Contacts of the helix formed by residues 141 - 152 (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 ARG 141 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123A LEU 3.7 13.7 - - - +
124A GLU 3.2 27.6 - - - +
125A ASN* 4.0 6.1 - - - +
126A TYR* 2.7 37.5 + - - +
127A HIS* 4.3 7.3 + - - +
128A PHE 4.8 0.2 - - - +
135A ASP* 3.0 27.5 + - - -
137A GLY* 3.1 21.8 + - - +
138A ILE* 3.3 28.7 - - + +
140A ILE* 1.3 77.3 - - - +
142A GLN* 1.3 62.3 + - + +
144A VAL* 3.3 3.4 - - - +
145A LYS* 3.1 39.2 + - - +
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Residues in contact with GLN 142 (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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138A ILE* 3.1 49.1 + - + +
139A ASN* 4.0 8.1 - - - +
141A ARG* 1.3 75.5 - - + +
143A LYS* 1.3 62.1 + - - +
145A LYS* 3.5 9.3 + - + +
146A GLU* 3.2 22.4 + - - +
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Residues in contact with LYS 143 (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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92A TYR* 3.7 22.0 - - + +
95A LEU* 3.8 20.2 - - + -
96A LEU* 3.2 41.2 - - - +
99A ALA* 3.8 25.1 - - - +
139A ASN 3.1 20.1 + - - +
140A ILE 3.8 2.9 - - - +
142A GLN* 1.3 75.5 - - - +
144A VAL* 1.3 65.2 + - - +
146A GLU* 3.4 26.2 + - + +
147A LEU* 3.0 24.9 + - + +
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Residues in contact with VAL 144 (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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95A LEU* 3.9 15.2 - - + +
120A LEU* 3.5 50.3 - - + +
121A ARG* 4.8 0.7 - - - +
123A LEU* 3.9 9.4 - - + -
124A GLU* 3.8 31.4 - - + +
140A ILE 2.8 20.0 + - - +
141A ARG 3.3 12.8 - - - +
143A LYS* 1.3 72.0 - - - +
145A LYS* 1.3 64.7 + - - +
147A LEU* 3.1 4.5 + - + -
148A VAL* 2.9 33.6 + - + +
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Residues in contact with LYS 145 (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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124A GLU* 3.7 53.6 + - + +
141A ARG* 3.1 25.8 + - - +
142A GLN* 3.7 7.9 - - - +
143A LYS 3.3 0.2 - - - -
144A VAL* 1.3 82.7 - - - +
146A GLU* 1.3 61.6 + - - +
148A VAL* 3.5 6.4 + - - +
149A GLU* 3.1 24.0 + - - +
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Residues in contact with GLU 146 (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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142A GLN 3.2 13.7 + - - +
143A LYS* 3.5 30.2 + - + +
145A LYS* 1.3 76.3 - - - +
147A LEU* 1.3 57.9 + - - +
149A GLU* 3.3 15.1 + - - +
150A PHE* 3.1 27.9 + - + +
156A ARG* 5.9 1.4 + - - +
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Residues in contact with LEU 147 (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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95A LEU* 3.8 40.2 - - + +
98A LEU* 3.8 29.4 - - + -
99A ALA* 3.8 27.6 - - + +
102A ILE* 4.3 20.0 - - + -
103A ARG* 5.1 0.7 - - - +
120A LEU* 4.4 11.2 - - + -
143A LYS* 3.0 19.7 + - + +
144A VAL* 3.1 4.7 + - - +
146A GLU* 1.3 75.7 - - + +
148A VAL* 1.3 55.8 + - - +
150A PHE* 3.3 11.4 + - + +
151A ALA* 2.8 36.6 + - + +
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Residues in contact with VAL 148 (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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117A ILE* 4.2 9.2 - - + -
120A LEU* 3.8 23.8 - - + -
121A ARG* 3.6 41.3 - - + -
124A GLU* 4.3 9.4 - - - +
144A VAL* 2.9 23.8 + - + +
145A LYS* 3.8 4.9 - - - +
147A LEU* 1.3 73.0 - - - +
149A GLU* 1.3 66.3 + - - +
151A ALA* 3.2 1.6 + - - +
152A GLN* 3.1 46.0 + - - +
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Residues in contact with GLU 149 (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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145A LYS 3.1 14.8 + - - +
146A GLU* 3.4 16.8 - - - +
148A VAL* 1.3 77.9 - - - +
150A PHE* 1.3 61.4 + - - +
152A GLN* 3.8 6.2 + - - +
153A ASP* 3.4 22.1 + - + +
156A ARG* 5.5 4.9 + - - -
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Residues in contact with PHE 150 (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* 3.7 16.6 - - + -
103A ARG* 3.4 45.3 - - + +
146A GLU* 3.1 15.9 + - + +
147A LEU* 3.4 12.6 - - + +
149A GLU* 1.3 75.2 + - - +
151A ALA* 1.3 66.0 + - - +
153A ASP* 2.9 24.9 + - - +
156A ARG* 3.6 52.3 - - + +
157A LEU* 3.5 35.1 - - + +
160A GLU* 3.6 26.0 - - + -
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Residues in contact with ALA 151 (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* 3.7 28.9 - - + -
113A ALA* 4.9 8.3 - - + -
114A ARG* 3.0 37.7 + - + -
117A ILE* 4.6 13.0 - - + -
120A LEU* 5.6 1.8 - - + -
147A LEU* 2.8 23.4 + - + +
148A VAL* 3.2 6.7 + - - +
150A PHE* 1.3 73.7 - - - +
152A GLN* 1.3 58.5 + - - +
153A ASP 3.3 0.2 - - - -
157A LEU* 3.7 5.5 - - - +
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Residues in contact with GLN 152 (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* 4.7 10.5 - - + +
117A ILE* 3.5 34.3 - - + +
118A TYR* 5.4 4.4 + - - -
121A ARG* 4.8 8.5 - - - +
148A VAL* 3.1 33.1 + - - +
149A GLU* 4.1 5.2 - - - +
151A ALA* 1.3 74.4 - - - +
153A ASP* 1.3 57.5 + - - +
154A ASP* 3.4 7.1 + - - +
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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