Contacts of the helix formed by residues 147 - 164 (chain W) in PDB entry 3SDI
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 GLU 147 (chain W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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208V ARG* 4.2 10.3 - - - +
9W LYS* 4.1 21.8 + - - +
145W ASN 3.6 5.8 + - - +
146W LEU* 1.3 72.9 - - - +
148W PRO* 1.3 81.8 - - + +
149W GLU* 4.0 11.7 - - - +
150W ASP* 2.8 23.1 + - - +
151W LEU 2.8 20.1 + - - -
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Residues in contact with PRO 148 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9W LYS 4.1 7.2 - - - +
11W CYS* 3.9 27.4 - - + -
146W LEU 3.7 0.2 - - - -
147W GLU* 1.3 94.8 - - + +
149W GLU* 1.3 69.6 + - - +
151W LEU* 3.9 2.8 - - + +
152W PHE* 3.1 26.7 + - - +
177W ILE* 4.0 28.3 - - + +
179W LYS* 3.9 33.0 - - + +
187W ARG* 5.5 0.6 + - - -
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Residues in contact with GLU 149 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208V ARG* 3.4 39.4 + - - +
147W GLU* 2.9 10.8 + - - +
148W PRO* 1.3 91.4 - - - +
150W ASP* 1.3 64.1 + - - +
152W PHE* 3.7 12.0 - - - +
153W GLU* 3.6 19.6 - - - +
179W LYS* 5.8 1.6 + - - -
187W ARG* 5.9 5.2 - - - +
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Residues in contact with ASP 150 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205V LYS* 3.5 32.9 + - + -
206V PHE 4.7 6.1 - - - +
208V ARG* 2.6 50.5 + - - +
146W LEU* 4.3 15.1 - - + +
147W GLU* 2.8 23.3 + - - +
149W GLU* 1.3 75.3 - - - +
151W LEU* 1.3 56.3 + - - +
152W PHE 3.1 1.1 - - - -
153W GLU* 2.8 28.5 + - - +
154W THR* 3.1 15.1 + - - +
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Residues in contact with LEU 151 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6W MET* 3.8 22.4 - - + -
7W THR 3.5 25.1 - - - +
8W GLY* 4.0 6.3 - - - +
11W CYS* 3.6 25.6 - - + -
12W VAL 4.0 2.2 - - - +
13W ALA* 3.5 35.4 - - + +
142W TYR* 4.9 0.2 - - + -
146W LEU* 3.9 26.9 - - + +
147W GLU 2.8 20.3 + - - +
148W PRO* 3.9 4.3 - - + +
150W ASP* 1.3 70.9 - - - +
152W PHE* 1.3 62.5 + - - +
154W THR* 3.9 1.4 - - - -
155W ILE* 3.1 27.1 + - + +
177W ILE* 4.7 4.9 - - + -
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Residues in contact with PHE 152 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211V THR* 4.2 12.8 - - + -
213V VAL* 3.7 32.3 - - + -
148W PRO 3.1 18.7 + - - +
149W GLU* 3.7 8.5 - - - +
150W ASP 3.1 1.0 - - - -
151W LEU* 1.3 77.7 - - - +
153W GLU* 1.3 82.0 + - - +
155W ILE* 3.4 2.2 - - - +
156W SER* 3.0 47.3 + - - -
175W VAL* 3.9 19.7 - - + -
177W ILE* 3.7 17.0 - - + +
187W ARG* 3.5 45.3 - - + +
189W LEU* 3.9 8.5 - - + -
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Residues in contact with GLU 153 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206V PHE* 3.9 26.7 - - + +
207V PRO 4.2 3.6 - - - +
208V ARG* 3.8 13.1 - - - +
209V GLY* 2.9 29.3 + - - -
210V THR* 3.5 6.7 + - - -
211V THR* 3.0 36.5 + - - +
149W GLU 3.6 14.9 - - - +
150W ASP* 2.8 16.4 + - - +
152W PHE* 1.3 88.0 - - - +
154W THR* 1.3 58.8 + - - +
156W SER* 3.1 2.8 + - - -
157W GLN* 2.9 33.8 + - + +
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Residues in contact with THR 154 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204V TYR 4.8 2.4 + - - -
205V LYS* 5.1 5.0 - - - +
206V PHE* 4.3 18.2 + - - -
6W MET* 3.7 25.4 - - + -
141W LEU* 3.8 33.7 + - + +
142W TYR* 4.4 2.0 - - - -
143W GLU* 5.9 0.3 - - - +
146W LEU* 3.8 24.7 - - + +
150W ASP 3.1 9.6 + - - -
151W LEU* 3.9 6.5 - - - -
153W GLU* 1.3 77.4 - - - +
155W ILE* 1.3 57.5 + - - +
157W GLN 3.5 0.3 + - - -
158W ALA* 3.0 27.4 + - - +
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Residues in contact with ILE 155 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4W VAL* 4.0 26.2 - - + +
5W ALA* 4.1 0.7 - - - -
6W MET* 3.7 36.3 - - + +
13W ALA* 3.6 40.8 - - + +
14W ILE 4.2 1.3 - - - +
15W ALA* 4.2 8.0 - - + +
151W LEU 3.1 21.5 + - - +
152W PHE* 3.4 9.9 - - - +
154W THR* 1.3 76.2 - - - +
156W SER* 1.3 62.2 + - - +
158W ALA* 3.7 1.0 - - - +
159W LEU* 3.0 27.2 + - - +
175W VAL* 3.7 22.7 - - + -
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Residues in contact with SER 156 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211V THR* 3.6 18.2 - - - -
