Contacts of the helix formed by residues 116 - 134 (chain A) in PDB entry 2QA5
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 LYS 116 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117A THR* 1.3 72.7 + - - +
118A ILE* 3.3 3.2 - - - +
119A ILE* 3.5 25.5 - - + +
120A SER* 3.5 21.0 + - - -
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Residues in contact with THR 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A THR* 4.3 23.0 + - - +
79A VAL* 4.3 12.4 - - - +
116A LYS* 1.3 85.3 - - - +
118A ILE* 1.3 68.4 + - + +
120A SER* 3.4 16.6 - - - -
121A TYR* 3.5 9.5 + - - +
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Residues in contact with ILE 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A MSE 4.1 25.6 - - + -
43A VAL* 3.6 4.0 - - + -
79A VAL* 5.0 5.2 - - + -
100A VAL* 3.2 42.6 - - + -
102A THR* 6.5 1.8 - - - -
116A LYS* 3.3 1.4 - - - +
117A THR* 1.3 82.0 - - + +
119A ILE* 1.3 69.9 + - + +
120A SER 3.1 2.0 - - - -
121A TYR* 3.2 7.4 + - - +
122A ILE* 3.2 24.1 + - + +
167A PHE* 3.6 38.6 - - + -
171A ILE* 4.6 4.0 - - + -
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Residues in contact with ILE 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A LYS* 3.5 33.4 - - + +
118A ILE* 1.3 77.8 - - + +
120A SER* 1.3 69.0 + - - +
122A ILE* 3.2 22.7 - - + +
123A ASP* 3.0 31.4 + - - +
167A PHE* 6.3 3.6 - - + -
170A ALA* 4.6 15.7 - - + +
171A ILE* 4.1 24.2 - - + -
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Residues in contact with SER 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A LYS 3.5 11.6 + - - -
117A THR* 3.4 13.7 - - - -
119A ILE* 1.3 84.5 - - - +
121A TYR* 1.3 57.1 + - - +
123A ASP* 3.5 4.0 - - - +
124A GLU* 2.8 31.0 + - - +
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Residues in contact with TYR 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A MSE 5.7 1.6 - - - -
79A VAL* 3.7 34.8 - - + -
81A ILE* 3.6 26.4 - - + +
98A THR* 4.2 17.3 - - + +
117A THR 3.5 8.7 + - - +
118A ILE 3.2 8.3 + - - +
120A SER* 1.3 78.5 - - - +
122A ILE* 1.3 72.7 + - + +
123A ASP 3.5 0.2 + - - -
124A GLU* 4.3 13.2 - - - -
125A GLN* 2.7 58.1 + - + +
144A ASN* 4.8 7.2 + - - +
146A VAL* 4.4 16.6 - - + -
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Residues in contact with ILE 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A MSE 3.5 30.5 - - - -
118A ILE* 3.2 10.7 + - + +
119A ILE* 3.2 30.1 - - + +
121A TYR* 1.3 83.8 - - + +
123A ASP* 1.3 62.4 + - + +
125A GLN* 3.6 15.7 - - - +
126A PHE* 3.7 18.4 + - + -
145A ARG* 5.5 0.3 - - - -
146A VAL* 4.0 21.8 + - + +
171A ILE* 3.6 36.3 - - + +
173A ASN 5.2 3.1 - - - +
175A VAL* 4.2 17.5 - - + -
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Residues in contact with ASP 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 ILE* 3.0 23.3 + - - +
120A SER* 3.6 4.0 - - - +
122A ILE* 1.3 79.8 - - - +
124A GLU* 1.2 65.7 + - - +
125A GLN 3.0 2.0 - - - -
126A PHE* 3.1 37.0 + - - +
127A GLU* 3.1 12.1 + - - +
298A ASN* 3.3 21.4 + - - +
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Residues in contact with GLU 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A SER* 2.8 19.8 + - - +
121A TYR* 3.8 12.3 - - - +
123A ASP* 1.2 72.4 - - - +
125A GLN* 1.3 69.1 + - - +
127A GLU* 2.9 10.5 + - + +
128A ARG* 2.6 40.4 + - + +
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Residues in contact with GLN 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 TYR* 2.7 45.9 + - + +
122A ILE* 3.6 12.6 - - - +
123A ASP 3.0 0.6 - - - -
124A GLU* 1.3 93.7 + - - +
126A PHE* 1.3 59.6 + - - +
128A ARG* 3.8 11.6 - - - +
129A TYR* 3.2 23.2 + - - +
143A ASP* 5.8 0.3 - - - +
144A ASN* 2.4 54.3 + - + +
145A ARG* 4.0 12.6 + - - +
