Contacts of the helix formed by residues 130 - 141 (chain C) 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 LEU 130 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108C LEU* 3.3 35.4 - - + +
131C SER* 1.3 73.0 + - - +
132C GLU* 2.5 27.4 + - - -
133C ARG* 2.6 59.4 + - + +
134C CYS* 3.2 8.5 + - - -
147C TRP* 4.1 25.6 - - + -
173C TYR* 4.2 19.3 - - + -
176C ILE* 4.0 24.2 - - + -
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Residues in contact with SER 131 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130C LEU* 1.3 77.0 - - - +
132C GLU* 1.3 75.7 + - - +
134C CYS* 2.9 12.7 + - - +
135C ALA* 3.0 15.0 + - - +
176C ILE* 3.7 21.3 - - - +
179C GLN* 5.7 1.7 - - - +
180C ASN* 3.2 29.3 + - - +
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Residues in contact with GLU 132 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130C LEU 2.5 37.1 + - - -
131C SER* 1.3 86.0 + - - +
133C ARG* 1.3 65.5 + - + +
134C CYS 3.1 0.2 + - - -
135C ALA* 3.6 5.1 + - - +
136C GLN* 3.2 21.1 + - - +
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Residues in contact with ARG 133 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108C LEU* 2.7 34.8 + - - +
109C ASP 3.9 11.3 - - - -
130C LEU* 2.6 45.6 + - + +
132C GLU* 1.3 77.3 - - + +
134C CYS* 1.3 54.8 + - - +
136C GLN* 3.6 6.3 - - - +
137C TYR* 2.9 57.3 + - + +
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Residues in contact with CYS 134 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108C LEU* 3.0 35.2 - - - -
130C LEU* 3.2 8.5 + - - -
131C SER 2.9 9.6 + - - +
133C ARG* 1.3 72.4 - - - +
135C ALA* 1.3 60.9 + - - +
136C GLN 2.8 0.9 - - - -
137C TYR* 2.5 35.0 + - - +
138C LYS* 2.9 10.8 + - - -
176C ILE* 4.2 13.9 - - - -
177C CYS* 4.4 7.6 - - - -
180C ASN* 3.2 25.1 - - + +
182C LEU* 4.2 15.9 - - + -
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Residues in contact with ALA 135 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131C SER* 3.0 9.6 + - - +
132C GLU* 4.0 5.4 - - - +
134C CYS* 1.3 75.4 - - - +
136C GLN* 1.3 63.2 + - - +
138C LYS* 3.5 8.5 + - - +
139C LYS* 3.4 27.3 + - - +
180C ASN* 3.0 27.8 + - - +
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Residues in contact with GLN 136 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84C TYR* 4.1 7.8 + - - +
132C GLU 3.2 14.3 + - - +
133C ARG* 3.6 8.1 - - - +
134C CYS 2.6 4.2 + - - -
135C ALA* 1.3 73.6 - - - +
137C TYR* 1.3 62.0 - - + +
139C LYS* 2.7 52.5 + - - +
140C ASP* 2.7 42.8 + - - +
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Residues in contact with TYR 137 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80C HIS* 3.7 30.9 + + - +
83C LEU* 3.9 15.3 - - + -
84C TYR* 3.6 29.4 - + - -
106C ILE* 3.5 26.4 - - + +
107C LYS 4.6 2.1 + - - -
108C LEU* 3.1 36.5 - - + -
133C ARG* 2.9 40.8 + - + +
134C CYS* 2.5 12.7 + - - +
136C GLN* 1.3 75.4 - - + +
138C LYS* 1.3 60.4 + - - +
140C ASP* 3.2 8.9 + - - +
141C GLY 3.0 7.4 + - - -
142C VAL* 3.0 32.8 + - + +
182C LEU* 4.9 1.8 - - + -
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Residues in contact with LYS 138 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C GLU* 3.1 30.5 + - - -
18C ILE* 3.5 9.7 - - - +
134C CYS 2.9 7.1 + - - +
135C ALA* 3.5 11.2 - - - +
137C TYR* 1.3 74.6 - - - +
139C LYS* 1.3 69.1 + - + +
141C GLY* 3.1 11.8 + - - -
142C VAL 2.8 23.3 - - - +
143C ASP* 2.6 29.4 + - - +
180C ASN 3.6 19.5 - - - +
181C GLY* 3.3 13.2 + - - +
182C LEU* 3.6 15.6 - - + +
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Residues in contact with LYS 139 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135C ALA* 3.4 19.4 + - - +
136C GLN* 2.7 32.0 + - - +
138C LYS* 1.3 75.7 - - - +
140C ASP* 1.3 67.5 + - - +
141C GLY* 2.9 3.3 + - - -
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Residues in contact with ASP 140 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83C LEU* 4.5 5.6 - - + -
84C TYR* 2.6 42.6 + - - +
94C ARG* 2.7 41.7 + - - +
136C GLN* 2.7 35.1 + - - +
137C TYR* 3.2 11.9 + - - +
139C LYS* 1.3 74.7 - - - +
141C GLY* 1.3 56.8 + - - +
142C VAL* 5.6 0.2 - - - -
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Residues in contact with GLY 141 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94C ARG* 4.3 2.9 - - - -
98C LYS* 2.7 41.7 + - - -
104C VAL* 3.9 5.2 - - - +
137C TYR 3.0 0.4 + - - -
138C LYS 3.1 5.6 + - - -
139C LYS 2.9 6.6 + - - -
140C ASP* 1.3 81.2 - - - +
142C VAL* 1.3 67.2 + - - +
143C ASP* 3.7 6.1 - - - +
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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