Contacts of the helix formed by residues 130 - 141 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126C GLN* 3.3 18.2 + - - +
128D LEU 3.1 2.0 + - - -
129D ASP* 1.3 70.6 - - - +
131D LEU* 1.3 64.6 + - - +
132D SER 3.2 3.1 - - - -
133D GLU* 3.1 23.6 + - - +
134D ARG* 3.1 27.8 + - - +
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Residues in contact with LEU 131 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109D VAL* 3.6 34.5 - - + +
127D GLY 3.7 7.2 - - - +
128D LEU* 3.1 22.0 + - + +
129D ASP 3.1 4.8 + - - -
130D GLY* 1.3 76.1 - - - +
132D SER* 1.3 57.0 + - - +
134D ARG* 3.2 21.6 + - + +
135D CYS* 2.8 43.8 + - - -
148D TRP* 4.4 4.5 - - + -
174D TYR* 4.0 28.7 - - + +
177D ILE* 4.0 30.3 - - + -
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Residues in contact with SER 132 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128D LEU 4.9 0.4 + - - -
130D GLY 3.2 0.8 - - - -
131D LEU* 1.3 78.2 - - - +
133D GLU* 1.3 75.7 + - - +
135D CYS 3.3 0.7 + - - -
136D ALA* 3.0 21.0 + - - +
177D ILE* 3.5 20.1 - - - +
180D GLN* 3.5 14.0 + - - -
181D ASN* 2.9 30.1 + - - +
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Residues in contact with GLU 133 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126C GLN* 5.3 2.6 + - - +
130D GLY* 3.1 27.1 + - - +
132D SER* 1.3 85.1 + - - +
134D ARG* 1.3 65.0 + - + +
136D ALA* 3.3 8.5 + - - +
137D GLN* 3.0 24.4 + - - +
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Residues in contact with ARG 134 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108D LYS 4.5 1.4 + - - -
109D VAL* 3.0 41.9 + - - +
110D ASP 5.1 0.6 + - - -
111D LYS* 3.7 25.1 - - - +
127D GLY 3.4 19.2 + - - -
129D ASP 4.4 3.8 - - - -
130D GLY* 3.1 20.3 + - - +
131D LEU* 3.5 16.8 - - + +
133D GLU* 1.3 75.1 - - + +
135D CYS* 1.3 59.5 + - - +
137D GLN* 3.1 8.0 + - - +
138D TYR* 2.8 62.8 + - + -
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Residues in contact with CYS 135 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109D VAL* 5.1 7.4 - - - -
131D LEU* 2.8 47.7 + - - +
132D SER 3.3 4.2 + - - +
134D ARG* 1.3 68.8 - - - +
136D ALA* 1.3 68.8 + - - +
137D GLN 3.0 0.2 + - - -
138D TYR* 3.0 5.8 + - - +
139D LYS* 2.8 25.8 + - - +
177D ILE* 4.8 0.4 - - - -
178D CYS* 4.0 29.8 - - - -
181D ASN* 3.7 21.1 - - + +
183D ILE* 3.6 16.4 - - + +
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Residues in contact with ALA 136 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132D SER 3.0 9.6 + - - +
133D GLU* 3.4 13.2 - - - +
135D CYS* 1.3 77.4 - - - +
137D GLN* 1.3 55.8 - - - +
139D LYS* 3.6 7.0 + - - +
140D LYS* 3.1 36.6 + - - +
181D ASN* 3.5 20.5 + - - +
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Residues in contact with GLN 137 (chain D).
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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85D TYR* 4.6 1.8 + - - +
133D GLU 3.0 13.8 + - - +
134D ARG* 3.3 11.7 - - - +
136D ALA* 1.3 73.2 - - - +
138D TYR* 1.3 70.3 + - + +
140D LYS* 2.9 37.5 + - - +
141D ASP* 2.9 50.7 + - - +
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Residues in contact with TYR 138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81D HIS* 2.6 46.0 + + - +
84D LEU* 3.7 15.6 - - + +
85D TYR* 3.6 16.2 - - - -
107D ILE* 3.8 37.2 - - + +
108D LYS 4.9 1.5 + - - -
109D VAL* 4.0 23.8 - - + -
134D ARG* 2.8 59.9 + - + +
135D CYS* 3.6 7.2 - - - +
137D GLN* 1.3 75.7 - - + +
139D LYS* 1.3 63.8 + - - +
141D ASP* 2.9 14.8 + - - +
142D GLY 3.2 0.7 + - - -
143D ALA* 3.0 22.4 + - + +
183D ILE* 4.5 1.8 - - + -
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Residues in contact with LYS 139 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D GLU* 2.9 28.7 + - - -
19D ILE* 3.7 5.9 - - - +
135D CYS 2.8 20.5 + - - +
136D ALA* 3.6 6.5 - - - +
138D TYR* 1.3 72.6 - - - +
140D LYS* 1.3 59.4 + - - +
142D GLY* 2.9 21.5 + - - -
143D ALA 3.2 21.0 + - - +
144D ASP* 2.9 22.4 + - - +
181D ASN 4.0 9.9 - - - +
182D GLY* 2.7 32.2 + - - +
183D ILE* 3.9 8.9 - - + +
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Residues in contact with LYS 140 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136D ALA* 3.1 18.1 + - - +
137D GLN* 2.9 35.5 + - - +
139D LYS* 1.3 80.1 - - - +
141D ASP* 1.3 63.2 + - - +
142D GLY 3.4 0.2 - - - -
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Residues in contact with ASP 141 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84D LEU* 4.7 8.7 - - + +
85D TYR* 2.6 44.2 + - + +
95D VAL* 3.8 19.8 - - - +
137D GLN* 2.9 30.7 + - - +
138D TYR* 2.9 11.3 + - - +
140D LYS* 1.3 85.4 - - - +
142D GLY* 1.3 56.0 + - - +
143D ALA 3.7 0.4 - - - -
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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