146A VAL* 5.2 0.7 - - + +
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Residues in contact with PHE 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 ILE* 3.8 19.7 - - + -
123A ASP* 3.1 31.0 + - - +
125A GLN* 1.3 78.2 - - - +
127A GLU* 1.3 56.3 + - - +
129A TYR* 3.5 4.6 + - - +
130A LEU* 2.9 26.7 + - - +
145A ARG* 4.0 20.6 - - + -
146A VAL 6.1 0.9 - - - -
173A ASN 4.8 12.3 - - - -
175A VAL* 5.6 7.9 - - + -
290A VAL* 4.3 11.9 - - + -
294A LEU* 3.9 31.9 - - + -
295A HIS* 3.7 41.9 - - + +
298A ASN* 3.3 26.3 - - + +
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Residues in contact with GLU 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A ASP 3.1 9.8 + - - +
124A GLU* 2.9 12.4 + - + +
126A PHE* 1.3 74.1 - - - +
128A ARG* 1.3 66.7 + - - +
129A TYR 3.2 0.2 - - - -
130A LEU* 3.9 9.5 - - + +
131A HIS* 3.0 26.0 + - - +
298A ASN* 4.4 3.1 + - - +
302A GLU* 6.3 2.7 - - + -
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Residues in contact with ARG 128 (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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124A GLU* 2.6 24.1 + - + +
125A GLN* 3.8 16.6 - - - +
127A GLU* 1.3 72.9 - - - +
129A TYR* 1.3 56.6 + - - +
131A HIS* 3.7 6.6 - - - +
132A ASP* 2.9 35.9 + - - +
144A ASN* 5.8 2.5 - - - +
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Residues in contact with TYR 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 GLN 3.2 15.8 + - - +
126A PHE 3.7 4.3 - - - +
127A GLU 3.2 0.2 - - - -
128A ARG* 1.3 77.3 - - - +
130A LEU* 1.3 55.3 + - - +
132A ASP* 4.2 3.6 - - + -
133A GLU* 2.5 80.2 + - + +
141A ILE* 4.3 36.9 - - + +
142A ILE 5.7 0.2 - - - -
143A ASP* 3.3 27.6 - - + -
145A ARG* 3.1 39.8 + - - -
295A HIS* 3.5 17.7 - + + -
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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 PHE 2.9 19.2 + - - +
127A GLU* 3.4 9.2 + - + +
129A TYR* 1.3 69.0 - - - +
131A HIS* 1.3 71.6 + - - +
133A GLU* 4.2 4.7 - - - +
134A SER* 3.1 32.7 + - - -
295A HIS* 4.4 9.0 - - + -
298A ASN* 4.2 11.2 - - - +
299A PHE* 4.1 31.2 - - + +
302A GLU* 3.3 31.6 - - + +
303A ARG 5.4 0.2 - - - +
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Residues in contact with HIS 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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127A GLU 3.0 18.5 + - - +
128A ARG* 3.7 5.4 - - - +
130A LEU* 1.3 82.3 - - - +
132A ASP* 1.3 87.9 + - - +
134A SER* 3.5 3.5 - - - -
135A GLY* 3.1 22.8 + - - -
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Residues in contact with ASP 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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128A ARG* 2.9 21.9 + - - +
129A TYR* 3.7 6.7 - - + +
131A HIS* 1.3 97.9 + - - +
133A GLU* 1.3 61.6 - - - +
135A GLY* 3.3 12.4 + - - +
137A ASN 3.9 10.6 - - - +
138A ARG* 4.1 0.7 - - - +
141A ILE* 3.6 39.0 + - + +
142A ILE* 4.6 7.6 + - - +
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Residues in contact with GLU 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 TYR* 2.5 53.5 + - + +
130A LEU* 4.2 4.2 - - - +
132A ASP* 1.3 72.0 - - - +
134A SER* 1.3 50.4 + - - +
135A GLY 3.2 0.2 - - - -
138A ARG* 2.2 60.1 + - - +
141A ILE* 4.1 8.2 - - + +
295A HIS* 3.2 19.2 + - - -
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Residues in contact with SER 134 (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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130A LEU* 3.1 26.9 + - - -
131A HIS* 3.5 4.3 - - - -
133A GLU* 1.3 76.2 - - - +
135A GLY* 1.3 61.8 + - - +
138A ARG* 3.9 6.1 - - - +
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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