Contacts of the helix formed by residues 116 - 132 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B ILE* 4.0 2.3 - - - +
115B LYS* 1.3 73.9 - - - +
117B LEU* 1.3 63.8 + - - +
118B GLN* 3.4 15.1 + - - +
119B ALA* 3.5 19.2 + - - +
120B TYR* 3.3 18.2 + - - +
261B ASN 4.0 4.9 - - - +
262B ALA* 3.2 31.5 + - - +
263B LYS* 4.4 7.4 - - + +
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Residues in contact with LEU 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B ARG* 4.5 33.4 - - + +
114B ILE* 5.1 8.5 - - + +
115B LYS 3.3 8.0 + - - +
116B ASP* 1.3 72.9 + - - +
118B GLN* 1.3 60.7 + - - +
119B ALA 3.5 0.2 - - - -
120B TYR* 3.6 7.7 - - + +
121B GLU* 3.1 54.1 + - + +
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Residues in contact with GLN 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B ASP* 3.3 7.7 + - - +
117B LEU* 1.3 79.3 - - - +
119B ALA* 1.3 63.5 + - - +
121B GLU* 3.3 21.1 + - - +
122B ASN* 3.0 42.0 + - - +
125B LYS* 4.8 4.9 - - - +
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Residues in contact with ALA 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B ASP* 3.5 23.1 + - - +
117B LEU 3.5 0.2 - - - -
118B GLN* 1.3 74.2 - - - +
120B TYR* 1.3 66.0 + - - +
122B ASN* 3.3 11.1 + - - +
123B ALA* 2.9 25.8 + - - +
260B LEU* 5.2 1.3 - - - -
261B ASN* 3.4 28.7 - - + +
262B ALA* 3.9 4.5 - - + -
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Residues in contact with TYR 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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44B ARG* 3.6 30.4 + - + -
45B ASN* 2.5 32.9 + - - -
48B LEU* 3.9 13.7 - - + -
108B THR* 3.4 5.2 - - - +
114B ILE* 3.7 35.0 - - + -
116B ASP 3.3 11.9 + - - +
117B LEU* 3.6 12.6 - - + +
119B ALA* 1.3 79.2 - - - +
121B GLU* 1.3 59.8 + - + +
122B ASN 3.2 0.3 + - - -
123B ALA* 3.2 4.5 + - + +
124B ILE* 2.9 52.8 + - + +
188B MET* 3.4 34.6 - - + +
260B LEU* 4.5 15.3 - - + -
262B ALA* 4.1 1.6 - - + +
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Residues in contact with GLU 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B ARG 5.4 2.1 - - - +
47B SER* 5.0 5.2 + - - -
48B LEU* 3.6 36.6 - - + +
117B LEU* 3.1 37.7 + - + +
118B GLN* 3.3 24.5 + - - +
120B TYR* 1.3 80.4 - - + +
122B ASN* 1.3 58.5 + - - +
124B ILE* 3.9 6.8 - - - +
125B LYS* 3.1 40.4 + - - +
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Residues in contact with ASN 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 GLN* 3.0 44.2 + - - +
119B ALA* 3.6 9.4 - - - +
121B GLU* 1.3 75.6 - - - +
123B ALA* 1.3 64.2 - - - +
125B LYS* 3.2 22.2 + - - +
126B LYS* 3.0 38.9 + - - +
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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
----------------------------------------------------------
119B ALA 2.9 16.4 + - - +
120B TYR* 3.6 3.4 - - + +
122B ASN* 1.3 74.9 - - - +
124B ILE* 1.3 63.7 + - + +
126B LYS* 3.3 8.5 + - - +
127B ALA* 3.0 23.4 + - - +
139B PHE* 4.0 13.0 - - + -
258B VAL* 3.8 25.6 - - + +
259B GLU 4.2 5.8 - - - +
260B LEU* 4.0 19.1 - - + -
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Residues in contact with ILE 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B LEU* 4.2 19.1 - - + -
106B ILE* 3.9 35.7 - - + -
120B TYR* 2.9 60.0 + - + +
121B GLU 3.9 4.9 - - - +
123B ALA* 1.3 75.1 - - + +
125B LYS* 1.3 59.9 + - + +
127B ALA* 3.2 4.2 + - - +
128B ILE* 2.8 39.0 + - + +
139B PHE* 3.8 22.2 - - + -
188B MET* 3.9 7.9 - - + -
190B VAL* 4.7 2.7 - - + -
