Contacts of the helix formed by residues 112 - 127 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106A ILE* 4.2 6.2 - - - +
107A GLU* 3.9 10.1 + - - -
110A PHE* 3.3 6.7 + - - +
111A GLY* 1.3 77.6 - - - +
113A PHE* 1.3 64.4 + - - +
114A ASP* 3.6 9.3 + - - +
115A ALA* 3.1 23.6 + - - +
116A PHE* 3.1 20.3 + - - +
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Residues in contact with PHE 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A GLY 3.8 14.1 - - - -
97A GLN* 3.5 39.5 - - - +
98A PRO* 3.4 33.2 - - + -
106A ILE* 4.2 10.4 - - + +
107A GLU* 4.7 5.9 - - + +
112A SER* 1.3 72.2 - - - +
114A ASP* 1.3 63.1 + - - +
116A PHE* 3.1 15.7 + + - +
117A LYS* 2.9 67.7 + - + +
187A TRP* 4.8 4.7 - + + -
192A TRP* 3.5 29.6 - + - -
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Residues in contact with ASP 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A GLN* 5.4 1.6 + - - +
112A SER* 3.3 8.5 + - - +
113A PHE* 1.3 82.3 - - - +
115A ALA* 1.3 62.9 + - - +
117A LYS* 3.3 27.3 + - - +
118A GLU* 3.1 36.5 + - - +
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Residues in contact with ALA 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A PHE* 3.3 25.4 - - - +
111A GLY* 5.1 0.4 - - - -
112A SER* 3.1 18.4 + - - +
114A ASP* 1.3 73.7 - - - +
116A PHE* 1.3 66.3 + - - +
118A GLU* 3.3 14.8 + - - +
119A GLU* 3.0 23.0 + - - +
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Residues in contact with PHE 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A ILE* 3.8 18.2 - - + -
110A PHE* 3.9 35.3 - + + +
112A SER 3.1 12.6 + - - +
113A PHE* 3.1 24.0 + + - +
115A ALA* 1.3 77.0 - - - +
117A LYS* 1.3 64.5 + - - +
119A GLU* 3.1 4.0 + - - +
120A PHE* 2.9 41.4 + + + +
135A LEU* 3.8 24.9 - - + -
144A VAL* 3.7 22.2 - - + -
162A ILE* 4.0 11.0 - - + -
187A TRP* 3.8 20.6 - + - -
192A TRP* 3.9 19.3 - + - -
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Residues in contact with LYS 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A GLN* 5.3 2.2 - - - +
113A PHE* 2.9 54.3 + - + +
114A ASP* 3.3 31.3 + - - +
116A PHE* 1.3 76.0 - - + +
118A GLU* 1.3 58.0 + - + +
120A PHE* 3.7 0.9 - - - +
121A ALA* 2.8 32.7 + - - +
187A TRP* 3.7 53.7 - - + +
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Residues in contact with GLU 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A ASP* 3.1 25.2 + - - +
115A ALA* 3.5 13.2 - - - +
117A LYS* 1.3 77.8 - - + +
119A GLU* 1.3 56.4 + - - +
121A ALA* 3.4 6.0 + - - +
122A LYS* 3.0 29.9 + - - +
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Residues in contact with GLU 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A PHE* 3.4 30.2 - - - -
115A ALA 3.0 13.0 + - - +
116A PHE* 3.1 8.9 + - - +
118A GLU* 1.3 76.1 - - - +
120A PHE* 1.3 57.0 + - - +
122A LYS* 3.4 8.6 + - + +
123A ALA* 3.0 26.2 + - - +
144A VAL* 3.8 27.5 + - + +
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Residues in contact with PHE 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A PHE* 2.9 37.0 + + + +
117A LYS 3.7 3.6 - - - +
119A GLU* 1.3 74.6 - - - +
121A ALA* 1.3 59.2 + - - +
