Contacts of the helix formed by residues 148 - 165 (chain W) in PDB entry 5A0Q
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 148 (chain W).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8W TYR* 3.2 36.6 + - + -
10W ASP* 3.9 21.2 + - - +
147W GLU* 1.3 77.7 - - - +
149W GLU* 1.3 71.7 + - + +
151W ALA* 3.8 6.4 - - - +
152W LYS* 2.4 41.2 + - - +
177W VAL* 4.9 1.7 - - - +
179W SER* 3.8 12.3 + - - -
181W ASN* 4.8 15.0 + - - +
182W LYS* 6.5 1.1 - - - -
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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
----------------------------------------------------------
147W GLU* 4.6 2.2 - - + +
148W GLU* 1.3 94.3 - - + +
150W GLU* 1.4 63.1 + - - +
151W ALA 3.2 2.2 - - - -
152W LYS* 3.2 41.2 + - - +
153W ASN* 3.8 7.8 + - - +
182W LYS* 5.7 3.1 + - - -
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Residues in contact with GLU 150 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143W ARG* 3.0 38.0 + - - +
146W MET* 3.4 20.7 - - + +
147W GLU* 3.1 41.4 + - + +
149W GLU* 1.4 74.0 - - - +
151W ALA* 1.4 60.1 + - - +
152W LYS 3.2 0.2 - - - -
153W ASN* 3.0 18.9 + - + +
154W LEU* 3.0 26.2 + - - +
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Residues in contact with ALA 151 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6W VAL* 4.3 3.8 - - + -
8W TYR* 4.2 10.3 - - + -
13W VAL* 3.4 31.2 - - + -
146W MET* 3.6 25.1 - - + -
147W GLU 4.2 0.4 + - - +
148W GLU 3.8 9.5 + - - +
149W GLU 3.2 0.4 - - - -
150W GLU* 1.4 77.9 - - - +
152W LYS* 1.3 59.6 + - - +
154W LEU* 2.9 14.6 + - - -
155W VAL* 3.0 21.8 + - - +
175W LEU* 4.3 0.5 - - - +
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Residues in contact with LYS 152 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8W TYR* 4.2 0.8 + - - -
13W VAL* 3.7 12.7 - - + +
148W GLU* 2.4 37.9 + - - +
149W GLU* 3.2 33.6 + - - +
151W ALA* 1.3 76.3 - - - +
153W ASN* 1.4 59.3 + - - +
154W LEU 3.2 0.9 - - - -
156W SER* 3.0 30.0 + - - -
175W LEU* 3.9 24.2 - - + +
177W VAL* 3.6 39.1 - - + +
186W LEU* 5.8 0.9 - - + -
189W TYR* 4.3 20.1 - - + +
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Residues in contact with ASN 153 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149W GLU 3.9 11.2 - - - +
150W GLU* 3.0 18.4 + - + +
152W LYS* 1.4 75.4 + - - +
154W LEU* 1.3 54.5 + - - +
156W SER* 4.4 1.2 + - - -
157W GLU* 2.7 38.7 + - - +
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Residues in contact with LEU 154 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6W VAL* 3.9 16.6 - - + -
137W VAL* 5.6 2.4 - - + +
138W PHE* 3.8 18.4 - - + -
141W LYS* 4.1 26.7 - - + +
142W PHE* 4.2 18.4 - - + +
146W MET* 3.0 37.7 - - + -
150W GLU* 3.0 15.5 + - - +
151W ALA* 2.9 8.3 + - - +
153W ASN* 1.3 79.9 - - - +
155W VAL* 1.3 58.8 + - + +
156W SER 3.7 0.2 - - - -
157W GLU* 4.4 1.7 - - - +
158W ALA* 3.3 21.8 + - + +
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Residues in contact with VAL 155 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4W ALA* 4.3 3.6 - - + -
5W GLY 5.1 0.2 - - - -
6W VAL* 3.4 33.4 - - + +
13W VAL* 3.9 11.2 - - + +
15W GLY* 3.7 32.3 - - - +
138W PHE* 4.0 16.6 - - + -
151W ALA 3.0 11.9 + - - +
154W LEU* 1.3 76.7 - - - +
156W SER* 1.3 62.1 + - - +
157W GLU 3.2 1.6 - - - -
158W ALA* 4.1 4.0 - - - -
159W ILE* 2.8 40.2 + - + +
173W ILE* 5.1 0.9 - - + -
175W LEU* 3.9 10.5 - - + -
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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
----------------------------------------------------------
152W LYS 3.0 19.5 + - - -
153W ASN* 4.4 1.9 + - - -
155W VAL* 1.3 79.1 - - - +
157W GLU* 1.4 77.3 + - - +
160W ALA* 3.2 11.4 + - - +
173W ILE* 2.9 42.3 - - - +
175W LEU* 4.3 5.9 - - - +
189W TYR* 5.3 1.1 - - - -
190W THR* 4.0 20.4 - - - +
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Residues in contact with GLU 157 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155N GLU* 5.5 6.5 - - - +
