Contacts of the helix formed by residues 101 - 115 (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 LEU 101 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38A GLU* 3.4 42.9 - - + +
39A LYS* 4.2 22.9 - - + +
42A PHE* 4.7 21.5 - - + -
95A PRO* 5.6 6.1 - - + -
96A GLU 5.7 1.8 - - - +
97A ASP 3.6 3.8 - - - +
98A HIS* 3.2 43.1 - - + +
100A THR* 1.3 78.8 - - + +
102A SER* 1.3 65.5 + - - +
103A GLN 3.2 1.3 - - - -
104A PHE* 3.2 23.4 - - - +
105A THR* 3.3 12.3 + - - -
164A HIS* 5.0 1.5 + - - +
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Residues in contact with SER 102 (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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38A GLU* 5.5 0.9 - - - -
98A HIS 3.7 7.9 + - - -
99A ARG* 3.2 27.9 + - - +
101A LEU* 1.3 79.8 - - - +
103A GLN* 1.3 61.8 + - - +
104A PHE 2.9 5.4 - - - -
105A THR* 3.8 8.5 - - - +
106A ASP* 3.2 31.8 + - - +
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Residues in contact with GLN 103 (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 PHE* 3.4 21.6 - - + -
99A ARG* 2.8 50.2 + - + +
100A THR* 3.6 6.5 - - - +
102A SER* 1.3 79.3 + - - +
104A PHE* 1.3 57.2 + - - +
106A ASP* 3.9 6.4 + - - +
107A ALA* 3.1 25.5 + - - +
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Residues in contact with PHE 104 (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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42A PHE* 3.4 43.3 - + + -
45A LEU* 3.8 34.1 - - + -
46A ARG* 4.3 6.7 - - + -
49A LEU* 4.5 1.1 - - + -
87A ILE* 3.7 30.5 - - + -
90A PHE* 3.4 25.0 - + + -
101A LEU 3.2 12.3 - - - +
103A GLN* 1.3 77.6 - - - +
105A THR* 1.3 58.3 + - - +
106A ASP 3.1 1.6 - - - -
107A ALA* 2.7 22.7 + - + +
108A LEU* 2.8 44.2 + - + +
164A HIS* 3.9 17.3 - - - -
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Residues in contact with THR 105 (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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38A GLU* 4.4 7.3 + - - -
101A LEU 3.3 11.8 + - - -
102A SER* 3.4 10.0 + - - -
104A PHE* 1.3 78.3 - - - +
106A ASP* 1.3 63.6 + - - +
108A LEU* 3.3 9.0 + - - +
109A VAL* 3.0 33.5 + - + +
164A HIS* 3.9 18.6 + - - -
165A THR* 4.2 25.5 - - + +
168A PHE* 4.8 13.3 + - - +
169A ASP* 5.7 4.3 - - - -
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Residues in contact with ASP 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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102A SER* 3.2 17.8 + - - +
103A GLN* 4.0 6.3 - - - +
104A PHE 3.1 0.6 - - - -
105A THR* 1.3 82.2 - - - +
107A ALA* 1.3 64.3 + - - +
109A VAL* 3.5 8.2 + - - +
110A THR* 2.9 32.6 + - - +
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Residues in contact with ALA 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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86A ASP* 4.6 11.3 - - - +
87A ILE* 5.9 0.9 - - + -
90A PHE* 3.7 23.1 - - + -
103A GLN 3.1 18.0 + - - +
104A PHE* 2.7 15.5 + - + +
106A ASP* 1.3 78.3 - - - +
108A LEU* 1.3 55.3 + - + -
110A THR* 3.7 5.0 + - - -
111A ILE* 2.9 37.5 + - + +
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Residues in contact with LEU 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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45A LEU* 4.3 5.8 - - + -
49A LEU* 3.7 25.8 - - + -
87A ILE* 4.5 9.9 - - + -
104A PHE* 2.8 38.8 + - + +
105A THR* 3.6 5.8 - - - +
