Contacts of the helix formed by residues 130 - 141 (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 GLY 130 (chain W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2W THR* 3.5 23.3 + - - +
128W GLY* 3.2 1.8 - - - -
129W SER* 1.3 74.9 - - - +
131W SER* 1.3 61.1 + - - +
132W LEU 3.3 4.5 + - - -
133W ALA* 3.4 8.6 + - - +
134W ALA* 3.0 22.5 + - - +
162W GLY* 4.5 3.2 - - - -
166W ASP* 3.0 21.5 + - - -
169W SER* 3.9 3.2 + - - -
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Residues in contact with SER 131 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25V TYR* 4.1 8.9 + - - -
126W THR* 3.2 14.0 + - - -
127W MET* 3.6 29.8 + - - -
128W GLY 3.2 17.5 + - - -
129W SER 3.2 2.9 + - - -
130W GLY* 1.3 77.8 - - - +
132W LEU* 1.4 70.2 + - - +
134W ALA* 3.8 4.3 - - - -
135W MET* 2.9 26.7 + - - +
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Residues in contact with LEU 132 (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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144N TYR* 3.3 56.4 - - + +
145N LEU* 4.3 7.6 - - + +
25V TYR* 3.3 56.8 + - + -
129W SER 4.8 6.0 + - - +
130W GLY 3.3 0.8 + - - -
131W SER* 1.4 81.9 + - - +
133W ALA* 1.3 63.1 + - - +
135W MET* 3.9 1.4 - - - +
136W ALA* 3.1 23.0 + - - +
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Residues in contact with ALA 133 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144N TYR* 3.2 16.2 - - + +
148N PRO* 3.4 29.0 - - + +
130W GLY* 3.4 10.7 + - - +
132W LEU* 1.3 82.1 - - - +
134W ALA* 1.3 57.9 + - - +
136W ALA* 3.9 2.3 + - - +
137W VAL* 3.4 23.9 + - - +
161W ALA* 4.0 16.0 - - - +
162W GLY* 4.8 1.8 - - - -
165W ASN* 4.5 8.1 - - + -
166W ASP* 5.9 2.0 - - + +
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Residues in contact with ALA 134 (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* 3.9 18.6 - - + -
126W THR* 3.7 19.1 - - + -
130W GLY 3.0 17.3 + - - +
131W SER 3.8 2.7 - - - +
133W ALA* 1.3 76.8 - - - +
135W MET* 1.4 59.5 + - - +
137W VAL* 3.1 7.3 + - - +
138W PHE* 2.9 32.2 + - + -
158W ALA* 3.9 20.1 - - - +
159W ILE* 5.5 0.2 - - - -
161W ALA* 4.7 0.9 - - - -
162W GLY 5.2 1.1 - - - +
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Residues in contact with MET 135 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25V TYR* 3.4 36.3 - - + +
26V ILE 5.6 2.2 - - - +
27V ALA* 5.7 4.0 - - - -
28V ASN 5.8 4.3 - - - +
29V ARG* 6.0 1.8 - - - -
114W TYR* 5.0 9.2 - - - +
122W LEU* 5.7 3.4 - - + -
124W TYR* 3.7 35.0 - - + +
125W VAL* 4.4 6.3 - - + -
126W THR* 3.2 47.1 + - + +
131W SER* 2.9 10.7 + - - +
132W LEU 4.2 1.3 - - - +
134W ALA* 1.4 73.9 - - - +
136W ALA* 1.3 58.5 + - - +
138W PHE* 4.2 4.9 - - + -
139W GLU* 2.8 30.5 + - - +
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Residues in contact with ALA 136 (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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145N LEU* 2.9 54.4 - - + +
148N PRO* 5.4 0.2 - - + -
149N LEU* 3.6 12.5 - - + +
175N VAL* 4.4 1.1 - - - +
132W LEU 3.1 11.9 + - - +
133W ALA 4.1 5.2 - - - +
134W ALA 3.3 0.2 - - - -
135W MET* 1.3 75.5 - - - +
137W VAL* 1.4 56.9 + - + +
139W GLU* 3.4 9.4 + - - +
140W ASP* 3.0 29.5 + - - +
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Residues in contact with VAL 137 (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* 4.0 7.2 - - + +
149N LEU* 3.8 10.8 - - + -
152N GLU* 3.4 25.8 - - + +
133W ALA 3.4 15.9 - - - +
134W ALA 3.1 7.7 + - - +
136W ALA* 1.4 72.0 - - - +
138W PHE* 1.4 59.8 + - - +
140W ASP* 3.4 0.8 + - - -
141W LYS* 3.0 42.3 + - + +
154W LEU* 5.6 2.9 - - + +
157W GLU* 5.0 6.5 - - + -
158W ALA* 4.2 22.7 - - + +
161W ALA* 3.7 18.6 - - + -
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Residues in contact with PHE 138 (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 ALA* 3.6 21.8 - - + -
5W GLY 4.2 4.9 - - - -
6W VAL* 4.0 23.8 - - + -
124W TYR* 3.6 36.0 - - + -
125W VAL 4.5 0.2 - - - -
126W THR* 3.2 34.5 - - + -
134W ALA* 2.9 22.2 + - + -
135W MET* 3.8 6.1 - - - +
137W VAL* 1.4 75.7 - - - +
139W GLU* 1.3 58.7 + - - +
142W PHE* 2.9 34.7 + - + +
154W LEU* 3.8 26.9 - - + -
155W VAL* 4.0 13.9 - - + -
158W ALA* 3.3 25.1 - - + -
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Residues in contact with GLU 139 (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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145N LEU* 5.0 4.9 - - - +
174N ARG 4.6 2.8 - - - +
175N VAL* 3.3 44.8 - - + +
29V ARG* 4.3 20.8 + - - +
124W TYR* 3.7 27.7 + - + +
135W MET 2.8 18.6 + - - +
136W ALA* 3.6 5.4 - - - +
138W PHE* 1.3 77.2 - - - +
140W ASP* 1.3 63.9 + - - +
141W LYS 3.4 0.3 + - - -
142W PHE* 4.2 9.2 - - - +
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Residues in contact with ASP 140 (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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149N LEU* 3.9 20.8 - - + +
152N GLU* 3.5 11.8 - - - +
171N ARG* 3.2 42.6 + - - +
172N CYS* 6.0 0.2 - - - -
174N ARG* 5.6 2.5 + - - +
175N VAL* 3.9 17.3 - - + +
136W ALA 3.0 18.7 + - - +
137W VAL 3.4 3.8 + - - +
139W GLU* 1.3 77.0 - - - +
141W LYS* 1.3 79.2 + - + +
142W PHE 4.9 0.6 - - - +
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Residues in contact with LYS 141 (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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152N GLU* 3.8 11.2 + - - +
171N ARG* 4.7 11.7 - - - +
137W VAL* 3.0 33.0 + - + +
140W ASP* 1.3 101.9 + - - +
142W PHE* 1.4 67.6 + - - +
143W ARG* 3.5 10.7 + - - +
154W LEU* 4.1 17.1 - - + +
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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