Contacts of the helix formed by residues 153 - 164 (chain A) in PDB entry 1XGW
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 ASP 153 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114A ARG* 4.6 0.2 - - - -
149A GLU 3.4 17.4 + - - +
150A PHE* 2.9 11.5 + - - +
151A ALA 3.3 0.2 - - - -
152A GLN* 1.3 74.7 - - - +
154A ASP* 1.3 60.1 + - - +
155A ASP* 4.4 7.0 - - - +
156A ARG* 3.0 33.4 + - + +
157A LEU* 2.9 29.3 + - - +
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Residues in contact with ASP 154 (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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114A ARG* 2.6 39.0 + - - +
152A GLN 3.4 5.8 + - - +
153A ASP* 1.3 73.8 + - - +
155A ASP* 1.3 54.8 + - - +
157A LEU* 3.6 0.9 - - - +
158A ARG* 2.6 72.8 + - - +
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Residues in contact with ASP 155 (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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153A ASP* 4.4 7.6 - - - +
154A ASP* 1.3 73.5 + - - +
156A ARG* 1.3 54.9 + - - +
158A ARG* 3.4 7.4 - - - +
159A GLU* 2.4 54.5 + - + +
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Residues in contact with ARG 156 (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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103A ARG* 4.4 11.9 - - - +
146A GLU* 5.9 1.6 + - - +
149A GLU* 5.5 4.9 + - - -
150A PHE* 3.6 39.6 - - + +
153A ASP* 3.0 30.6 + - + +
155A ASP* 1.3 77.5 + - - +
157A LEU* 1.3 54.9 + - - +
159A GLU* 4.0 5.8 - - - +
160A GLU* 2.7 44.2 + - + +
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Residues in contact with LEU 157 (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 ILE* 3.5 36.8 - - + +
103A ARG* 5.1 0.4 - - - -
110A VAL* 3.7 22.7 - - + -
114A ARG* 3.5 24.5 - - - +
150A PHE* 3.5 34.8 - - + +
151A ALA* 3.7 11.9 - - - +
153A ASP 2.9 18.5 + - - +
154A ASP* 3.7 4.3 - - - +
156A ARG* 1.3 79.1 - - - +
158A ARG* 1.3 59.3 + - - +
160A GLU 3.7 0.2 - - - -
161A ARG* 2.8 46.8 + - + +
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Residues in contact with ARG 158 (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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107A GLU* 2.7 43.6 + - - -
110A VAL* 4.0 7.5 - - - +
114A ARG* 3.4 16.1 - - - +
154A ASP* 2.6 59.6 + - - +
155A ASP* 3.4 7.9 - - - +
157A LEU* 1.3 74.7 - - - +
159A GLU* 1.3 68.7 + - - +
161A ARG* 3.2 18.7 + - - +
162A LYS* 3.2 23.8 + - - +
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Residues in contact with GLU 159 (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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155A ASP* 2.4 52.2 + - + +
156A ARG* 4.0 4.9 - - - +
158A ARG* 1.3 72.4 - - - +
160A GLU* 1.3 64.9 + - - +
162A LYS* 2.9 54.7 + - - +
163A LYS* 3.9 9.0 + - - +
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Residues in contact with GLU 160 (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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103A ARG* 2.7 57.2 + - + +
150A PHE* 3.6 15.3 - - + -
156A ARG* 2.7 31.2 + - + +
157A LEU 3.9 0.4 - - - +
159A GLU* 1.3 73.2 - - - +
161A ARG* 1.3 61.5 + - + +
163A LYS* 3.6 37.9 + - - +
164A ALA* 4.2 2.4 + - - +
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Residues in contact with ARG 161 (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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64A PHE* 5.9 0.6 - - - -
101A LEU 3.8 4.8 + - - -
102A ILE* 2.8 25.5 + - - +
103A ARG* 4.1 17.3 + - - +
105A GLY 2.5 33.3 + - - +
106A SER 3.2 13.3 + - - -
107A GLU* 3.9 18.8 + - - +
110A VAL* 3.4 20.4 - - - +
157A LEU* 2.8 38.2 + - + +
158A ARG* 3.3 22.9 - - - +
159A GLU 3.1 0.2 - - - -
160A GLU* 1.3 75.8 - - - +
162A LYS* 1.3 65.6 + - - +
164A ALA* 3.2 23.0 + - - +
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Residues in contact with LYS 162 (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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158A ARG 3.2 10.0 + - - +
159A GLU* 2.9 60.1 + - - +
161A ARG* 1.3 74.7 - - - +
163A LYS* 1.3 76.4 + - - +
164A ALA 2.9 11.8 - - - +
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Residues in contact with LYS 163 (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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159A GLU* 3.9 12.8 + - - +
160A GLU* 3.6 38.6 + - - +
162A LYS* 1.3 87.6 - - - +
164A ALA* 1.3 59.7 + - - +
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Residues in contact with ALA 164 (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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103A ARG 4.5 6.5 - - - +
104A ASN* 3.2 33.4 - - - +
160A GLU 4.2 1.9 + - - +
161A ARG 3.2 18.6 + - - +
162A LYS* 2.9 14.0 - - - +
163A LYS* 1.3 78.8 - - + +
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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