Contacts of the helix formed by residues 116 - 133 (chain A) in PDB entry 2QH5
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 ASP 116 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A ILE* 3.8 1.6 - - - +
115A LYS* 1.3 72.5 - - - +
117A LEU* 1.3 60.5 + - - +
118A GLN* 3.3 9.9 + - - +
119A ALA* 3.0 33.3 + - - +
120A TYR* 3.3 17.7 + - - +
261A ASN 4.6 2.2 - - - +
262A ALA* 3.0 34.3 + - - +
263A LYS* 4.9 1.5 - - + +
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Residues in contact with LEU 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A ARG* 4.3 35.4 - - + +
48A LEU* 6.0 1.3 - - + -
114A ILE* 5.0 7.2 - - - +
115A LYS 3.1 9.7 + - - +
116A ASP* 1.3 71.6 + - - +
118A GLN* 1.3 61.6 + - - +
120A TYR* 3.5 11.9 - - + +
121A GLU* 3.1 41.6 + - - +
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Residues in contact with GLN 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A ASP* 3.3 7.5 + - - +
117A LEU* 1.3 77.2 - - - +
119A ALA* 1.3 60.1 + - - +
120A TYR 3.2 0.4 - - - -
121A GLU* 3.3 22.0 + - - +
122A ASN* 2.9 54.2 + - - +
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Residues in contact with ALA 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A ASP* 3.0 24.1 + - - +
118A GLN* 1.3 73.8 - - - +
120A TYR* 1.3 64.2 + - - +
122A ASN* 3.9 10.7 - - - +
123A ALA* 3.3 22.3 + - - +
259A GLU 5.5 0.7 - - - +
260A LEU* 4.9 1.2 - - - +
261A ASN* 3.3 29.9 + - + +
262A ALA* 4.1 3.6 - - + -
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Residues in contact with TYR 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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44A ARG* 3.5 27.8 + - + -
45A ASN* 2.4 30.9 + - - -
48A LEU* 3.7 13.2 - - + -
108A THR* 3.6 1.7 - - - +
114A ILE* 3.6 43.3 - - + -
116A ASP 3.3 13.3 + - - +
117A LEU* 3.5 15.0 - - + +
119A ALA* 1.3 78.3 - - - +
121A GLU* 1.3 65.0 + - + +
123A ALA* 3.4 4.2 + - - +
124A ILE* 3.1 48.4 + - + +
139A PHE* 6.3 0.2 - + - -
188A MET* 3.4 30.9 - - + +
260A LEU* 4.2 16.6 - - + -
262A ALA* 4.2 1.3 - - - +
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Residues in contact with GLU 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A SER* 5.9 0.3 - - - -
48A LEU* 3.6 30.5 - - + +
117A LEU* 3.1 33.7 + - - +
118A GLN* 3.3 24.3 + - - +
120A TYR* 1.3 84.7 - - + +
122A ASN* 1.3 62.1 + - - +
124A ILE* 3.5 6.0 + - - +
125A LYS* 3.2 34.9 + - + +
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Residues in contact with ASN 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 GLN* 2.9 42.3 + - - +
119A ALA* 3.9 10.3 - - - +
121A GLU* 1.3 73.9 - - - +
123A ALA* 1.3 60.0 + - - +
125A LYS* 3.3 14.3 + - - +
126A LYS* 3.0 47.6 + - - +
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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 ALA 3.3 15.4 + - - +
120A TYR 3.4 4.5 + - - +
122A ASN* 1.3 77.3 - - - +
124A ILE* 1.3 57.1 + - + +
126A LYS* 3.5 5.4 + - - +
127A ALA* 2.9 29.6 + - - +
139A PHE* 3.7 20.6 - - + -
258A VAL* 3.8 19.3 - - + +
259A GLU 4.1 13.2 - - - +
260A LEU* 4.3 10.1 - - + -
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Residues in contact with ILE 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A ASN* 4.7 0.4 - - - +
48A LEU* 3.9 22.7 - - + +
106A ILE* 4.0 38.4 - - + -
120A TYR* 3.1 57.6 + - + +
121A GLU 3.7 5.6 - - - +
122A ASN 3.2 0.4 - - - -
123A ALA* 1.3 75.7 - - - +
125A LYS* 1.3 60.2 + - + +
127A ALA* 3.2 4.7 + - - +
128A ILE* 2.9 38.9 + - + +
139A PHE* 4.0 19.5 - - + -
188A MET* 4.1 4.9 - - + -
190A VAL* 4.8 2.2 - - + -
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Residues in contact with LYS 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A GLU* 3.2 24.7 + - + +
122A ASN* 3.3 13.2 + - - +
