Contacts of the helix formed by residues 112 - 127 (chain B) in PDB entry 1XUQ
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 SER 112 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106B ILE* 4.4 5.8 - - - -
107B GLU* 4.3 9.4 - - - +
110B PHE* 3.3 5.6 + - - +
111B GLY* 1.3 77.4 - - - +
113B PHE* 1.3 65.4 + - - +
114B ASP* 3.6 8.5 + - - +
115B ALA* 3.1 22.1 + - - +
116B PHE* 3.1 22.7 + - - +
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Residues in contact with PHE 113 (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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96B GLY 3.8 12.6 - - - -
97B GLN* 3.7 32.8 - - - +
98B PRO* 3.3 37.0 - - + -
106B ILE* 4.1 10.9 - - + +
107B GLU* 4.9 5.6 - - + +
112B SER* 1.3 71.2 - - - +
114B ASP* 1.3 64.6 + - - +
116B PHE* 3.3 11.0 + + - +
117B LYS* 2.9 71.3 + - + +
187B TRP* 4.7 4.5 - + + -
192B TRP* 3.4 34.3 - + - -
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Residues in contact with ASP 114 (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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97B GLN* 5.6 0.7 + - - +
112B SER* 3.3 8.1 + - - +
113B PHE* 1.3 82.7 - - - +
115B ALA* 1.3 60.0 + - - +
117B LYS* 3.3 27.2 + - - +
118B GLU* 3.1 34.5 + - - +
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Residues in contact with ALA 115 (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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110B PHE* 3.4 24.7 - - - +
111B GLY* 5.0 0.4 - - - -
112B SER* 3.1 19.1 + - - +
114B ASP* 1.3 74.0 - - - +
116B PHE* 1.3 66.3 + - - +
118B GLU* 3.2 14.8 + - - +
119B GLU* 3.1 21.7 + - - +
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Residues in contact with PHE 116 (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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106B ILE* 3.9 13.9 - - + -
110B PHE* 3.8 38.2 - + + +
112B SER 3.1 14.1 + - - +
113B PHE* 3.5 22.2 - + - +
115B ALA* 1.3 73.4 - - - +
117B LYS* 1.3 69.9 + - - +
119B GLU* 3.1 3.0 + - - +
120B PHE* 2.9 39.7 + + + +
135B LEU* 3.9 32.5 - - + -
144B VAL* 3.7 24.2 - - + -
162B ILE* 4.2 6.1 - - + -
187B TRP* 3.7 24.9 - + - -
192B TRP* 3.9 13.2 - + - -
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Residues in contact with LYS 117 (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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97B GLN* 5.5 0.8 + - - -
113B PHE* 2.9 58.3 + - + +
114B ASP* 3.6 26.9 + - - +
116B PHE* 1.3 77.5 - - + +
118B GLU* 1.3 58.1 + - + +
120B PHE* 3.7 1.6 - - - +
121B ALA* 2.9 31.8 + - - +
187B TRP* 3.6 54.2 - - + +
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Residues in contact with GLU 118 (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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114B ASP* 3.1 27.0 + - - +
115B ALA* 3.4 12.6 - - - +
116B PHE 3.1 0.2 - - - -
117B LYS* 1.3 78.0 - - + +
119B GLU* 1.3 56.6 + - - +
121B ALA* 3.5 5.3 + - - +
122B LYS* 3.0 29.6 + - - +
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Residues in contact with GLU 119 (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 LYS* 5.7 2.3 + - - -
110B PHE* 3.4 28.8 - - - -
115B ALA 3.1 12.8 + - - +
116B PHE* 3.1 7.2 + - - +
118B GLU* 1.3 75.7 - - - +
120B PHE* 1.3 57.7 + - - +
122B LYS* 3.4 6.5 + - - +
123B ALA* 3.0 28.2 + - - +
144B VAL* 3.7 30.4 + - + +
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Residues in contact with PHE 120 (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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116B PHE* 2.9 37.7 + + + +
