Contacts of the helix formed by residues 105 - 115 (chain A) in PDB entry 1BMO
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 SER 105 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62A HIS* 5.9 1.0 - - - -
92A GLU 4.1 1.0 + - - -
94A VAL* 3.4 27.8 - - - +
104A SER* 1.3 72.4 - - - +
106A CYS* 1.3 55.8 + - - +
108A PHE* 4.1 1.6 - - - -
109A PHE* 2.7 63.6 + - - -
126A LEU* 4.7 5.2 - - - -
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Residues in contact with CYS 106 (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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63A GLY* 5.3 0.9 - - - -
79A GLN* 3.2 23.1 - - - -
84A CYS* 2.0 45.8 - - + -
85A PRO* 4.6 8.5 - - + -
104A SER* 3.0 9.9 + - - +
105A SER* 1.3 81.7 + - - +
107A HIS* 1.3 51.9 + - - +
109A PHE* 3.2 4.7 + - - +
110A ALA* 2.8 36.0 + - - +
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Residues in contact with HIS 107 (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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81A PRO* 2.8 37.5 + - + +
82A THR* 4.7 4.3 - - + +
84A CYS* 3.7 16.2 + - + +
85A PRO 3.6 20.0 - - - -
86A ALA* 4.6 1.3 - - - -
87A PRO* 4.3 6.1 - - + -
102A PHE* 4.2 4.0 - - + -
103A ASP* 3.3 37.1 + - + +
104A SER* 2.6 34.0 + - - +
106A CYS* 1.3 78.8 - - - +
108A PHE* 1.3 57.5 + - - +
110A ALA* 3.1 5.7 + - - +
111A THR* 2.8 33.8 + - - +
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Residues in contact with PHE 108 (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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94A VAL* 3.9 17.5 - - + -
96A SER* 3.6 24.5 - - - -
102A PHE* 3.5 33.1 - + + -
104A SER 2.8 12.4 + - - +
105A SER 3.5 5.8 - - - +
107A HIS* 1.3 75.8 - - - +
109A PHE* 1.3 95.4 + + - +
111A THR* 3.1 4.0 + - - -
112A LYS* 2.8 39.1 + - + +
124A LEU* 3.8 24.2 - - + -
125A HIS* 3.4 10.5 - - - -
126A LEU* 3.3 33.0 - - + -
233A THR* 4.7 0.4 - - - -
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Residues in contact with PHE 109 (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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62A HIS* 4.3 32.4 - + + +
63A GLY* 3.2 31.1 - - - +
105A SER* 2.7 53.3 + - - +
106A CYS* 4.0 3.8 - - - +
108A PHE* 1.3 98.1 - + - +
110A ALA* 1.3 57.1 + - - +
112A LYS* 4.3 14.7 - - + +
113A CYS* 3.1 20.7 + - - +
126A LEU* 4.0 9.6 - - + -
224A HIS* 5.2 9.0 - + + -
233A THR* 3.6 32.1 - - + -
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Residues in contact with ALA 110 (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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63A GLY* 4.0 9.2 - - - -
78A CYS* 4.8 0.2 - - - +
79A GLN* 3.5 32.0 - - + +
80A ASP 4.4 0.4 - - - -
81A PRO* 3.5 24.7 - - + +
84A CYS* 4.4 2.9 - - - -
106A CYS 2.8 18.2 + - - +
107A HIS 3.2 5.8 - - - +
108A PHE 3.1 0.2 - - - -
109A PHE* 1.3 75.1 - - - +
111A THR* 1.3 66.9 + - - +
113A CYS* 3.1 18.4 - - - +
114A THR* 3.9 6.6 + - - +
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Residues in contact with THR 111 (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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81A PRO* 4.5 12.3 - - - +
102A PHE* 3.3 32.1 - - + -
107A HIS* 2.8 14.3 + - - +
108A PHE 3.3 7.0 - - - -
110A ALA* 1.3 77.4 - - - +
112A LYS* 1.3 64.0 + - - +
113A CYS 3.0 1.2 + - - -
114A THR* 3.1 23.7 + - - +
115A LEU* 4.4 3.0 + - + +
124A LEU* 5.1 5.8 - - + -
80B ASP* 3.9 22.9 - - - +
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Residues in contact with LYS 112 (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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108A PHE* 2.8 36.4 + - + +
109A PHE* 4.3 16.7 - - + +
111A THR* 1.3 73.3 - - - +
113A CYS* 1.3 63.2 + - - +
115A LEU* 2.9 22.4 + - + +
116A GLU* 4.1 1.2 + - - +
121A GLY 3.5 15.5 - - - +
122A HIS* 5.7 0.4 - - - +
124A LEU* 2.9 57.7 + - + +
125A HIS* 3.5 20.6 + - - -
233A THR* 4.4 4.4 + - - -
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Residues in contact with CYS 113 (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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62A HIS 5.6 0.9 - - - +
63A GLY* 3.7 7.4 - - - +
64A LYS* 3.5 30.7 - - - -
78A CYS* 2.0 53.7 - - + -
109A PHE 3.1 17.1 + - - +
110A ALA 3.1 15.0 - - - +
111A THR 3.0 0.6 + - - -
112A LYS* 1.3 76.7 - - - +
114A THR* 1.3 59.0 + - - +
115A LEU 3.0 1.6 + - - -
116A GLU* 3.3 22.8 + - - +
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Residues in contact with THR 114 (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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78A CYS* 4.0 14.8 - - + -
110A ALA 4.4 5.6 - - - +
111A THR* 3.1 16.8 + - - +
113A CYS* 1.3 74.3 - - - +
115A LEU* 1.3 69.3 + - - +
116A GLU 3.4 1.9 + - - +
77B VAL* 3.5 24.4 - - - +
78B CYS* 3.9 29.1 + - + +
79B GLN 5.5 2.9 - - - +
80B ASP* 5.5 6.6 + - - +
81B PRO* 6.4 1.3 - - + -
114B THR* 4.3 19.5 - - + -
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Residues in contact with LEU 115 (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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111A THR* 4.9 2.7 - - + +
112A LYS* 2.9 13.1 + - - +
114A THR* 1.3 94.5 - - - +
116A GLU* 1.3 66.0 + - - +
117A GLY 3.2 0.5 + - - -
118A THR* 2.9 27.5 + - + +
120A LYS* 3.8 28.9 - - + -
121A GLY* 3.4 36.1 - - - +
124A LEU* 4.0 22.9 - - + -
67B GLU* 5.2 3.1 - - + -
77B VAL* 4.6 12.8 - - + -
78B CYS 5.4 0.9 - - - +
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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