124A ILE* 1.3 80.9 - - + +
126A LYS* 1.3 60.1 + - - +
128A ILE* 3.7 10.2 - - + +
129A ASP* 3.3 20.1 + - - +
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Residues in contact with LYS 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 ASN* 3.0 30.4 + - - +
123A ALA* 3.5 9.2 - - - +
125A LYS* 1.3 72.8 - - - +
127A ALA* 1.3 61.7 + - - +
129A ASP* 2.9 23.1 + - - +
130A LEU* 3.2 16.0 + - + +
258A VAL* 4.0 25.1 - - + -
129B ASP* 3.8 32.6 + - - -
133B LYS* 5.7 3.8 - - - +
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Residues in contact with ALA 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A ALA 2.9 18.7 + - - +
124A ILE 3.2 4.0 + - - +
126A LYS* 1.3 74.9 - - - +
128A ILE* 1.3 56.6 + - - +
130A LEU* 3.5 1.4 + - - -
131A ALA* 3.0 26.0 + - - +
137A VAL* 3.4 30.6 - - + +
139A PHE* 3.4 26.9 - - + -
190A VAL* 3.8 13.0 - - + -
258A VAL* 4.2 3.8 - - + +
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Residues in contact with ILE 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A LEU* 6.3 0.9 - - + -
3A ILE* 4.2 22.2 - - + -
104A LEU* 3.9 22.4 - - + -
106A ILE* 3.9 25.6 - - + -
124A ILE* 2.9 31.2 + - + +
125A LYS* 3.7 11.0 - - + +
127A ALA* 1.3 74.8 - - - +
129A ASP* 1.3 63.1 + - - +
131A ALA* 3.2 7.0 + - - +
132A GLN* 3.1 31.9 + - - +
190A VAL* 3.9 19.1 - - + -
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Residues in contact with ASP 129 (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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125A LYS 3.3 9.5 + - - +
126A LYS* 2.9 12.3 + - - +
128A ILE* 1.3 80.3 - - - +
130A LEU* 1.3 63.1 + - + +
132A GLN* 3.2 27.1 + - - +
133A LYS* 3.3 32.6 + - - +
126B LYS* 3.8 34.0 + - - +
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Residues in contact with LEU 130 (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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126A LYS* 3.2 10.9 + - + +
127A ALA 3.7 1.8 - - - +
129A ASP* 1.3 76.6 - - + +
131A ALA* 1.3 61.9 + - - +
133A LYS* 3.1 18.3 + - + +
135A PHE* 3.3 28.4 + - + -
137A VAL* 3.7 19.1 - - + -
159A LEU* 4.3 16.8 - - + -
256A LYS* 4.0 23.6 - - + -
257A MET 4.4 0.2 - - - +
258A VAL* 3.8 28.9 - - + -
159B LEU* 3.9 28.7 - - + -
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Residues in contact with ALA 131 (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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104A LEU* 4.0 16.1 - - + +
127A ALA 3.0 17.5 + - - +
128A ILE 3.2 6.9 + - - +
130A LEU* 1.3 75.8 - - - +
132A GLN* 1.3 61.6 + - - +
134A GLY* 3.2 14.0 + - - -
135A PHE 3.7 12.6 + - - +
137A VAL* 3.8 2.2 - - + +
190A VAL* 3.9 20.9 - - + -
191A PHE* 4.0 16.8 - - - +
192A GLN* 4.5 10.0 + - - +
195A VAL* 5.0 0.3 - - - +
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Residues in contact with GLN 132 (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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1A LEU* 3.7 30.7 - - + +
104A LEU* 4.1 23.1 - - + -
128A ILE* 3.1 24.2 + - - +
129A ASP* 3.2 20.3 + - - +
131A ALA* 1.3 76.3 - - - +
133A LYS* 1.3 60.9 + - + +
134A GLY* 3.2 0.7 + - - -
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Residues in contact with LYS 133 (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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129A ASP* 3.3 33.0 - - - +
130A LEU* 3.1 16.1 + - + +
132A GLN* 1.3 79.2 - - + +
134A GLY* 1.3 58.4 + - - +
135A PHE* 3.7 15.0 - - + -
126B LYS* 5.9 2.6 - - - +
157B ASN* 3.9 34.2 - - - +
158B GLY 3.0 21.5 + - - +
159B LEU* 4.4 15.4 - - + +
258B VAL* 5.4 2.0 - - - +
259B GLU* 2.8 35.3 + - - +
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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