Contacts of the helix formed by residues 115 - 123 (chain A) in PDB entry 2BKG
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 THR 115 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85A HIS* 3.9 3.1 - - - -
106A VAL 4.8 2.5 - - - -
107A ASN* 4.0 20.2 - - + +
108A ALA 3.3 12.1 - - - +
109A ASP* 4.4 4.9 - - + -
113A GLY 4.2 5.6 - - - +
114A SER* 1.3 78.4 - - - +
116A PRO* 1.3 74.7 - - - +
117A LEU* 3.5 10.9 + - - +
118A HIS* 2.9 41.7 + - - +
119A LEU* 3.2 13.5 + - - +
138A ASP 5.2 0.9 + - - +
141A ALA* 4.1 21.5 - - + +
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Residues in contact with PRO 116 (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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82A THR* 5.1 0.4 - - - +
84A LEU* 3.8 34.3 - - + +
85A HIS* 3.7 21.3 - - + +
88A ALA* 3.9 12.1 - - + +
105A ASP 4.5 2.5 - - - +
106A VAL 3.5 19.3 - - - +
108A ALA 3.3 14.4 - - - +
115A THR* 1.3 87.2 - - - +
117A LEU* 1.3 60.4 + - - +
119A LEU* 3.2 5.0 + - + +
120A ALA* 2.9 26.0 + - - +
132A LEU* 3.6 18.6 - - + +
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Residues in contact with LEU 117 (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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106A VAL 5.0 1.4 + - - -
115A THR* 3.2 9.7 + - - +
116A PRO* 1.3 78.5 - - - +
118A HIS* 1.3 63.1 + - + +
120A ALA* 4.1 0.2 - - - +
121A ALA* 2.9 26.5 + - - +
129A VAL* 3.9 32.5 - - + +
132A LEU* 3.6 12.3 - - + +
133A LEU* 4.1 17.5 - - + -
137A ALA* 4.1 24.0 - - + +
138A ASP 3.7 23.3 - - - +
139A VAL* 4.0 12.6 - - - -
149A ALA* 3.6 22.9 - - + -
165A LEU* 4.1 7.9 - - + -
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Residues in contact with HIS 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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113A GLY 3.9 15.5 - - - -
114A SER* 4.3 12.3 - - - +
115A THR* 2.9 39.4 + - - +
117A LEU* 1.3 79.9 - - + +
119A LEU* 1.3 59.9 + - + +
121A ALA* 3.7 1.7 - - - +
122A ASP* 2.9 31.1 + - - +
138A ASP 5.8 0.2 - - - -
141A ALA* 3.1 30.8 + - + -
143A ASP* 3.6 10.4 + - + -
147A LYS 2.8 29.0 + - - -
148A THR* 3.7 2.0 - - - -
149A ALA* 3.7 14.6 - - + -
152A ILE* 3.6 28.7 - - + +
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Residues in contact with LEU 119 (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 SER* 6.0 0.2 - - - +
85A HIS* 3.5 47.1 - - + +
86A LEU* 6.1 1.1 - - + -
89A LYS* 4.0 43.2 - - + +
110A ASP* 4.9 5.2 - - - +
114A SER* 3.9 22.9 - - - +
115A THR 3.2 9.6 + - - +
116A PRO* 3.2 7.6 + - + +
118A HIS* 1.3 77.7 - - + +
120A ALA* 1.3 60.3 + - - +
122A ASP* 3.4 7.1 + - + +
123A THR* 3.0 29.9 + - - +
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Residues in contact with ALA 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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88A ALA* 3.8 11.6 + - + +
116A PRO 2.9 16.4 + - - +
117A LEU 4.1 0.9 - - - +
119A LEU* 1.3 74.7 - - - +
121A ALA* 1.3 65.8 + - - +
123A THR* 3.4 6.6 + - - -
124A GLY 3.1 3.5 + - - -
125A HIS* 3.0 28.0 + - + +
128A ILE* 3.6 32.8 - - + -
129A VAL* 4.0 14.1 - - + -
132A LEU* 4.2 2.7 - - + -
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Residues in contact with ALA 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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117A LEU 2.9 19.0 + - - +
118A HIS 3.7 3.4 - - - +
120A ALA* 1.3 77.8 - - - +
122A ASP* 1.3 61.0 + - - +
124A GLY* 3.2 6.6 + - - -
129A VAL* 3.9 6.1 - - + +
149A ALA* 4.0 15.0 - - + +
152A ILE* 4.0 5.1 - - + +
156A ASN* 4.0 7.4 + - - -
158A ASN* 5.3 0.5 + - - +
161A LEU* 3.1 36.7 - - + +
165A LEU* 3.9 18.8 - - + -
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Residues in contact with ASP 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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89A LYS* 5.9 0.7 + - - -
118A HIS 2.9 17.6 + - - +
119A LEU* 3.8 10.6 - - + +
120A ALA 3.3 0.2 - - - -
121A ALA* 1.3 76.5 - - - +
123A THR* 1.3 64.6 + - + +
124A GLY 3.8 0.2 + - - -
152A ILE* 3.4 22.1 - - + +
156A ASN* 3.1 30.1 + - - +
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Residues in contact with THR 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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89A LYS* 3.3 29.6 + - + +
119A LEU 3.0 17.5 + - - +
120A ALA* 3.5 4.0 + - - -
121A ALA 3.2 0.2 - - - -
122A ASP* 1.3 81.7 - - + +
124A GLY* 1.3 62.2 + - - +
125A HIS* 2.8 39.8 + - - -
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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