Contacts of the helix formed by residues 124 - 143 (chain A) in PDB entry 2Q24
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 124 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123A GLY* 1.3 74.6 - - - -
125A SER* 1.3 63.4 + - - +
126A ARG 3.3 2.5 - - - -
127A GLN* 3.1 35.5 + - + +
128A LEU* 3.0 21.5 + - - +
17B ARG* 3.9 14.9 + - - -
18B ASP* 4.7 0.2 - - - +
64B ALA 4.6 0.3 - - - +
67B ARG* 4.5 1.7 - - - +
68B ASN* 2.8 49.0 + - - +
71B ALA* 3.6 23.2 - - + +
72B ARG* 5.6 0.3 - - - +
195B CL 3.1 16.2 - - + +
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Residues in contact with SER 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A TYR* 3.3 34.5 - - - -
67A ARG* 5.4 1.4 - - - +
70A VAL* 3.6 24.2 - - - +
122A TYR* 2.6 25.9 + - - -
123A GLY 3.3 1.0 + - - -
124A ASP* 1.3 76.8 - - - +
126A ARG* 1.3 64.3 + - - +
128A LEU* 3.2 6.4 + - - +
129A ILE* 2.9 31.2 + - - +
67B ARG* 4.3 5.0 + - - -
195B CL 4.0 0.6 - - - +
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Residues in contact with ARG 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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123A GLY 5.0 0.6 + - - -
124A ASP 3.3 0.4 - - - -
125A SER* 1.3 78.7 - - - +
127A GLN* 1.3 68.4 + - + +
129A ILE* 3.5 3.6 + - - +
130A GLN* 3.0 50.3 + - - +
156A PHE* 3.8 32.5 - - + -
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Residues in contact with GLN 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 GLY 4.3 2.8 - - - +
124A ASP* 3.1 46.8 + - + +
126A ARG* 1.3 88.8 + - + +
128A LEU* 1.3 56.0 + - - +
130A GLN* 3.5 10.4 + - - +
131A SER* 2.9 25.3 + - - -
17B ARG* 5.6 7.3 - - - +
18B ASP* 5.1 6.3 + - - -
71B ALA* 5.4 0.4 - - + -
75B ASP* 3.3 19.1 - - - +
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Residues in contact with LEU 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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70A VAL* 4.3 11.7 - - + -
74A CYS* 3.5 21.0 - - + +
124A ASP 3.0 17.3 + - - +
125A SER* 3.2 11.2 + - - +
127A GLN* 1.3 76.5 - - - +
129A ILE* 1.3 63.3 + - - +
131A SER* 3.3 4.7 + - - -
132A ALA* 3.1 17.0 + - - +
71B ALA* 3.8 26.2 - - + -
74B CYS* 4.3 12.1 - - + -
75B ASP* 3.5 18.0 - - - +
128B LEU* 3.9 34.5 - - + -
195B CL 4.1 19.7 - - + -
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Residues in contact with ILE 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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70A VAL* 4.1 12.3 - - + -
73A LEU* 4.1 9.6 - - + -
74A CYS* 3.7 18.8 - - - -
93A TRP* 3.8 23.9 - - + -
97A PHE* 4.2 9.0 - - + -
100A TYR* 3.7 40.8 - - + +
125A SER* 2.9 22.5 + - - +
126A ARG* 3.9 3.4 - - - +
128A LEU* 1.3 73.9 - - - +
130A GLN* 1.3 65.1 + - - +
132A ALA* 3.1 3.3 + - - +
133A LEU* 3.0 22.2 + - - +
156A PHE* 3.5 25.6 - - + -
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Residues in contact with GLN 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 ARG* 3.0 38.1 + - - +
127A GLN* 3.7 9.6 - - - +
129A ILE* 1.3 78.4 - - - +
131A SER* 1.3 56.6 + - - +
133A LEU* 3.3 6.4 + - - +
134A THR* 2.9 33.3 + - - +
152A SER* 4.4 4.5 + - - +
153A THR* 3.9 22.4 + - - -
156A PHE* 3.6 41.7 - - + +
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Residues in contact with SER 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 GLN 2.9 11.3 + - - -
128A LEU 3.6 3.1 - - - -
129A ILE 3.2 0.2 - - - -
130A GLN* 1.3 74.1 - - - +
132A ALA* 1.3 59.8 + - - +
134A THR* 3.2 7.5 + - - -
135A ALA* 2.9 28.6 + - - +
74B CYS 4.6 0.7 + - - -
75B ASP* 3.2 48.0 + - - -
78B PRO* 3.4 18.7 - - - +
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Residues in contact with ALA 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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74A CYS* 4.0 24.5 - - + +
77A VAL* 3.8 24.0 - - + +
93A TRP* 4.0 10.1 - - + -
128A LEU 3.1 12.2 + - - +
129A ILE 3.1 8.6 + - - +
131A SER* 1.3 75.6 - - - +
133A LEU* 1.3 64.7 + - - +
135A ALA* 3.2 8.6 + - - +
136A LEU* 3.1 26.1 + - - +
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Residues in contact with LEU 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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90A LEU* 3.7 27.6 - - + -
93A TRP* 3.9 20.3 - - + -
129A ILE 3.0 13.2 + - - +
130A GLN* 3.6 8.5 - - - +
132A ALA* 1.3 79.0 - - - +
134A THR* 1.3 57.0 + - - +
136A LEU* 3.2 7.1 + - - +
137A MSE 2.9 48.4 + - - +
152A SER* 3.6 11.9 - - - +
155A MSE 3.8 14.4 - - + -
156A PHE* 3.5 41.7 - - + +
