Contacts of the helix formed by residues 129 - 140 (chain Z) 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 Z).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128Z ASP* 1.3 82.1 + - - +
130Z LEU* 1.3 56.2 + - - +
131Z SER 4.6 0.2 - - - +
132Z GLU* 2.6 27.5 + - - +
133Z ARG* 2.9 33.7 + - - +
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Residues in contact with LEU 130 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108Z LEU* 3.7 33.0 - - + +
128Z ASP* 4.0 14.1 - - - +
129Z GLY* 1.3 78.8 - - - +
131Z SER* 1.3 58.0 + - - +
132Z GLU 2.9 5.4 - - - -
133Z ARG* 2.9 38.4 - - + +
134Z CYS* 3.0 40.4 + - - -
147Z TRP* 3.3 31.4 - - + -
173Z TYR* 4.2 28.7 - - + +
176Z ILE* 4.2 11.9 - - + -
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Residues in contact with SER 131 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128Z ASP* 5.8 0.2 - - - +
129Z GLY 4.6 0.2 - - - +
130Z LEU* 1.3 77.4 - - - +
132Z GLU* 1.3 72.2 + - - +
135Z ALA* 3.8 5.9 - - - +
176Z ILE* 3.4 31.1 - - - +
179Z GLN* 5.5 3.3 - - - +
180Z ASN* 3.4 25.6 + - - +
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Residues in contact with GLU 132 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129Z GLY* 2.6 44.8 + - - +
130Z LEU 2.9 0.2 - - - -
131Z SER* 1.3 97.0 - - - +
133Z ARG* 1.3 65.2 + - + +
134Z CYS 3.1 1.1 - - - -
135Z ALA* 3.2 7.7 + - - +
136Z GLN* 3.1 22.0 + - - +
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Residues in contact with ARG 133 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108Z LEU* 3.1 17.6 + - - +
109Z ASP* 5.1 1.6 + - - +
128Z ASP 3.8 8.9 + - - -
129Z GLY* 2.9 26.8 + - - +
130Z LEU* 2.9 38.7 - - + +
132Z GLU* 1.3 78.7 - - + +
134Z CYS* 1.3 57.7 + - - +
136Z GLN* 3.6 6.6 + - - +
137Z TYR* 2.9 50.3 + - + -
147Z TRP* 4.7 7.1 - - - -
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Residues in contact with CYS 134 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108Z LEU* 3.2 34.3 - - - -
130Z LEU* 3.0 27.0 + - - +
133Z ARG* 1.3 73.3 - - - +
135Z ALA* 1.3 68.3 + - - +
136Z GLN 3.0 1.1 - - - -
137Z TYR* 2.9 10.3 + - - +
138Z LYS* 2.9 24.1 + - - +
176Z ILE* 4.6 5.8 - - - -
177Z CYS* 4.6 7.6 - - - -
180Z ASN* 3.0 27.1 - - + +
182Z LEU* 3.8 19.1 - - + +
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Residues in contact with ALA 135 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131Z SER 3.8 13.2 - - - +
132Z GLU* 3.2 11.8 + - - +
134Z CYS* 1.3 79.2 - - - +
136Z GLN* 1.3 65.0 + - - +
138Z LYS* 3.5 4.8 + - - +
139Z LYS* 3.0 37.5 + - - +
180Z ASN* 3.6 19.6 - - + +
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Residues in contact with GLN 136 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84Z TYR* 5.0 4.7 + - - +
132Z GLU 3.1 8.0 + - - +
133Z ARG* 3.6 9.9 - - - +
134Z CYS 3.0 0.8 - - - -
135Z ALA* 1.3 76.2 - - - +
137Z TYR* 1.3 57.5 + - + +
139Z LYS* 2.6 48.5 + - - +
140Z ASP* 3.0 32.7 + - - +
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Residues in contact with TYR 137 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80Z HIS* 3.1 37.7 + + - +
83Z LEU* 3.1 36.8 - - + -
84Z TYR* 5.1 4.3 - + - -
106Z ILE* 3.3 22.8 - - + +
107Z LYS 4.7 3.7 + - - -
108Z LEU* 3.6 29.8 - - + -
133Z ARG* 2.9 39.1 + - + -
134Z CYS* 2.9 12.8 + - - +
136Z GLN* 1.3 72.4 - - + +
138Z LYS* 1.3 61.2 + - - +
140Z ASP* 3.1 12.4 + - + -
142Z VAL* 2.8 36.5 + - + +
182Z LEU* 4.7 4.0 - - + -
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Residues in contact with LYS 138 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14Z GLU* 4.0 22.0 + - - -
18Z ILE* 3.8 10.5 - - - +
134Z CYS 2.9 11.5 + - - +
135Z ALA* 3.7 10.8 - - - +
136Z GLN 2.8 3.8 + - - -
137Z TYR* 1.3 71.3 - - - +
139Z LYS* 1.3 60.4 + - + +
141Z GLY* 2.8 23.4 + - - -
142Z VAL 3.0 24.7 + - - +
143Z ASP* 2.4 36.3 + - - +
180Z ASN 3.9 14.8 - - - +
181Z GLY* 2.9 31.0 + - - +
182Z LEU* 3.8 4.4 - - + +
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Residues in contact with LYS 139 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94Z ARG* 5.1 1.0 + - - -
135Z ALA* 3.0 34.8 + - - +
136Z GLN* 2.6 32.4 + - - +
138Z LYS* 1.3 75.0 - - + +
140Z ASP* 1.3 58.9 + - - +
141Z GLY* 2.9 6.1 + - - -
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Residues in contact with ASP 140 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83Z LEU* 3.8 15.8 - - + +
84Z TYR* 2.3 42.9 + - - +
94Z ARG* 3.3 39.2 + - - +
136Z GLN* 3.0 37.6 + - - +
137Z TYR* 3.1 13.8 + - - +
139Z LYS* 1.3 75.3 - - - +
141Z GLY* 1.3 59.9 + - - +
142Z VAL 3.7 0.2 + - - -
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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