Contacts of the helix formed by residues 107 - 114 (chain A) in PDB entry 3BWB
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 GLY 107 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104A GLY 3.2 11.8 + - - -
105A GLY 3.2 4.4 - - - -
106A ASP* 1.3 77.0 + - - +
108A GLY* 1.3 58.8 + - - +
109A VAL 3.5 2.2 - - - -
110A LEU* 3.6 10.2 - - - +
111A ARG* 2.9 24.8 + - - +
142A ILE 3.2 16.0 - - - +
143A SER 5.3 0.2 - - - -
145A SER* 4.3 2.4 - - - -
146A LEU* 3.9 21.1 - - - -
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Residues in contact with GLY 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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82A HIS* 3.5 17.4 - - - +
104A GLY 4.9 0.2 + - - -
106A ASP* 2.8 17.4 + - - -
107A GLY* 1.3 74.7 - - - +
109A VAL* 1.3 63.8 + - - +
111A ARG* 3.5 13.2 + - - +
112A GLU* 3.5 25.3 + - - +
142A ILE* 3.5 14.8 - - - +
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Residues in contact with VAL 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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82A HIS* 3.8 25.4 - - + -
85A LEU* 3.9 28.7 - - + -
86A GLY 4.3 8.1 - - - +
101A ILE* 4.1 14.6 - - + -
104A GLY* 5.4 4.9 + - - -
106A ASP* 4.6 0.4 + - - -
108A GLY* 1.3 72.2 - - - +
110A LEU* 1.3 59.6 + - - +
112A GLU* 3.3 3.3 + - - +
113A VAL* 3.0 29.2 + - + +
174A ILE* 3.7 38.4 - - + -
176A ASP* 4.2 16.2 - - + +
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Residues in contact with LEU 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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101A ILE* 3.7 6.3 - - + +
104A GLY 5.6 0.4 + - - -
107A GLY* 3.4 10.8 + - - +
108A GLY 3.3 0.4 - - - -
109A VAL* 1.3 76.1 - - - +
111A ARG* 1.3 66.8 + - - +
113A VAL* 3.0 9.4 - - + +
114A LEU* 3.0 41.0 + - + +
122A CYS* 3.6 36.8 - - + +
124A LEU* 3.9 28.6 - - + +
145A SER* 3.5 24.5 - - - +
146A LEU* 4.0 15.0 - - + -
151A ALA* 3.8 15.9 - - + -
153A VAL* 4.4 4.0 - - + -
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Residues in contact with ARG 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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78A GLU* 3.1 28.5 + - - -
79A PHE* 4.9 5.5 - - - +
82A HIS* 4.6 2.0 + - - +
107A GLY 2.9 14.2 + - - +
108A GLY* 3.6 17.6 - - - +
109A VAL 3.3 0.2 - - - -
110A LEU* 1.3 76.8 - - - +
112A GLU* 1.3 86.3 + - - +
114A LEU* 3.6 3.8 + - - +
115A ARG* 3.6 37.1 + - - +
141A GLN 3.3 20.6 + - - -
142A ILE* 3.6 24.9 - - - +
144A ARG* 5.6 4.7 - - - +
145A SER* 3.3 25.9 + - - +
280A LYS* 5.8 4.4 - - - +
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Residues in contact with GLU 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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82A HIS* 3.4 31.7 - - + +
83A GLU* 3.6 25.4 - - - +
86A GLY* 4.3 4.3 - - - -
87A HIS* 2.7 49.8 + - + +
108A GLY 3.5 12.8 + - - +
109A VAL 3.3 4.6 + - - +
110A LEU 3.2 0.4 - - - -
111A ARG* 1.3 103.0 + - - +
113A VAL* 1.3 65.9 + - - +
114A LEU 3.2 0.2 - - - -
115A ARG* 2.9 37.0 + - - +
116A HIS* 3.5 2.3 - - - -
279A LEU* 3.7 1.4 - - - +
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Residues in contact with VAL 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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86A GLY* 4.3 6.7 - - - -
90A LEU* 3.9 21.1 - - + -
99A VAL* 4.6 7.2 - - + -
101A ILE* 4.2 4.7 - - + -
109A VAL* 3.0 17.7 + - + +
110A LEU* 3.0 39.3 - - + +
112A GLU* 1.3 75.2 - - - +
114A LEU* 1.3 60.9 + - + +
116A HIS* 3.2 19.8 + - - +
119A VAL* 3.5 20.9 - - + +
122A CYS* 3.9 14.6 - - + -
174A ILE* 3.9 26.9 - - + -
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Residues in contact with LEU 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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110A LEU* 3.0 34.1 + - + +
111A ARG* 3.9 5.4 - - - +
112A GLU 3.2 0.4 - - - -
113A VAL* 1.3 77.1 - - + +
115A ARG* 1.3 63.6 + - - +
116A HIS 3.2 1.7 - - - +
119A VAL* 4.5 5.6 - - + -
122A CYS* 4.4 11.0 - - + -
145A SER* 3.7 26.7 - - - +
148A ASP* 3.4 35.4 - - + +
150A ARG* 3.0 63.2 + - + +
151A ALA* 4.4 1.1 - - + -
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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