Contacts of the helix formed by residues 106 - 116 (chain A) in PDB entry 2W9M
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 106 (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 3.7 4.8 + - - -
105A LEU* 1.3 75.8 - - - +
107A PRO* 1.3 76.3 - - - +
108A LYS* 3.3 14.6 - - - -
109A LYS* 3.2 9.0 + - - +
110A ILE* 2.9 23.9 + - - +
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Residues in contact with PRO 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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22A ASP* 3.6 48.9 - - + +
25A ASP* 5.0 7.2 - - + -
26A ILE* 4.1 16.4 - - + +
106A GLY* 1.3 84.1 - - - +
108A LYS* 1.3 73.8 + - - +
110A ILE* 3.4 4.2 + - + +
111A ARG* 3.0 30.7 + - - +
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Residues in contact with LYS 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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106A GLY* 3.8 11.0 - - - -
107A PRO* 1.3 100.8 - - - +
109A LYS* 1.3 79.1 + - + +
111A ARG* 3.6 7.7 + - - +
112A SER* 3.1 26.0 + - - -
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Residues in contact with LYS 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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104A GLY 4.5 11.6 + - - +
105A LEU* 4.1 16.4 - - + -
106A GLY 3.2 9.8 + - - +
108A LYS* 1.3 93.6 - - + +
110A ILE* 1.3 59.3 + - - +
111A ARG 3.1 1.6 - - - -
112A SER* 3.1 8.9 + - - -
113A LEU* 2.8 34.8 + - - +
138A GLY* 3.3 29.8 + - - -
139A PHE* 3.7 35.9 - - + -
143A SER* 4.3 13.1 - - - -
147A ILE* 4.9 2.6 - - - +
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Residues in contact with ILE 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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26A ILE* 4.0 13.2 - - + -
96A LEU* 3.7 28.7 - - + -
99A LEU* 3.5 36.1 - - + +
100A LEU* 3.5 28.9 - - + -
105A LEU* 3.7 30.1 - - + +
106A GLY 2.9 19.9 + - - +
107A PRO* 3.9 3.8 - - + +
109A LYS* 1.3 75.4 - - - +
111A ARG* 1.3 57.2 + - - +
113A LEU* 3.5 9.1 + - - +
114A TRP* 3.1 26.0 + - - +
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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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25A ASP 3.5 12.4 + - - -
26A ILE* 3.2 29.0 + - - +
27A LEU* 2.9 30.9 + - - +
107A PRO 3.0 18.1 + - - +
108A LYS* 3.8 9.2 - - - +
110A ILE* 1.3 79.7 - - - +
112A SER* 1.3 57.1 + - - +
114A TRP* 3.5 6.2 + - - +
115A LEU* 3.1 54.5 + - + +
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Residues in contact with SER 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 LYS 3.1 14.2 + - - -
109A LYS* 3.1 10.5 + - - -
111A ARG* 1.3 76.3 - - - +
113A LEU* 1.3 66.5 + - - +
115A LEU* 3.5 8.5 + - - +
116A ALA* 3.0 24.9 + - - +
136A LEU* 4.5 5.1 - - - +
137A LYS 4.6 6.5 + - - -
139A PHE* 3.6 20.3 - - - -
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Residues in contact with LEU 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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99A LEU* 4.5 11.0 - - + -
105A LEU* 3.6 36.6 - - + -
109A LYS 2.8 19.7 + - - +
110A ILE* 3.7 6.1 - - - +
112A SER* 1.3 77.6 + - - +
114A TRP* 1.3 60.7 + - - +
116A ALA* 3.0 11.7 + - - +
117A GLY 3.1 0.2 + - - -
118A ILE* 2.9 50.7 + - + +
124A LEU* 4.4 16.8 - - + -
133A LEU* 4.0 10.3 - - + -
136A LEU* 3.8 17.3 - - + -
139A PHE* 3.7 21.5 - - + -
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Residues in contact with TRP 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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26A ILE* 5.9 2.0 - - + +
27A LEU* 5.0 10.3 - - + +
93A PRO* 3.9 20.6 - - + -
95A GLY* 5.0 0.4 - - - -
96A LEU* 3.7 50.3 - - + -
99A LEU* 4.3 6.7 - - + -
110A ILE 3.1 16.5 + - - +
111A ARG* 3.6 7.6 - - - +
113A LEU* 1.3 76.7 - - - +
115A LEU* 1.3 59.9 + - + +
117A GLY 3.0 15.1 + - - -
118A ILE 3.8 13.2 + - - +
119A ASP* 3.6 34.5 - - + -
339A ASP 3.0 19.7 + - - -
340A GLY 3.6 10.2 - - - -
341A GLY* 3.7 26.5 - - - +
518A HIS* 3.6 27.2 + - + -
519A VAL* 3.5 18.8 - - + +
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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 ARG* 3.1 52.8 + - + +
112A SER* 4.1 7.2 - - - +
113A LEU 3.3 0.2 - - - -
114A TRP* 1.3 77.7 - - + +
116A ALA* 1.3 58.4 + - - +
117A GLY 3.3 1.5 + - - -
336A THR* 4.8 7.9 - - - +
340A GLY 5.1 1.8 - - - +
341A GLY* 3.8 33.4 - - - +
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Residues in contact with ALA 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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112A SER 3.0 18.4 + - - +
113A LEU 3.0 5.8 + - - +
115A LEU* 1.3 77.1 - - - +
117A GLY* 1.3 59.9 + - - +
118A ILE* 3.4 5.6 - - + +
123A ARG* 4.9 1.4 + - - -
132A GLU* 4.3 14.3 - - - +
136A LEU* 3.9 33.9 - - + -
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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