Contacts of the helix formed by residues 140 - 156 (chain A) in PDB entry 3EXF
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 ALA 140 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A ASN* 5.6 3.1 - - + -
137A ILE* 3.3 37.0 - - + +
138A VAL 2.8 3.0 + - - -
139A GLY* 1.3 77.7 - - - +
141A GLN* 1.3 60.1 + - - +
142A VAL 3.3 0.4 + - - -
143A PRO* 3.8 2.8 - - - +
144A LEU* 3.6 16.6 - - + +
174A GLN* 3.3 15.9 - - - +
91B ASP* 4.4 4.7 - - - +
92B GLN* 3.3 24.2 + - - +
95B ASN* 6.5 0.2 - - + -
96B SER* 5.1 3.8 - - - +
127D GLN* 6.3 0.4 - - - +
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Residues in contact with GLN 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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86A ILE* 3.7 22.4 - - + +
87A THR* 3.6 22.9 - - - +
88A ALA* 4.0 16.8 - - - +
135A ASN* 3.9 11.6 - - + +
137A ILE 3.9 5.0 + - - +
138A VAL* 4.7 0.2 - - - -
139A GLY* 3.2 11.7 + - - +
140A ALA* 1.3 86.2 + - - +
142A VAL* 1.3 60.7 + - - +
144A LEU* 3.7 9.7 - - - +
145A GLY 2.9 22.3 + - - -
163A THR* 3.5 6.5 - - + +
164A LEU 2.6 29.9 + - - +
165A TYR* 3.5 20.6 - - - +
169A ALA* 5.6 0.6 - - - +
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Residues in contact with VAL 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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139A GLY 3.4 3.3 + - - +
141A GLN* 1.3 79.1 - - - +
143A PRO* 1.4 75.3 - - + +
145A GLY* 3.1 3.5 + - - -
146A ALA* 2.8 20.3 + - - +
163A THR* 3.5 11.3 - - + +
165A TYR* 3.6 31.9 - - + -
175A ILE* 3.6 34.5 - - + -
178A ALA* 4.0 9.9 - - + -
191A PHE* 3.4 35.2 - - + -
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Residues in contact with PRO 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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139A GLY 3.4 15.3 - - - +
140A ALA 3.8 3.1 - - - +
142A VAL* 1.4 89.3 - - + +
144A LEU* 1.3 57.5 + - - +
146A ALA* 3.0 3.9 + - + +
147A GLY 2.8 24.4 + - - -
174A GLN* 3.4 40.4 - - + +
178A ALA* 4.2 9.6 - - + -
61B GLY* 3.4 31.0 - - - +
64B GLY* 3.6 12.8 - - - -
65B ILE* 3.5 9.9 - - + -
92B GLN* 4.2 4.0 - - - +
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Residues in contact with LEU 144 (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 ILE* 3.7 16.2 - - + -
135A ASN* 3.8 22.7 - - - +
140A ALA* 3.6 16.2 - - + +
141A GLN* 3.5 6.3 + - - +
142A VAL 3.1 1.0 - - - -
143A PRO* 1.3 78.9 - - - +
145A GLY* 1.3 57.6 + - - +
147A GLY* 2.9 3.6 + - - -
148A ILE* 2.8 34.3 + - + +
64B GLY 3.4 11.0 + - - +
67B VAL* 3.5 23.3 - - + -
68B GLY* 3.4 25.8 - - - +
71B MET* 4.2 17.0 - - + -
92B GLN* 4.1 2.7 - - - +
96B SER* 3.5 21.5 - - - +
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Residues in contact with GLY 145 (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 ILE* 3.7 14.0 - - - +
141A GLN 2.9 15.1 + - - -
142A VAL 3.6 1.3 - - - -
144A LEU* 1.3 68.9 - - - +
146A ALA* 1.3 65.3 + - - +
148A ILE* 3.2 6.6 + - - -
149A ALA* 2.9 23.7 + - - +
161A CYS* 3.5 7.9 - - - +
163A THR* 3.0 26.7 - - - -
189A CYS* 4.4 1.2 - - - -
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Residues in contact with ALA 146 (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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142A VAL 2.8 13.5 + - - +
143A PRO* 3.5 9.6 - - + +
145A GLY* 1.3 75.1 - - - +
147A GLY* 1.3 57.3 + - - +
149A ALA* 2.9 26.7 - - - +
150A LEU* 2.9 10.2 + - - +
163A THR* 4.2 0.2 + - - -
178A ALA* 4.4 15.0 - - + +
182A ALA* 5.1 1.1 - - + -
187A LEU* 3.8 12.6 - - + +
189A CYS* 4.1 13.8 - - - -
191A PHE* 4.6 4.5 - - + -
65B ILE* 4.2 19.3 - - + -
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Residues in contact with GLY 147 (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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143A PRO 2.8 11.5 + - - -
144A LEU 2.9 4.0 + - - -
146A ALA* 1.3 73.2 - - - +
148A ILE* 1.3 67.8 + - - +
150A LEU* 3.1 5.6 + - - +
151A ALA 3.0 14.4 + - - -
65B ILE* 3.0 37.8 - - - +
69B ALA* 3.6 15.6 + - - -
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Residues in contact with ILE 148 (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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84A HIS* 3.9 36.6 - - + +
86A ILE* 4.2 16.4 - - + -