117B LYS 3.7 3.4 - - - +
119B GLU* 1.3 78.8 - - - +
121B ALA* 1.3 55.6 + - - +
123B ALA* 3.2 3.6 + - - +
124B GLY* 2.9 25.9 + - - -
133B ALA* 3.6 25.7 - - + +
134B TRP* 3.5 38.1 - - - -
135B LEU 3.7 3.4 - - - -
144B VAL* 4.1 10.0 - - + +
162B ILE* 4.1 10.5 - - + -
163B GLY 4.4 0.4 - - - -
164B LEU* 4.0 24.5 - - + -
183B ILE* 4.5 5.4 - - + -
186B PHE* 3.9 25.8 - + - -
187B TRP* 3.7 23.8 - + + -
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Residues in contact with ALA 121 (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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117B LYS 2.9 17.9 + - - +
118B GLU* 3.8 5.6 - - - +
120B PHE* 1.3 77.0 - - - +
122B LYS* 1.3 57.7 + - - +
124B GLY* 3.7 0.7 - - - +
125B ALA* 2.8 31.0 + - - +
180B PRO* 6.6 0.2 - - + -
183B ILE* 3.9 30.6 - - + +
187B TRP* 5.3 3.4 - - + +
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Residues in contact with LYS 122 (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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118B GLU 3.0 19.1 + - - +
119B GLU* 3.8 7.0 - - - +
121B ALA* 1.3 74.3 - - - +
123B ALA* 1.3 62.0 + - - +
125B ALA* 4.5 8.2 - - + +
126B THR* 2.8 62.9 + - + +
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Residues in contact with ALA 123 (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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119B GLU 3.0 6.8 + - - +
120B PHE* 3.5 8.1 - - - +
122B LYS* 1.3 75.6 - - - +
124B GLY* 1.3 61.4 + - - +
126B THR* 4.0 4.8 - - - +
127B ARG* 3.3 24.6 + - - +
133B ALA* 4.5 3.4 - - + -
144B VAL* 3.6 28.7 - - + -
145B THR 4.2 16.4 - - - +
146B SER* 3.9 9.4 - - - -
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Residues in contact with GLY 124 (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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120B PHE* 2.9 14.9 + - - -
121B ALA 3.7 3.4 - - - -
122B LYS 3.3 0.2 - - - -
123B ALA* 1.3 78.8 - - - +
125B ALA* 1.3 57.5 + - - +
127B ARG* 3.7 5.8 + - - +
133B ALA* 3.9 16.9 - - - +
166B VAL* 4.2 8.2 - - - +
179B ARG* 2.8 27.2 + - - -
183B ILE* 4.0 15.3 - - - -
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Residues in contact with ALA 125 (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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121B ALA 2.8 21.3 + - - +
122B LYS* 4.0 12.1 - - - +
124B GLY* 1.3 74.6 - - - +
126B THR* 1.3 60.7 + - - +
127B ARG 3.6 1.9 + - - +
179B ARG* 3.8 18.6 + - - +
180B PRO* 5.0 14.8 - - + -
183B ILE* 4.0 5.3 - - + +
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Residues in contact with THR 126 (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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122B LYS* 2.8 43.4 + - + +
123B ALA* 4.0 4.9 - - - +
125B ALA* 1.3 75.4 - - - +
127B ARG* 1.3 58.5 + - - +
128B PHE* 3.1 12.5 + - - +
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Residues in contact with ARG 127 (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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123B ALA 3.3 16.1 + - - +
124B GLY* 4.0 6.7 - - - +
125B ALA 3.4 1.9 - - - +
126B THR* 1.3 73.9 - - - +
128B PHE* 1.3 70.9 + - - +
129B GLY 3.5 3.5 + - - +
130B SER 3.9 13.4 + - - +
131B GLY* 4.1 9.6 - - - +
132B TRP 4.4 1.6 - - - +
146B SER* 2.9 47.0 + - - +
147B THR 3.6 10.5 + - - +
148B PRO* 3.5 37.9 - - - +
166B VAL* 4.0 20.4 - - + -
179B ARG* 2.8 25.9 + - - +
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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