Contacts of the helix formed by residues 129 - 140 (chain A) in PDB entry 1XDM
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 129 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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127A LEU 3.6 1.4 + - - -
128A ASP* 1.3 77.3 + - - +
130A LEU* 1.3 51.9 + - - +
132A GLU* 2.6 28.0 + - - +
133A ARG* 2.8 48.9 + - - +
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Residues in contact with LEU 130 (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* 4.0 25.8 - - + +
126A GLY 4.8 0.4 - - - +
127A LEU* 3.7 33.0 + - + +
128A ASP 3.3 2.4 + - - -
129A GLY* 1.3 74.0 - - - +
131A SER* 1.3 60.0 + - - +
132A GLU 2.9 4.4 + - - -
133A ARG* 3.0 35.0 - - + +
134A CYS* 2.8 47.8 + - - -
147A TRP* 3.7 26.2 - - + -
173A TYR* 4.2 21.8 - - + +
176A ILE* 4.0 9.2 - - + -
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Residues in contact with SER 131 (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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127A LEU 4.9 1.0 + - - -
129A GLY 3.5 0.4 - - - -
130A LEU* 1.3 76.4 - - - +
132A GLU* 1.3 74.2 + - - +
135A ALA* 3.7 7.3 - - - +
176A ILE* 3.5 25.0 - - - +
179A GLN* 5.7 2.3 - - - +
180A ASN* 3.4 24.4 + - - +
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Residues in contact with GLU 132 (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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129A GLY* 2.6 41.2 + - - +
130A LEU 2.9 0.6 - - - -
131A SER* 1.3 99.0 + - - +
133A ARG* 1.3 65.4 + - - +
134A CYS 3.1 1.3 - - - -
135A ALA* 3.2 7.5 + - - +
136A GLN* 3.1 22.3 + - - +
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Residues in contact with ARG 133 (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* 3.6 16.9 + - + +
126A GLY 4.1 10.7 + - - -
128A ASP 2.8 27.5 + - - -
129A GLY* 2.8 23.9 + - - +
130A LEU* 3.0 35.2 - - + +
132A GLU* 1.3 73.2 - - - +
134A CYS* 1.3 56.7 + - - +
136A GLN* 3.6 5.9 + - - +
137A TYR* 2.8 49.3 + - + -
147A TRP* 4.5 1.4 - - - -
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Residues in contact with CYS 134 (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* 3.3 34.5 - - - -
130A LEU* 2.8 29.8 + - - +
133A ARG* 1.3 74.8 - - - +
135A ALA* 1.3 64.6 + - - +
136A GLN 3.0 1.1 - - - -
137A TYR* 2.9 10.4 + - - +
138A LYS* 2.9 24.3 + - - +
176A ILE* 4.5 4.9 - - - -
177A CYS* 4.6 6.5 - - - -
180A ASN* 2.9 33.9 - - + +
182A LEU* 3.9 13.3 - - + +
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Residues in contact with ALA 135 (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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131A SER 3.7 13.7 - - - +
132A GLU* 3.2 12.0 + - - +
134A CYS* 1.3 79.0 - - - +
136A GLN* 1.3 66.9 + - - +
138A LYS* 3.5 4.9 + - - +
139A LYS* 3.0 37.5 + - - +
180A ASN* 3.6 19.1 - - - +
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Residues in contact with GLN 136 (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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84A TYR* 5.0 4.0 + - - +
132A GLU 3.1 8.6 + - - +
133A ARG* 3.6 9.6 - - - +
134A CYS 3.0 0.4 - - - -
135A ALA* 1.3 76.6 - - - +
137A TYR* 1.3 58.2 + - + +
139A LYS* 2.6 48.3 + - - +
140A ASP* 3.0 34.1 + - - +
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Residues in contact with TYR 137 (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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80A HIS* 3.1 37.5 + + - +
83A LEU* 3.2 35.0 - - + -
84A TYR* 5.1 4.0 - - - -
106A ILE* 3.2 24.9 - - + +
107A LYS 4.7 4.9 + - - -
108A LEU* 3.5 30.5 - - + -
133A ARG* 2.8 39.5 + - + -
134A CYS* 2.9 13.4 + - - +
136A GLN* 1.3 71.4 - - + +
138A LYS* 1.3 63.0 + - - +
140A ASP* 3.1 12.2 + - + -
142A VAL* 2.9 33.8 + - + +
182A LEU* 4.7 4.0 - - + -
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Residues in contact with LYS 138 (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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14A GLU* 4.1 20.8 + - - -
18A ILE* 3.8 10.9 - - - +
134A CYS 2.9 11.6 + - - +
135A ALA* 3.6 9.9 - - - +
136A GLN 2.8 4.0 + - - -
137A TYR* 1.3 70.3 - - - +
139A LYS* 1.3 59.5 + - + +
141A GLY* 2.8 22.9 + - - -
142A VAL 2.9 24.2 + - - +
143A ASP* 2.4 34.4 + - - +
180A ASN 3.9 15.9 - - - +
181A GLY* 2.8 31.2 + - - +
182A LEU* 3.8 3.7 - - + +
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Residues in contact with LYS 139 (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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94A ARG* 4.9 1.4 + - - -
135A ALA* 3.0 33.8 + - - +
136A GLN* 2.6 32.1 + - - +
138A LYS* 1.3 73.9 - - + +
140A ASP* 1.3 59.2 + - - +
141A GLY* 2.9 6.2 + - - -
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Residues in contact with ASP 140 (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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83A LEU* 3.7 16.5 - - + +
84A TYR* 2.3 43.2 + - - +
94A ARG* 3.3 39.2 + - - +
136A GLN* 3.0 37.6 + - - +
137A TYR* 3.1 14.3 + - - +
139A LYS* 1.3 75.1 - - - +
141A GLY* 1.3 58.7 + - - +
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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