132A TYR* 3.7 37.9 - - + +
144A LEU* 2.8 18.3 + - + +
145A GLY* 3.2 14.1 + - - +
147A GLY* 1.3 73.2 - - - +
149A ALA* 1.3 55.3 + - - +
151A ALA* 2.6 27.7 + - - +
152A CYS* 3.0 13.3 + - - -
161A CYS* 3.9 5.4 - - - -
68B GLY* 3.9 14.6 - - - +
71B MET* 5.5 1.3 - - + -
72B ALA* 3.9 20.4 - - + -
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Residues in contact with ALA 149 (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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145A GLY 2.9 12.7 + - - +
146A ALA* 2.9 13.7 - - - +
148A ILE* 1.3 71.5 - - - +
150A LEU* 1.3 63.1 - - - +
152A CYS* 3.2 9.4 + - - +
153A LYS* 3.0 21.0 + - - +
161A CYS* 3.9 11.4 - - + +
187A LEU* 4.0 12.8 - - + -
188A PRO* 3.6 13.7 - - - +
189A CYS* 3.7 26.7 - - + -
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Residues in contact with LEU 150 (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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146A ALA 2.9 10.7 + - - +
147A GLY* 3.1 12.5 + - - +
148A ILE 3.1 0.2 + - - -
149A ALA* 1.3 76.0 - - - +
151A ALA* 1.3 57.0 + - - +
153A LYS* 3.6 5.6 + - + +
154A TYR* 2.8 36.2 + - + +
185A TRP* 4.2 22.0 - - + -
187A LEU* 3.5 25.7 - - + +
24B PHE* 4.0 31.9 - - + -
26B LEU* 5.7 3.1 - - + -
53B ILE* 4.9 12.6 - - + -
65B ILE* 4.3 15.5 - - + -
66B ALA 5.8 0.2 - - - +
69B ALA* 4.3 9.6 - - + -
74B LEU* 4.9 2.2 - - + -
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Residues in contact with ALA 151 (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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147A GLY 3.0 8.1 + - - +
148A ILE 2.6 15.2 + - - +
150A LEU* 1.3 71.3 - - - +
152A CYS* 1.3 51.4 + - - +
154A TYR* 2.9 1.2 + - - +
155A ASN* 2.6 46.6 + - - +
69B ALA* 4.4 1.6 - - - -
72B ALA* 3.6 27.1 - - + +
74B LEU* 3.5 34.8 - - + -
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Residues in contact with CYS 152 (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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84A HIS* 3.7 32.3 - - - -
148A ILE* 3.0 15.0 + - - -
149A ALA* 3.3 11.9 - - - +
151A ALA* 1.3 75.5 - - - +
153A LYS* 1.3 66.4 + - - +
155A ASN* 3.1 3.8 + - - +
156A GLY* 2.9 21.8 + - - -
157A LYS 3.7 5.0 + - - -
158A ASP 4.7 2.3 + - - -
159A GLU* 3.8 41.1 - - + +
160A VAL 4.4 5.6 - - - -
188A PRO* 4.2 3.1 - - + -
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Residues in contact with LYS 153 (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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149A ALA 3.0 10.8 + - - +
150A LEU* 3.8 6.5 - - + +
152A CYS* 1.3 78.3 - - - +
154A TYR* 1.3 60.2 + - + +
156A GLY* 3.3 11.3 + - - -
185A TRP* 2.9 34.4 + - - +
186A LYS* 3.5 22.4 - - - +
187A LEU* 4.2 10.2 - - + +
188A PRO* 3.7 21.5 - - + +
50B LYS* 5.5 0.7 - - - -
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Residues in contact with TYR 154 (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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150A LEU* 2.8 27.0 + - + +
151A ALA* 2.9 4.9 + - - +
153A LYS* 1.3 72.0 - - + +
155A ASN* 1.3 68.3 + - - +
156A GLY* 3.0 5.0 + - - -
21B GLU 2.5 30.7 + - - -
22B LYS* 3.9 5.0 - - - -
23B VAL 3.8 5.7 + - - -
24B PHE* 4.0 19.3 - + - +
50B LYS* 3.6 66.0 + - + +
51B ARG* 3.0 18.9 + - - -
74B LEU* 3.7 36.8 - - + -
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Residues in contact with ASN 155 (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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151A ALA* 2.6 31.7 + - - +
152A CYS* 4.0 4.4 - - - +
154A TYR* 1.3 77.8 - - - +
156A GLY* 1.3 61.8 + - - +
157A LYS* 3.4 35.7 + - - +
159A GLU* 5.6 0.6 + - - -
22B LYS* 5.8 2.6 - - - +
72B ALA 4.7 7.1 + - - -
74B LEU* 3.7 27.6 - - - +
19G GLU* 5.1 6.7 - - - +
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Residues in contact with GLY 156 (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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152A CYS 2.9 11.0 + - - -
153A LYS* 3.6 10.1 - - - -
154A TYR 3.0 4.0 - - - -
155A ASN* 1.3 79.3 - - - +
157A LYS* 1.3 55.7 + - - -
158A ASP* 3.3 6.4 + - - +
19G GLU* 5.9 2.0 - - - -
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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