123A ALA* 3.2 3.5 + - - +
124A GLY* 3.0 25.6 + - - -
133A ALA* 3.5 26.8 - - + +
134A TRP* 3.7 35.9 - - - -
135A LEU 3.9 2.9 - - - -
144A VAL* 4.0 10.7 - - + +
162A ILE* 4.1 10.5 - - + -
163A GLY 4.4 1.6 - - - -
164A LEU* 3.9 25.8 - - + -
183A ILE* 4.6 3.1 - - + -
186A PHE* 3.9 24.2 - + - -
187A TRP* 3.6 23.8 - + + -
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Residues in contact with ALA 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A LYS 2.8 19.2 + - - +
118A GLU* 3.6 7.6 - - - +
120A PHE* 1.3 76.1 - - - +
122A LYS* 1.3 56.9 + - - +
124A GLY* 3.4 1.3 + - - +
125A ALA* 2.8 31.2 + - - +
183A ILE* 3.9 30.6 - - + +
187A TRP* 5.2 2.9 - - + +
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Residues in contact with LYS 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A GLU 3.0 17.5 + - - +
119A GLU* 3.6 7.6 - - - +
120A PHE 3.3 0.2 - - - -
121A ALA* 1.3 74.5 - - - +
123A ALA* 1.3 63.0 + - - +
125A ALA* 4.5 4.3 - - - -
126A THR* 2.8 47.7 + - + +
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Residues in contact with ALA 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A GLU 3.0 7.8 + - - +
120A PHE 3.2 5.6 + - - +
122A LYS* 1.3 74.0 - - - +
124A GLY* 1.3 61.2 + - - +
126A THR* 3.4 7.1 + - - -
127A ARG* 3.3 22.9 + - - +
133A ALA* 4.6 4.5 - - + -
144A VAL* 3.6 31.2 - - + -
145A THR* 4.3 16.2 - - - +
146A SER* 4.1 9.9 + - - -
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Residues in contact with GLY 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A PHE* 3.0 14.7 + - - -
121A ALA 3.8 2.7 - - - -
123A ALA* 1.3 74.4 - - - +
125A ALA* 1.3 55.2 + - - +
126A THR 3.4 0.3 + - - -
127A ARG* 3.5 6.4 + - - +
133A ALA* 3.9 17.4 - - - +
166A VAL* 4.2 7.9 - - - +
179A ARG* 2.7 34.0 + - - -
183A ILE* 3.9 15.5 - - - -
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Residues in contact with ALA 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A ALA 2.8 19.6 + - - +
122A LYS* 4.0 5.4 - - - +
123A ALA 3.4 0.2 - - - -
124A GLY* 1.3 77.4 - - - +
126A THR* 1.3 63.6 + - + +
127A ARG 3.6 1.6 + - - +
128A PHE* 5.8 0.2 - - - -
179A ARG* 3.8 18.3 + - - +
180A PRO* 5.0 15.3 - - + -
183A ILE* 3.8 5.0 - - + +
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Residues in contact with THR 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A LYS* 2.8 37.1 + - + +
123A ALA* 3.4 9.7 + - - -
125A ALA* 1.3 80.5 - - + +
127A ARG* 1.3 59.4 + - - +
128A PHE* 2.9 13.0 + - - +
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Residues in contact with ARG 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A ALA 3.3 15.4 + - - +
124A GLY* 3.9 7.6 - - - +
125A ALA 3.4 2.5 - - - +
126A THR* 1.3 72.9 - - - +
128A PHE* 1.3 70.9 + - - +
129A GLY 3.5 4.3 + - - +
130A SER 3.8 12.8 - - - +
131A GLY* 4.1 11.0 - - - +
132A TRP 4.4 1.6 - - - +
146A SER* 2.9 47.3 + - - +
147A THR* 3.5 14.0 + - - +
148A PRO* 3.3 34.2 - - - +
166A VAL* 4.0 19.7 - - + -
179A ARG* 2.8 26.2 + - - +
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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