137W VAL* 5.0 7.9 - - + +
153W ASN* 2.7 45.5 + - - +
154W LEU* 5.1 2.0 - - - -
155W VAL 3.2 0.6 - - - +
156W SER* 1.4 88.5 + - - +
158W ALA* 1.4 59.6 + - - +
160W ALA* 3.1 8.5 + - + +
161W ALA* 2.9 27.1 + - - +
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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
----------------------------------------------------------
134W ALA* 3.9 14.2 - - - +
137W VAL* 4.2 20.8 - - + +
138W PHE* 3.3 39.9 - - + -
154W LEU 3.3 18.2 + - - +
155W VAL 3.3 2.5 + - - +
157W GLU* 1.4 74.1 - - - +
159W ILE* 1.4 62.4 + - - +
161W ALA* 3.1 20.1 + - - +
162W GLY 3.4 3.8 + - - -
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Residues in contact with ILE 159 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2W THR* 3.5 34.4 + - + +
4W ALA* 3.6 29.8 - - + +
15W GLY 4.0 9.0 - - - +
16W ALA 4.3 1.3 - - - +
17W ASP* 4.1 17.3 - - + -
138W PHE* 5.6 0.2 - - + -
155W VAL* 2.8 36.7 + - + +
158W ALA* 1.4 71.6 - - - +
160W ALA* 1.4 56.3 + - - +
162W GLY* 3.0 6.4 + - - +
163W ILE* 3.0 39.7 + - + +
173W ILE* 4.0 22.7 - - + -
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Residues in contact with ALA 160 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155N GLU* 4.9 13.2 - - - +
156W SER 3.2 21.3 + - - +
157W GLU* 3.1 12.8 + - + +
159W ILE* 1.4 75.2 - - - +
161W ALA* 1.4 58.4 + - - +
163W ILE* 3.0 25.1 + - + +
164W PHE* 3.1 22.7 + - + +
173W ILE* 4.1 5.1 - - + +
192W PRO* 4.9 13.7 - - + -
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Residues in contact with ALA 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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148N PRO* 4.3 7.6 - - + -
133W ALA* 4.0 13.1 - - - +
137W VAL* 3.7 29.4 - - + -
157W GLU 2.9 10.5 + - - +
158W ALA 3.1 13.9 + - - +
160W ALA* 1.4 75.4 - - - +
162W GLY* 1.3 55.8 + - - +
164W PHE* 5.4 0.4 - - - -
165W ASN* 3.0 38.3 + - - +
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Residues in contact with GLY 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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2W THR* 3.6 21.3 - - - -
130W GLY* 4.5 9.9 - - - -
133W ALA* 4.8 1.8 - - - +
134W ALA* 5.2 0.8 - - - +
158W ALA 3.4 4.2 + - - -
159W ILE 3.0 9.8 + - - -
161W ALA* 1.3 78.3 - - - +
163W ILE* 1.3 61.1 + - - +
164W PHE 3.4 0.2 - - - -
166W ASP* 3.1 28.9 - - - +
169W SER* 3.4 9.1 - - - -
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Residues in contact with ILE 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 THR* 5.5 0.2 - - - +
17W ASP* 4.4 4.9 - - + -
159W ILE* 3.0 24.3 + - + +
160W ALA* 3.0 10.0 + - - +
162W GLY* 1.3 77.0 - - - +
164W PHE* 1.3 76.2 + - + +
166W ASP 3.6 3.8 - - - +
169W SER* 3.2 17.1 - - - +
170W GLY* 3.9 22.6 - - - +
171W SER* 2.9 33.4 - - - +
173W ILE* 3.7 26.9 - - + -
192W PRO* 4.1 16.2 - - + -
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Residues in contact with PHE 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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28M ARG* 5.7 1.6 + - - -
35M ILE* 3.3 18.4 - - - +
38M ARG* 3.5 35.0 + - - +
155N GLU* 4.4 26.0 - - + -
160W ALA* 3.1 20.0 + - + +
161W ALA* 5.4 0.2 - - - -
163W ILE* 1.3 92.1 - - + +
165W ASN* 1.3 66.7 + - - +
166W ASP 3.5 5.7 + - - +
167W LEU* 5.0 1.0 - - - +
192W PRO* 4.1 33.0 - - + -
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Residues in contact with ASN 165 (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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33M PHE 3.9 6.8 - - - +
34M SER* 4.8 2.3 - - - -
35M ILE* 3.3 23.6 + - - +
38M ARG* 3.4 2.7 + - - +
144N TYR* 5.9 1.4 - - - -
147N GLN* 5.4 1.1 - - + -
148N PRO* 3.6 38.6 - - + +
151N ARG* 2.6 49.4 + - - +
133W ALA* 4.5 7.2 - - + -
161W ALA* 3.0 30.1 + - - +
164W PHE* 1.3 79.1 - - - +
166W ASP* 1.3 57.3 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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