159A LEU* 4.1 9.9 - - + -
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Residues in contact with THR 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 GLN* 2.9 15.2 + - - +
131A SER* 3.2 11.7 + - - -
133A LEU* 1.3 77.6 - - - +
135A ALA* 1.3 53.5 + - - +
137A MSE 4.1 1.7 - - - +
138A ASP* 2.8 61.8 + - - +
152A SER* 2.6 32.1 + - - +
78B PRO* 4.1 11.9 - - + -
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Residues in contact with ALA 135 (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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77A VAL* 4.0 17.0 - - + -
81A LEU* 4.3 6.3 - - + +
131A SER 2.9 13.7 + - - +
132A ALA* 3.5 10.5 - - - +
134A THR* 1.3 76.0 - - - +
136A LEU* 1.3 61.1 + - - +
138A ASP* 3.8 3.8 - - - +
139A ALA* 3.1 23.7 + - - +
78B PRO* 4.3 18.3 - - + +
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Residues in contact with LEU 136 (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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77A VAL* 3.9 27.6 - - + +
80A LEU* 5.2 1.3 - - + -
81A LEU* 4.1 8.7 - - + +
86A PRO* 4.7 3.9 - - - +
89A ALA* 4.0 30.3 - - + +
90A LEU* 4.0 25.1 - - + +
93A TRP* 3.3 47.3 - - + -
132A ALA 3.1 14.3 + - - +
133A LEU* 3.2 6.9 + - - +
135A ALA* 1.3 77.2 - - - +
137A MSE 1.3 58.9 + - - +
139A ALA* 3.3 6.6 + - - +
140A ALA* 2.9 29.0 + - - +
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Residues in contact with MSE 137 (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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90A LEU* 4.3 16.6 - - + -
133A LEU* 2.9 32.9 + - + +
134A THR* 4.1 3.8 - - - +
136A LEU* 1.3 72.6 - - - +
138A ASP* 1.3 63.3 + - - +
140A ALA* 4.5 0.7 - - - -
141A ALA* 2.9 33.8 + - - +
146A ILE* 3.6 17.4 - - + +
147A ARG 5.6 0.9 - - - +
150A ILE* 3.6 44.9 - - + +
151A ARG 4.3 2.7 - - - +
152A SER* 3.9 11.7 - - - -
155A MSE 3.6 32.1 - - + -
186A LEU* 4.2 12.3 - - + -
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Residues in contact with ASP 138 (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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134A THR* 2.8 45.8 + - - +
135A ALA* 3.8 4.9 - - - +
137A MSE 1.3 73.1 - - - +
139A ALA* 1.3 58.9 + - - +
141A ALA* 4.0 4.4 - - - +
142A ALA* 3.0 30.9 + - - +
78B PRO* 4.0 20.6 - - - +
82B ALA* 4.9 7.3 - - - +
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Residues in contact with ALA 139 (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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81A LEU* 3.9 28.9 - - + -
86A PRO* 3.8 6.5 - - + +
135A ALA 3.1 17.6 + - - +
136A LEU 3.7 4.5 - - - +
137A MSE 3.2 0.2 - - - -
138A ASP* 1.3 78.3 - - - +
140A ALA* 1.3 61.7 + - - +
142A ALA* 3.4 7.0 + - - +
143A ALA* 3.1 24.6 + - - +
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Residues in contact with ALA 140 (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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86A PRO* 3.5 15.0 - - + +
87A ALA* 3.9 22.2 - - + +
90A LEU* 4.8 3.4 - - + -
136A LEU 2.9 17.2 + - - +
137A MSE 4.5 0.7 - - - -
139A ALA* 1.3 76.5 - - - +
141A ALA* 1.3 60.1 + - - +
143A ALA* 3.3 2.4 + - - -
144A GLY 3.2 3.5 + - - -
145A GLU* 3.0 27.1 + - - +
146A ILE* 3.6 32.1 - - + +
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Residues in contact with ALA 141 (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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137A MSE 2.9 18.6 + - - +
138A ASP* 4.0 4.5 - - - +
140A ALA* 1.3 74.7 - - - +
142A ALA* 1.3 58.9 + - - +
144A GLY* 3.0 19.2 + - - -
146A ILE* 3.5 14.3 - - + +
147A ARG 3.9 17.3 - - - +
148A SER* 4.0 21.8 - - - -
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Residues in contact with ALA 142 (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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138A ASP 3.0 20.0 + - - +
139A ALA* 3.7 6.7 - - - +
141A ALA* 1.3 75.5 - - - +
143A ALA* 1.3 60.4 + - - +
144A GLY 3.5 0.7 + - - -
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Residues in contact with ALA 143 (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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86A PRO* 3.7 21.8 - - + -
139A ALA 3.1 17.6 + - - +
140A ALA 3.8 2.7 - - - +
141A ALA 3.2 0.4 - - - -
142A ALA* 1.3 77.8 - - - +
144A GLY* 1.3 56.9 + - - +
145A GLU* 3.2 17.8 + - + +
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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