152W PHE* 3.0 38.3 + - - -
153W GLU 3.1 4.8 + - - -
155W ILE* 1.3 80.0 - - - +
157W GLN* 1.3 57.5 + - - +
159W LEU* 3.4 3.0 + - - +
160W LEU* 2.9 36.6 + - - +
175W VAL* 3.5 7.9 - - - +
189W LEU* 3.4 27.5 - - - +
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Residues in contact with GLN 157 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140L ASN* 3.0 26.9 + - - -
144L ASN* 3.3 34.5 + - - +
206V PHE* 3.5 41.5 - - + -
210V THR* 4.3 4.4 - - + +
211V THR* 3.1 26.6 + - - +
137W MET* 3.8 0.5 - - - +
141W LEU* 4.0 4.3 - - + -
153W GLU 2.9 17.9 + - - +
154W THR 3.9 0.9 - - - +
156W SER* 1.3 75.0 - - - +
158W ALA* 1.3 66.9 + - - +
160W LEU* 4.1 8.8 - - - +
161W ASN* 2.6 39.4 + - - +
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Residues in contact with ALA 158 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4W VAL* 5.3 1.1 - - + -
6W MET* 4.0 17.9 - - + -
134W LEU* 4.3 4.9 - - + -
137W MET* 3.5 26.7 - - + +
138W CYS* 4.2 10.8 - - - +
141W LEU* 3.7 6.2 - - + +
154W THR 3.0 17.7 + - - +
155W ILE 3.7 4.9 - - - +
156W SER 3.3 0.2 - - - -
157W GLN* 1.3 77.1 - - - +
159W LEU* 1.3 62.3 + - - +
162W ALA* 3.1 26.5 + - - +
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Residues in contact with LEU 159 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2W ILE* 3.8 25.8 - - + +
4W VAL* 3.5 26.4 - - + +
15W ALA* 4.1 7.6 - - + +
16W CYS* 4.0 31.0 - - - +
17W ASP* 4.5 2.5 - - + +
134W LEU* 4.1 8.3 - - + -
155W ILE 3.0 18.1 + - - +
156W SER* 3.8 3.1 - - - +
157W GLN 3.3 0.2 - - - -
158W ALA* 1.3 77.2 - - - +
160W LEU* 1.3 59.1 + - + +
162W ALA* 3.6 1.4 - - - +
163W ALA* 2.8 37.8 + - + +
173W ALA* 3.4 33.9 - - + -
174W VAL 5.1 0.2 - - - +
175W VAL* 5.4 0.4 - - + -
189W LEU* 4.9 5.2 - - + -
191W MET* 5.9 0.4 - - - -
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Residues in contact with LEU 160 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144L ASN* 3.7 41.1 - - - +
211V THR* 4.0 17.0 - - + -
212V ALA 5.7 0.4 - - - +
156W SER 2.9 20.9 + - - +
157W GLN* 4.1 7.2 - - - +
159W LEU* 1.3 75.1 - - + +
161W ASN* 1.3 57.4 + - - +
163W ALA* 3.6 4.8 - - - +
164W ASP* 3.2 34.3 + - - +
173W ALA* 4.3 6.3 - - + -
189W LEU* 3.6 33.9 - - + -
190W LYS 4.5 9.0 - - - +
191W MET* 3.9 32.9 - - + +
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Residues in contact with ASN 161 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136L PRO* 3.5 25.0 - - - +
139L ASP* 4.8 4.5 - - + +
140L ASN* 3.2 38.2 + - - +
144L ASN* 2.9 37.3 - - - +
137W MET* 3.8 13.4 - - + +
157W GLN* 2.6 37.5 + - - +
160W LEU* 1.3 74.6 - - - +
162W ALA* 1.3 65.1 + - - +
164W ASP* 3.4 10.9 + - - +
165W ARG* 3.6 8.0 + - - +
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Residues in contact with ALA 162 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136L PRO* 4.4 0.4 - - - -
2W ILE* 4.9 0.4 - - + -
130W ALA* 3.8 9.7 - - + +
133W GLN* 3.7 23.1 - - + +
134W LEU* 3.6 42.4 - - + +
137W MET* 4.0 4.6 - - + +
158W ALA 3.1 19.0 + - - +
159W LEU 3.6 2.9 - - - +
161W ASN* 1.3 75.9 - - - +
163W ALA* 1.3 65.2 + - - +
164W ASP 3.3 0.5 + - - -
165W ARG 3.3 9.0 + - - -
166W ASP 3.7 5.4 + - - -
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Residues in contact with ALA 163 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2W ILE* 3.9 19.0 - - + +
17W ASP* 5.6 1.1 - - + -
130W ALA* 5.0 0.2 - - - -
159W LEU* 2.8 20.2 + - + +
160W LEU 3.6 6.3 - - - +
161W ASN 3.3 0.2 - - - -
162W ALA* 1.3 76.7 - - - +
164W ASP* 1.3 53.3 + - - +
166W ASP* 2.9 16.4 + - - +
169W SER* 4.4 5.4 - - - -
170W GLY* 4.3 13.7 - - - +
191W MET* 3.9 20.0 - - + -
202W MG 2.3 25.6 - - - -
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Residues in contact with ASP 164 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19K ARG* 5.1 2.9 + - - -
26K VAL* 4.1 15.2 - - - +
29K GLN* 4.9 12.0 + - - +
139L ASP* 5.9 1.6 - - - +
144L ASN* 3.1 28.2 + - - +
160W LEU 3.2 12.7 + - - +
161W ASN* 3.4 6.9 + - - +
162W ALA 3.2 1.0 - - - -
163W ALA* 1.3 79.2 - - - +
165W ARG* 1.3 60.7 + - + +
166W ASP 3.4 1.3 - - - +
191W MET* 3.3 21.6 - - - +
192W ARG* 3.2 36.4 - - - +
194W ASP* 5.4 0.5 - - - +
202W MG 3.9 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