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Residues in contact with LYS 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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118B GLN* 4.8 4.6 - - - +
121B GLU* 3.1 31.5 + - - +
122B ASN* 3.2 25.8 + - - +
124B ILE* 1.3 77.5 - - + +
126B LYS* 1.3 61.0 + - + +
128B ILE* 3.5 9.6 + - + +
129B ASP* 3.2 20.4 + - - +
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Residues in contact with LYS 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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129A ASP* 3.8 31.6 + - - +
133A LYS* 5.9 3.0 - - - +
122B ASN* 3.0 28.8 + - - +
123B ALA* 3.6 7.6 - - - +
125B LYS* 1.3 72.3 - - + +
127B ALA* 1.3 62.1 + - - +
129B ASP* 3.1 8.3 + - - +
130B LEU* 2.9 31.9 + - + +
258B VAL* 4.3 25.8 - - + +
259B GLU 5.7 2.4 + - - -
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Residues in contact with ALA 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 3.0 7.5 + - - +
124B ILE 3.4 8.1 - - - +
126B LYS* 1.3 73.7 - - - +
128B ILE* 1.3 56.4 + - - +
130B LEU* 3.3 3.5 + - - +
131B ALA* 2.8 36.7 + - - +
137B VAL* 3.6 21.4 - - + +
139B PHE* 3.4 33.4 - - + -
190B VAL* 3.8 14.6 - - + -
258B VAL* 4.1 3.3 - - + +
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Residues in contact with ILE 128 (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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3B ILE* 4.2 23.6 - - + -
104B LEU* 3.8 18.3 - - + +
106B ILE* 3.6 29.4 - - + -
124B ILE* 2.8 28.3 + - + +
125B LYS* 3.6 11.0 - - + +
127B ALA* 1.3 74.9 - - - +
129B ASP* 1.3 63.3 + - - +
131B ALA* 3.2 7.6 + - - +
132B GLN* 3.1 38.6 + - - +
190B VAL* 3.9 12.6 - - + -
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Residues in contact with ASP 129 (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 LYS* 3.8 29.0 + - - -
125B LYS 3.2 9.0 + - - +
126B LYS* 3.1 10.5 + - - +
128B ILE* 1.3 78.6 - - - +
130B LEU* 1.3 63.8 + - - +
132B GLN* 3.2 24.4 + - - +
133B LYS* 3.3 34.4 + - - +
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Residues in contact with LEU 130 (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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159A LEU* 3.8 30.7 - - + -
126B LYS* 2.9 13.2 + - + +
127B ALA 3.6 7.4 - - - +
129B ASP* 1.3 77.3 - - - +
131B ALA* 1.3 61.5 + - - +
133B LYS* 3.1 19.4 + - + -
135B PHE* 3.3 34.2 + - + +
137B VAL* 3.7 11.7 - - + -
159B LEU* 3.9 18.4 - - + -
256B LYS* 3.9 20.2 - - + -
257B MET 3.9 0.4 - - - +
258B VAL* 3.8 28.5 - - + -
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Residues in contact with ALA 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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104B LEU* 4.4 8.1 - - + -
127B ALA 2.8 20.6 + - - +
128B ILE* 3.2 6.9 + - - +
130B LEU* 1.3 72.7 - - - +
132B GLN* 1.3 57.7 + - - +
133B LYS 3.2 0.4 - - - -
134B GLY* 3.2 18.4 + - - -
135B PHE 3.7 12.3 + - - +
137B VAL* 3.7 3.7 - - + +
190B VAL* 4.0 9.0 - - + -
191B PHE* 3.8 30.1 - - - +
192B GLN* 4.3 16.7 + - - +
195B VAL* 4.9 0.2 - - - +
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Residues in contact with GLN 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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1B LEU* 4.2 19.8 - - + +
104B LEU* 3.9 26.0 - - + +
128B ILE* 3.1 29.4 + - - +
129B ASP* 3.7 16.2 - - - +
130B LEU 3.2 1.0 - - - -
131B ALA* 1.3 74.7 - - - +
133B LYS* 1.3 59.2 + - + +
134B GLY 3.2 3.5 + - - -
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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