Contacts of the helix formed by residues 130 - 141 (chain C) in PDB entry 1XFB
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 130 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128C LEU 3.1 2.2 + - - -
129C ASP* 1.3 71.8 - - - +
131C LEU* 1.3 64.7 + - - +
132C SER 3.2 3.1 - - - -
133C GLU* 3.1 24.1 + - - +
134C ARG* 3.1 26.7 + - - +
126D GLN* 3.2 17.8 + - - +
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Residues in contact with LEU 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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109C VAL* 3.6 33.7 - - + -
127C GLY 3.7 7.2 - - - +
128C LEU* 3.1 21.7 + - + +
129C ASP 3.1 4.4 + - - -
130C GLY* 1.3 76.5 - - - +
132C SER* 1.3 57.8 + - - +
134C ARG* 3.2 22.0 + - + +
135C CYS* 2.8 42.7 + - - -
148C TRP* 4.4 4.5 - - + -
174C TYR* 4.0 29.4 - - + +
177C ILE* 4.0 31.0 - - + -
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Residues in contact with SER 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 GLY 3.2 1.0 - - - -
131C LEU* 1.3 77.5 - - - +
133C GLU* 1.3 76.0 + - - +
135C CYS 3.3 0.7 + - - -
136C ALA* 3.0 20.4 + - - +
177C ILE* 3.5 20.9 - - - +
180C GLN* 3.5 14.0 + - - -
181C ASN* 2.9 30.8 + - - +
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Residues in contact with GLU 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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130C GLY* 3.3 27.7 - - - +
132C SER* 1.3 85.8 + - - +
134C ARG* 1.3 64.5 + - + +
136C ALA* 3.3 9.7 + - - +
137C GLN* 3.0 23.7 + - - +
126D GLN* 5.2 3.1 + - - +
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Residues in contact with ARG 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 LYS 4.5 1.4 + - - -
109C VAL* 3.0 41.3 + - - +
110C ASP 5.1 0.2 + - - -
111C LYS* 3.7 24.7 - - - +
127C GLY 3.4 20.0 + - - -
129C ASP 4.4 3.8 - - - -
130C GLY* 3.1 20.1 + - - +
131C LEU* 3.5 16.4 - - + +
133C GLU* 1.3 76.0 - - + +
135C CYS* 1.3 59.4 + - - +
137C GLN* 3.1 8.7 + - - +
138C TYR* 2.8 61.6 + - + -
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Residues in contact with CYS 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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107C ILE* 6.5 0.2 - - - -
109C VAL* 5.1 7.2 - - - -
131C LEU* 2.8 47.9 + - - +
132C SER 3.7 4.3 - - - +
134C ARG* 1.3 69.9 - - - +
136C ALA* 1.3 68.0 + - - +
137C GLN 3.0 0.2 + - - -
138C TYR* 3.0 5.1 + - - +
139C LYS* 2.8 26.5 + - - +
177C ILE* 4.8 0.4 - - - -
178C CYS* 4.0 30.1 - - - -
181C ASN* 3.7 20.9 - - + +
183C ILE* 3.6 17.3 - - + +
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Residues in contact with ALA 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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132C SER 3.0 9.2 + - - +
133C GLU* 3.4 12.1 - - - +
135C CYS* 1.3 77.6 - - - +
137C GLN* 1.3 55.8 + - - +
139C LYS* 3.6 7.4 - - - +
140C LYS* 3.1 36.8 + - - +
181C ASN* 3.5 21.0 + - - +
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Residues in contact with GLN 137 (chain C).
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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85C TYR* 4.6 1.2 + - - +
133C GLU 3.0 13.4 + - - +
134C ARG* 3.3 11.4 - - - +
135C CYS 3.0 0.2 - - - -
136C ALA* 1.3 74.3 - - - +
138C TYR* 1.3 69.6 + - + +
140C LYS* 2.9 37.4 + - - +
141C ASP* 2.9 51.5 + - - +
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Residues in contact with TYR 138 (chain C).
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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81C HIS* 2.6 45.2 + + - +
84C LEU* 3.7 14.7 - - + +
85C TYR* 3.6 15.7 - - - -
107C ILE* 3.8 36.7 - - + +
108C LYS 4.9 1.5 + - - -
109C VAL* 4.0 22.4 - - + -
134C ARG* 2.8 58.1 + - + +
135C CYS* 3.6 6.7 - - - +
137C GLN* 1.3 74.8 - - + +
139C LYS* 1.3 63.4 + - - +
141C ASP* 2.9 14.0 + - - +
142C GLY 3.2 0.7 + - - -
143C ALA* 3.0 21.7 + - + +
183C ILE* 4.5 1.8 - - + -
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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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15C GLU* 2.9 29.2 + - - -
19C ILE* 3.7 5.3 - - - +
135C CYS 2.8 18.8 + - - +
136C ALA* 3.6 6.3 - - - +
138C TYR* 1.3 71.5 - - - +
140C LYS* 1.3 60.2 - - - +
142C GLY* 2.9 21.1 + - - -
143C ALA 3.2 20.9 + - - +
144C ASP* 2.9 22.0 + - - +
181C ASN 4.0 10.3 - - - +
182C GLY* 2.7 33.3 + - - +
183C ILE* 3.9 9.8 - - + +
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Residues in contact with LYS 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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136C ALA* 3.1 18.9 + - - +
137C GLN* 2.9 37.1 + - - +
139C LYS* 1.3 78.7 - - - +
141C ASP* 1.3 64.7 + - - +
142C GLY 3.4 0.6 + - - -
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Residues in contact with ASP 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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84C LEU* 4.7 8.8 - - + +
85C TYR* 2.6 42.9 + - + +
95C VAL* 3.8 19.8 - - - +
137C GLN* 2.9 30.5 + - - +
138C TYR* 2.9 11.3 + - - +
140C LYS* 1.3 86.6 - - - +
142C GLY* 1.3 55.2 + - - +
143C ALA 3.7 0.6 + - - -
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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