Contacts of the helix formed by residues 140 - 156 (chain U) in PDB entry 3EXG
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 U).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135U ASN* 5.4 5.6 - - + -
137U ILE* 3.2 33.1 + - + +
138U VAL 3.2 0.8 - - - -
139U GLY* 1.3 75.2 - - - +
141U GLN* 1.3 60.4 + - - +
142U VAL 3.3 0.7 + - - -
143U PRO* 3.4 10.4 - - - +
144U LEU* 3.5 16.6 - - + +
174U GLN* 3.2 18.4 - - - +
91V ASP* 4.3 8.1 - - - +
92V GLN* 3.5 11.4 + - - +
96V SER* 4.2 15.7 - - - +
127X GLN* 6.3 0.9 - - - +
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Residues in contact with GLN 141 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86U ILE* 3.8 10.8 - - + +
87U THR* 3.5 27.1 - - - +
88U ALA* 3.8 18.5 - - - +
135U ASN* 3.7 17.3 - - - +
137U ILE 3.8 5.4 - - - +
138U VAL* 4.8 0.6 - - - +
139U GLY 2.8 24.3 + - - +
140U ALA* 1.3 68.2 + - - +
142U VAL* 1.3 63.4 + - + +
144U LEU* 3.7 10.7 - - - +
145U GLY* 2.9 24.1 + - - -
163U THR* 3.6 5.3 - - + +
164U LEU 3.1 28.7 + - - +
165U TYR* 3.6 19.0 - - - +
166U GLY 5.0 0.4 - - - +
169U ALA* 5.2 1.4 - - - +
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Residues in contact with VAL 142 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139U GLY 2.7 15.8 + - - +
141U GLN* 1.3 77.4 - - + +
143U PRO* 1.4 68.8 - - + +
145U GLY 3.1 0.5 + - - -
146U ALA* 3.0 19.2 + - - +
163U THR* 3.5 13.1 - - + +
165U TYR* 3.3 38.4 - - + -
175U ILE* 3.4 37.0 - - + -
178U ALA* 3.6 21.3 - - + -
191U PHE* 4.0 17.0 - - + -
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Residues in contact with PRO 143 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139U GLY 3.4 6.7 - - - +
140U ALA 3.4 9.9 - - - +
142U VAL* 1.4 92.3 - - + +
144U LEU* 1.3 64.9 + - - +
146U ALA* 3.0 10.0 + - + +
147U GLY 2.8 18.2 + - - -
174U GLN* 3.4 40.6 - - + +
178U ALA* 4.3 5.6 - - + -
61V GLY* 3.6 28.0 - - - +
64V GLY* 3.8 12.6 - - - -
65V ILE* 3.6 8.0 - - + -
92V GLN* 3.9 3.6 - - - +
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Residues in contact with LEU 144 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86U ILE* 3.9 15.3 - - + -
135U ASN* 3.8 24.2 - - + +
140U ALA 3.5 16.3 + - - +
141U GLN* 3.5 8.9 + - - +
142U VAL 3.3 0.2 - - - -
143U PRO* 1.3 77.8 - - - +
145U GLY* 1.3 64.8 + - - +
147U GLY 3.0 1.9 + - - -
148U ILE* 2.9 23.4 + - + +
64V GLY 3.4 20.8 + - - +
67V VAL* 3.5 27.8 - - + -
68V GLY* 3.4 13.6 - - - +
71V MET* 4.4 15.0 - - + -
92V GLN* 4.0 9.6 - - - +
96V SER* 3.7 19.5 - - - +
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Residues in contact with GLY 145 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86U ILE* 3.7 13.4 - - - +
141U GLN 2.9 15.4 + - - -
142U VAL 3.1 2.2 + - - -
144U LEU* 1.3 77.4 - - - +
146U ALA* 1.3 56.4 + - - +
148U ILE* 3.2 9.9 + - - +
149U ALA* 2.9 24.4 + - - +
161U CYS* 3.6 8.0 - - - -
163U THR* 3.3 22.6 + - - -
189U CYS* 4.6 0.2 - - - -
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Residues in contact with ALA 146 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142U VAL 3.0 12.0 + - - +
143U PRO* 3.0 11.9 + - + +
145U GLY* 1.3 74.6 - - - +
147U GLY* 1.3 59.0 + - - +
149U ALA* 3.1 10.2 + - - +
150U LEU* 2.9 23.4 + - - +
163U THR* 4.2 0.4 + - - -
178U ALA* 4.4 13.9 - - + +
182U ALA* 5.0 2.2 - - + -
187U LEU* 3.4 14.4 - - + +
189U CYS* 4.3 5.6 - - - -
191U PHE* 4.7 11.2 - - + -
65V ILE* 4.0 19.2 - - + +
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Residues in contact with GLY 147 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143U PRO 2.8 11.6 + - - -
144U LEU 3.0 4.0 + - - -
146U ALA* 1.3 75.7 - - - +
148U ILE* 1.3 59.2 + - - +
150U LEU* 3.1 3.5 + - - +
151U ALA* 2.9 27.4 + - - +
65V ILE* 3.4 36.1 - - - +
69V ALA* 3.6 12.4 + - - -
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Residues in contact with ILE 148 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84U HIS* 3.5 37.5 - - + +
