Contacts of the helix formed by residues 130 - 141 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126A GLN* 3.1 18.2 + - - +
128B LEU 3.1 2.2 + - - -
129B ASP* 1.3 71.8 - - - +
131B LEU* 1.3 64.5 + - - +
132B SER 3.2 3.1 - - - -
133B GLU* 3.1 23.2 + - - +
134B ARG* 3.1 26.7 + - - +
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Residues in contact with LEU 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109B VAL* 3.6 34.1 - - + +
127B GLY 3.7 7.4 - - - +
128B LEU* 3.1 22.2 + - + +
129B ASP 3.1 4.6 + - - -
130B GLY* 1.3 76.3 - - - +
132B SER* 1.3 58.4 + - - +
134B ARG* 3.2 21.2 + - + +
135B CYS* 2.8 42.8 + - - -
148B TRP* 4.4 4.3 - - + -
174B TYR* 4.0 29.6 - - + +
177B ILE* 4.0 30.5 - - + -
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Residues in contact with SER 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B GLY 3.2 1.0 - - - -
131B LEU* 1.3 78.6 - - - +
133B GLU* 1.3 76.0 + - - +
135B CYS 3.3 0.7 + - - -
136B ALA* 3.0 20.3 + - - +
177B ILE* 3.5 20.3 - - - +
180B GLN* 3.5 14.1 + - - -
181B ASN* 2.9 29.9 + - - +
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Residues in contact with GLU 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A GLN* 5.5 1.0 + - - +
130B GLY* 3.3 28.3 - - - +
132B SER* 1.3 85.7 + - - +
134B ARG* 1.3 64.9 + - + +
136B ALA* 3.3 8.8 + - - +
137B GLN* 3.0 24.2 + - - +
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Residues in contact with ARG 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B LYS 4.5 1.4 + - - -
109B VAL* 3.0 41.9 + - - +
110B ASP 5.1 0.4 + - - -
111B LYS* 3.7 24.5 - - - +
127B GLY 3.4 20.4 + - - -
129B ASP 4.4 4.0 - - - -
130B GLY* 3.1 19.3 + - - +
131B LEU* 3.5 16.1 - - + +
132B SER 3.2 0.2 - - - -
133B GLU* 1.3 76.0 - - + +
135B CYS* 1.3 58.9 + - - +
137B GLN* 3.1 8.6 + - - +
138B TYR* 2.8 62.8 + - + +
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Residues in contact with CYS 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B ILE* 6.5 0.2 - - - -
109B VAL* 5.1 7.4 - - - -
131B LEU* 2.8 48.1 + - - +
132B SER 3.7 4.0 - - - +
134B ARG* 1.3 70.3 - - - +
136B ALA* 1.3 68.0 + - - +
137B GLN 3.0 0.2 + - - -
138B TYR* 3.0 5.5 + - - +
139B LYS* 2.8 26.5 + - - +
177B ILE* 4.8 0.4 - - - -
178B CYS* 4.0 30.3 - - - -
181B ASN* 3.7 20.9 - - + +
183B ILE* 3.6 16.5 - - + +
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Residues in contact with ALA 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132B SER 3.0 9.6 + - - +
133B GLU* 3.4 12.3 - - - +
135B CYS* 1.3 77.6 - - - +
137B GLN* 1.3 56.1 + - - +
139B LYS* 3.6 6.9 - - - +
140B LYS* 3.1 35.8 + - - +
181B ASN* 3.5 21.0 + - - +
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Residues in contact with GLN 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85B TYR* 4.6 1.4 + - - +
133B GLU 3.0 13.6 + - - +
134B ARG* 3.3 11.7 - - - +
135B CYS 3.0 0.2 - - - -
136B ALA* 1.3 73.9 - - - +
138B TYR* 1.3 71.0 + - + +
140B LYS* 2.9 36.8 + - - +
141B ASP* 2.9 51.3 + - - +
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Residues in contact with TYR 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81B HIS* 2.6 45.7 + + - +
84B LEU* 3.7 15.6 - - + +
85B TYR* 3.6 15.9 - - - -
107B ILE* 3.8 36.3 - - + -
108B LYS 4.9 1.3 + - - -
109B VAL* 4.0 22.7 - - + -
134B ARG* 2.8 59.5 + - + +
135B CYS* 3.6 6.7 - - - +
137B GLN* 1.3 74.8 - - + +
139B LYS* 1.3 62.7 + - - +
141B ASP* 2.9 14.5 + - - +
142B GLY 3.2 0.7 + - - -
143B ALA* 3.0 21.8 + - + +
183B ILE* 4.5 2.0 - - + -
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Residues in contact with LYS 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B GLU* 2.9 29.0 + - - -
19B ILE* 3.7 5.5 - - - +
135B CYS 2.8 19.0 + - - +
136B ALA* 3.6 6.7 - - - +
138B TYR* 1.3 71.3 - - - +
140B LYS* 1.3 60.9 + - - +
142B GLY* 2.9 21.5 + - - -
143B ALA 3.2 20.7 + - - +
144B ASP* 2.9 22.2 + - - +
181B ASN 4.0 10.3 - - - +
182B GLY* 2.7 32.7 + - - +
183B ILE* 3.9 9.3 - - + +
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Residues in contact with LYS 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136B ALA* 3.1 18.5 + - - +
137B GLN* 2.9 36.0 + - - +
139B LYS* 1.3 79.3 - - - +
141B ASP* 1.3 63.9 + - - +
142B GLY 3.4 0.8 + - - -
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Residues in contact with ASP 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84B LEU* 4.7 9.2 - - + +
85B TYR* 2.6 43.6 + - + +
95B VAL* 3.8 19.9 - - - +
137B GLN* 2.9 30.4 + - - +
138B TYR* 2.9 10.8 + - - +
140B LYS* 1.3 85.6 - - - +
142B GLY* 1.3 55.4 + - - +
143B 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