107A ALA* 1.3 77.0 - - - +
109A VAL* 1.3 61.7 + - - +
110A THR 3.0 1.3 - - - -
111A ILE* 2.9 8.8 + - + +
112A ARG* 2.8 31.2 + - - +
161A ILE* 4.1 21.7 - - + +
164A HIS* 3.6 41.1 - - + -
165A THR* 4.0 11.7 - - + -
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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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105A THR* 3.0 24.4 + - + +
106A ASP* 3.9 8.3 - - - +
108A LEU* 1.3 75.4 - - - +
110A THR* 1.3 55.6 + - - +
112A ARG* 3.7 30.2 + - - +
113A ASN* 2.7 47.7 + - - +
165A THR* 3.7 20.2 - - + -
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Residues in contact with THR 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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86A ASP* 4.9 2.0 - - - +
106A ASP* 2.9 21.5 + - - +
107A ALA* 3.9 6.9 - - - -
108A LEU 3.0 0.8 - - - -
109A VAL* 1.3 77.9 - - - +
111A ILE* 1.3 64.9 + - - +
113A ASN* 3.5 6.9 + - - +
114A ARG* 3.0 43.7 + - + +
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Residues in contact with ILE 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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53A LEU* 6.0 2.9 - - + -
83A SER* 2.8 41.1 - - - +
86A ASP* 4.0 9.0 - - + +
87A ILE* 3.4 40.2 - - + -
107A ALA 2.9 25.0 + - - +
108A LEU* 2.9 13.5 + - + +
110A THR* 1.3 77.4 - - - +
112A ARG* 1.3 63.9 + - - +
114A ARG* 3.1 19.6 + - - +
115A HIS* 2.8 32.9 - - + +
157A ILE* 6.2 1.3 - - + -
161A ILE* 4.6 12.6 - - + -
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Residues in contact with ARG 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 LEU 2.8 14.4 + - - +
109A VAL* 3.7 37.1 + - - +
111A ILE* 1.3 78.2 - - - +
113A ASN* 1.3 72.6 + - - +
115A HIS* 3.2 15.1 + - - +
116A ASN* 3.2 14.4 + - - +
158A ARG* 3.5 31.9 + - + +
161A ILE* 4.2 19.4 - - + +
162A ASN* 3.0 28.9 + - - +
165A THR* 3.5 22.2 + - - +
166A LEU* 4.4 7.3 - - - +
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Residues in contact with ASN 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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109A VAL* 2.7 33.0 + - - +
110A THR* 3.5 7.2 + - - +
111A ILE 3.3 0.2 - - - -
112A ARG* 1.3 85.0 + - - +
114A ARG* 1.3 64.5 + - - +
115A HIS 3.0 3.1 + - - -
116A ASN* 3.1 34.5 + - - +
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Residues in contact with ARG 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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79A TRP* 3.7 55.5 + - + +
82A GLN* 3.7 12.0 - - - +
83A SER* 3.2 32.3 + - - +
86A ASP* 2.8 42.9 + - - -
110A THR* 3.0 32.1 + - + +
111A ILE* 3.1 17.6 + - - +
113A ASN* 1.3 78.0 - - - +
115A HIS* 1.3 60.8 + - + +
116A ASN 3.9 0.3 + - - -
117A ASP 5.1 0.3 + - - -
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Residues in contact with HIS 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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53A LEU* 5.5 1.8 - - + -
79A TRP* 3.5 18.4 + - + +
80A TYR* 3.2 55.6 + + - +
83A SER* 2.7 29.3 + - - -
111A ILE* 2.8 29.2 + - + +
112A ARG* 3.2 10.6 + - - +
113A ASN 3.0 0.4 - - - -
114A ARG* 1.3 85.2 - - + +
116A ASN* 1.3 61.5 + - - +
117A ASP 3.2 2.9 - - - -
118A VAL* 2.9 23.7 - - + +
154A ARG* 2.9 23.7 + - + +
158A ARG* 5.9 3.4 - - + +
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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