Contacts of the helix formed by residues 101 - 112 (chain A) in PDB entry 2BWJ
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 GLU 101 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72A SER* 3.7 11.6 + - - -
99A PRO* 3.5 7.0 - - - +
100A ARG* 1.3 109.7 + - - +
102A VAL* 1.3 63.4 + - - +
103A LYS* 3.9 20.7 - - + +
104A GLN* 3.4 15.8 + - + +
105A GLY 3.3 15.1 + - - -
162A PRO* 5.9 2.9 - - - -
163A VAL* 3.7 11.0 - - - -
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Residues in contact with VAL 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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99A PRO* 5.5 0.7 - - - -
101A GLU* 1.3 71.7 - - - +
103A LYS* 1.3 61.4 + - - +
105A GLY* 2.9 5.1 + - - +
106A GLU* 2.8 40.9 + - - +
162A PRO* 3.6 39.2 - - + +
163A VAL* 4.1 4.7 - - - +
166A TYR* 3.8 38.1 - - + -
167A TYR* 6.3 1.1 - - - -
134F GLN* 4.6 11.9 - - - +
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Residues in contact with LYS 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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72A SER* 5.9 1.1 - - - +
101A GLU* 3.9 20.8 - - + +
102A VAL* 1.3 78.6 - - - +
104A GLN* 1.3 60.5 + - + +
106A GLU* 3.4 17.6 + - - +
107A GLU* 2.9 30.0 + - - +
110A ARG* 4.4 4.4 + - - +
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Residues in contact with GLN 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 THR* 5.4 0.6 + - - -
72A SER* 4.0 30.0 + - - +
75A VAL* 4.5 12.3 - - - +
76A LEU* 5.4 0.6 - - + +
98A TYR* 3.3 37.1 + - - +
99A PRO* 4.0 2.2 - - + -
100A ARG* 2.8 57.5 + - - +
101A GLU* 3.4 18.3 + - + +
102A VAL 3.1 0.4 - - - -
103A LYS* 1.3 82.3 - - + +
105A GLY* 1.3 56.4 + - - +
107A GLU* 3.5 7.1 + - - +
108A PHE* 3.0 27.2 + - - +
66B ARG 5.5 0.4 + - - -
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Residues in contact with GLY 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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99A PRO* 3.6 14.7 - - - +
101A GLU 3.3 5.7 + - - -
102A VAL 2.9 7.4 + - - -
104A GLN* 1.3 75.9 - - - +
106A GLU* 1.3 63.6 + - - +
108A PHE* 3.4 7.5 + - - +
109A GLY* 3.1 18.7 + - - -
166A TYR* 5.1 2.0 - - - -
167A TYR* 3.2 30.2 + - - -
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Residues in contact with GLU 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 VAL* 2.8 28.4 + - - +
103A LYS* 3.4 21.4 + - - +
105A GLY* 1.3 70.7 - - - +
107A GLU* 1.3 57.0 + - - +
109A GLY* 3.2 3.7 + - - +
110A ARG* 3.1 52.9 + - - +
166A TYR* 3.4 36.4 + - + +
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Residues in contact with GLU 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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72A SER* 6.3 4.3 - - - -
73A GLY* 6.5 0.7 - - - -
76A LEU* 3.8 22.4 - - + -
103A LYS 2.9 18.1 + - - +
104A GLN* 3.6 8.7 - - + +
106A GLU* 1.3 73.2 - - - +
108A PHE* 1.3 64.9 + - - +
110A ARG* 3.3 22.9 + - - +
111A ARG* 2.9 37.1 + - + +
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Residues in contact with PHE 108 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A ILE* 4.0 12.6 - - + -
15A PHE* 3.7 20.4 - + + -
76A LEU* 3.9 20.5 - - + +
79A LEU* 3.8 16.4 - - + -
83A MET* 4.3 2.0 - - - -
95A ILE* 3.7 25.8 - - + -
98A TYR* 3.6 29.4 - + + +
104A GLN 3.0 14.8 + - - +
105A GLY* 3.4 11.4 + - - +
107A GLU* 1.3 74.3 - - - +
109A GLY* 1.3 56.3 + - - +
112A ILE* 2.7 55.6 + - + +
113A GLY 3.0 40.5 + - - -
115A PRO* 4.8 1.8 - - + -
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Residues in contact with GLY 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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9A ARG* 2.9 33.3 + - - -
105A GLY 3.1 13.3 + - - -
106A GLU* 3.2 5.3 + - - -
108A PHE* 1.3 78.7 - - - +
110A ARG* 1.3 57.8 + - - +
113A GLY* 3.4 15.4 + - - -
114A ASP* 3.7 14.8 - - - -
115A PRO* 5.6 1.1 - - - -
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Residues in contact with ARG 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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9A ARG* 3.5 12.9 + - - +
103A LYS* 4.4 4.9 + - - +
106A GLU* 3.1 47.9 + - - +
107A GLU* 3.7 27.9 - - - +
109A GLY* 1.3 77.0 - - - +
111A ARG* 1.3 65.4 + - + +
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Residues in contact with ARG 111 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5A MET* 5.8 3.6 - - - +
8A LEU* 5.3 0.5 - - - +
9A ARG* 5.0 0.4 - - - -
76A LEU* 4.0 23.8 - - + -
80A LYS* 3.9 25.3 + - + +
107A GLU* 2.9 26.1 + - + +
108A PHE 4.4 0.2 - - - +
110A ARG* 1.3 83.3 - - + +
112A ILE* 1.3 66.9 + - + +
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Residues in contact with ILE 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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5A MET 4.6 0.2 - - - +
8A LEU* 3.7 18.6 - - + +
9A ARG* 3.4 33.8 + - - +
13A ILE* 4.5 2.0 - - + -
76A LEU* 3.8 27.1 - - + -
79A LEU* 4.6 1.1 - - + -
80A LYS* 3.7 43.3 - - + +
83A MET* 3.7 31.0 - - + -
108A PHE* 2.7 34.8 + - + +
110A ARG 3.5 0.4 - - - -
111A ARG* 1.3 82.2 - - + +
113A GLY* 1.3 58.9 + - - +
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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