* 2.7 53.7 + + + +
134A GLY 3.4 21.9 + - - -
139A SER* 2.8 32.5 + - - -
143A ILE* 4.2 22.4 - - + -
299A MET* 4.9 2.5 - - - -
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Residues in contact with LYS 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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126A VAL* 2.9 18.6 + - + +
127A LEU* 3.3 19.9 + - + +
129A TYR* 1.3 77.6 - - + +
131A ASP* 1.3 62.9 + - - +
134A GLY* 2.9 34.7 + - - -
135A ASP* 3.7 28.5 + - + +
299A MET* 3.5 42.6 + - + +
300A TYR* 5.1 3.6 - - - +
302A THR* 3.6 31.2 + - - -
304A PRO 5.4 3.8 - - - -
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Residues in contact with ASP 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* 3.2 35.7 + - - +
128A GLU* 4.1 2.9 - - - +
130A LYS* 1.3 80.0 - - - +
132A THR* 1.3 62.1 + - - +
134A GLY 4.7 0.4 - - - -
304A PRO 5.7 3.0 - - - +
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Residues in contact with THR 132 (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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128A GLU* 2.8 29.8 + - - +
129A TYR* 3.9 0.9 - - - -
131A ASP* 1.3 80.8 - - - +
133A TYR* 1.3 96.0 + - + +
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Residues in contact with TYR 133 (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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66A ARG* 3.8 51.2 - - + +
70A THR* 6.4 0.4 - - + -
129A TYR* 2.7 50.9 + + + +
132A THR* 1.3 107.5 - - + +
134A GLY* 1.3 59.5 + - - +
136A ASP* 4.3 6.9 - - - +
139A SER* 5.4 0.2 + - - -
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Residues in contact with GLY 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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129A TYR* 3.4 27.8 + - - -
130A LYS* 2.9 23.2 + - - -
131A ASP 4.7 0.2 - - - -
132A THR 3.9 0.6 - - - -
133A TYR* 1.3 79.0 - - - +
135A ASP* 1.3 61.6 + - - -
136A ASP* 3.7 7.3 + - - +
139A SER* 4.1 0.2 + - - -
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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