86U ILE* 4.5 7.6 - - + -
132U TYR* 3.2 46.4 - - + +
144U LEU* 2.9 20.3 + - + +
145U GLY* 3.5 13.5 - - - +
147U GLY* 1.3 75.8 - - - +
149U ALA* 1.3 61.1 + - - +
151U ALA* 3.2 8.1 + - - +
152U CYS* 3.1 21.4 + - - -
161U CYS* 3.7 10.3 - - + -
68V GLY* 3.5 19.3 - - - +
71V MET* 5.1 2.7 - - + -
72V ALA* 4.4 7.9 - - + -
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Residues in contact with ALA 149 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145U GLY 2.9 10.3 + - - +
146U ALA 3.4 9.0 - - - +
147U GLY 3.1 0.4 - - - -
148U ILE* 1.3 76.2 - - - +
150U LEU* 1.3 65.8 + - - +
152U CYS* 2.9 15.9 + - - +
153U LYS 3.1 10.9 + - - -
161U CYS* 4.2 7.8 - - + +
187U LEU* 4.0 7.6 - - + -
188U PRO* 3.6 22.9 - - - +
189U CYS* 3.5 32.8 - - + -
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Residues in contact with LEU 150 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146U ALA 2.9 12.6 + - - +
147U GLY* 3.4 10.3 - - - +
149U ALA* 1.3 76.3 - - - +
151U ALA* 1.3 58.7 + - - +
153U LYS* 3.5 6.1 + - + +
154U TYR* 2.9 36.8 + - + +
185U TRP* 4.4 15.5 - - + -
187U LEU* 3.7 29.7 - - + +
24V PHE* 4.1 32.1 - - + -
26V LEU* 5.2 2.2 - - + -
53V ILE* 4.5 14.6 - - + -
65V ILE* 4.5 16.2 - - + -
69V ALA* 4.8 3.8 - - + -
74V LEU* 5.7 0.4 - - + -
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Residues in contact with ALA 151 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147U GLY 2.9 10.8 + - - +
148U ILE 3.3 10.8 - - - +
149U ALA 3.1 0.2 - - - -
150U LEU* 1.3 77.6 - - - +
152U CYS* 1.3 56.8 + - - +
154U TYR* 3.6 1.6 + - - +
155U ASN* 2.9 38.1 + - - +
69V ALA* 4.4 2.5 - - - -
72V ALA* 3.5 29.4 - - + -
74V LEU* 3.6 24.9 - - + -
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Residues in contact with CYS 152 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84U HIS* 3.6 33.9 - - - -
148U ILE* 3.1 22.0 + - - -
149U ALA* 2.9 8.7 + - - +
151U ALA* 1.3 73.9 - - - +
153U LYS* 1.3 69.8 + - - +
154U TYR 3.1 0.9 - - - -
155U ASN* 2.8 16.7 + - - +
156U GLY* 3.1 8.7 + - - -
157U LYS* 4.0 6.4 + - + -
158U ASP 5.2 0.2 + - - -
159U GLU* 3.4 42.0 - - + +
160U VAL* 4.0 8.5 - - - -
188U PRO* 4.2 2.2 - - + -
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Residues in contact with LYS 153 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149U ALA 3.1 5.6 + - - +
150U LEU* 3.9 10.1 - - + +
152U CYS* 1.3 77.7 - - - +
154U TYR* 1.3 63.7 + - - +
156U GLY* 3.2 12.4 + - - -
185U TRP* 2.8 27.0 + - - +
186U LYS* 3.1 27.3 - - - +
187U LEU* 4.6 7.1 - - + +
188U PRO* 4.0 19.0 - - + +
50V LYS* 5.3 1.0 + - - -
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Residues in contact with TYR 154 (chain U).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150U LEU* 2.9 29.6 + - + +
151U ALA* 3.7 6.7 - - - +
152U CYS 3.1 0.2 - - - -
153U LYS* 1.3 77.8 - - - +
155U ASN* 1.3 65.8 + - - +
156U GLY 3.5 0.3 + - - -
21V GLU* 2.6 32.1 + - + -
22V LYS* 4.1 2.7 - - + -
23V VAL 3.5 6.4 + - - -
24V PHE* 4.0 22.1 - + + +
50V LYS* 3.2 70.3 + - + +
51V ARG* 3.0 16.0 + - - -
53V ILE* 5.7 1.1 - - + -
74V LEU* 3.9 28.9 - - + -
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Residues in contact with ASN 155 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151U ALA* 2.9 25.5 + - - +
152U CYS* 2.8 14.3 + - - +
154U TYR* 1.3 78.4 - - - +
156U GLY* 1.3 68.3 + - - +
157U LYS* 3.4 19.7 - - + +
159U GLU* 5.5 4.2 + - - +
22V LYS* 5.0 10.9 + - - +
72V ALA 4.9 7.9 + - - -
74V LEU* 4.2 24.3 - - - +
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Residues in contact with GLY 156 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152U CYS 3.1 5.6 + - - -
153U LYS* 3.2 11.8 + - - -
154U TYR 3.3 1.2 + - - -
155U ASN* 1.3 79.6 - - - +
157U LYS* 1.3 64.3 + - - +
158U ASP* 3.7 3.8 - - - -
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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