Contacts of the helix formed by residues 146 - 161 (chain A) in PDB entry 3S5O
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 SER 146 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143A GLY 5.3 0.9 + - - -
144A ARG* 3.0 13.4 + - - -
145A MET* 1.3 75.5 - - - +
147A SER* 1.3 64.7 + - - +
148A ALA* 3.4 9.5 + - - +
149A ALA* 3.0 22.1 + - - +
150A LEU* 3.0 22.8 + - - +
179A PRO* 5.1 0.9 - - - -
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Residues in contact with SER 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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146A SER* 1.3 72.3 - - - +
148A ALA* 1.3 58.6 + - - +
150A LEU* 3.3 3.2 + - - +
151A ILE* 2.8 40.1 + - - +
179A PRO* 3.3 20.0 - - - +
181A ASP* 2.7 37.4 + - - -
182A ALA* 4.0 12.3 - - - +
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Residues in contact with ALA 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A SER* 3.2 7.8 + - - +
147A SER* 1.3 78.2 - - - +
149A ALA* 1.3 57.6 + - - +
151A ILE* 3.4 11.2 + - - +
152A HIS* 2.9 31.4 + - - +
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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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144A ARG 3.7 17.9 - - - +
145A MET* 4.3 13.9 - - + -
146A SER* 3.0 22.5 + - - +
148A ALA* 1.3 75.5 - - - +
150A LEU* 1.3 59.4 + - - +
152A HIS* 3.4 6.4 + - - +
153A HIS* 2.9 28.5 + - - +
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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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137A THR* 4.2 14.1 - - + -
138A PRO* 3.9 33.9 - - + +
145A MET* 3.6 32.3 - - + +
146A SER 3.0 13.2 + - - +
147A SER* 3.8 3.8 - - - +
149A ALA* 1.3 72.8 - - - +
151A ILE* 1.3 66.2 + - - +
153A HIS* 3.3 4.3 + - + +
154A TYR* 2.9 37.0 + - + -
176A LEU* 4.3 14.8 - - + -
178A LEU* 3.7 28.3 - - + -
179A PRO* 3.7 17.5 - - + -
182A ALA* 4.9 0.7 - - + -
186A LEU* 4.7 0.7 - - - -
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Residues in contact with ILE 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 SER* 2.8 30.4 + - - +
148A ALA* 3.6 8.5 - - - +
150A LEU* 1.3 75.6 - - - +
152A HIS* 1.3 56.2 + - - +
154A TYR 3.4 0.2 + - - -
155A THR* 2.7 46.9 + - - +
181A ASP* 4.8 2.0 - - - +
182A ALA* 3.7 33.7 - - + +
185A THR* 4.1 31.6 - - + +
186A LEU* 3.5 11.6 - - + +
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Residues in contact with HIS 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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115A THR* 5.1 7.7 - - + +
148A ALA 2.9 17.3 + - - +
149A ALA* 3.7 6.3 - - - +
151A ILE* 1.3 77.5 - - - +
153A HIS* 1.3 68.7 + - - +
155A THR* 3.9 4.7 - - - -
156A LYS* 3.0 38.7 + - + +
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Residues in contact with HIS 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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112A CYS 4.3 0.8 + - - -
113A GLU 4.7 0.4 + - - -
114A SER 4.0 0.7 - - - -
115A THR* 2.8 54.1 + - + +
118A THR* 3.6 22.3 + - - +
135A VAL* 4.2 12.1 - - - +
136A VAL 4.6 0.2 + - - -
138A PRO* 3.3 42.7 - - + +
149A ALA 2.9 17.6 + - - +
150A LEU* 3.3 7.8 + - + +
152A HIS* 1.3 78.5 - - - +
154A TYR* 1.3 82.3 + + - +
156A LYS* 3.4 2.4 + - - +
157A VAL* 3.1 28.8 + - + +
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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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135A VAL* 2.7 52.7 + - + -
136A VAL 4.3 1.1 - - - -
137A THR* 3.1 32.2 + - + +
150A LEU* 2.9 35.3 + - + +
153A HIS* 1.3 85.2 - + - +
155A THR* 1.3 57.8 + - - +
157A VAL* 3.4 4.5 + - + +
158A ALA* 2.8 32.6 + - - +
165A VAL* 4.6 7.4 - - + +
167A LEU* 3.4 24.0 - - + -
168A TYR 3.7 4.0 + - - -
178A LEU* 3.9 27.3 - - + +
186A LEU* 3.7 28.9 - - + -
192A ILE* 4.1 2.8 - - + +
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Residues in contact with THR 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 ILE* 2.7 32.1 + - - +
152A HIS* 3.9 5.8 - - - -
154A TYR* 1.3 76.7 - - - +
156A LYS* 1.3 57.5 + - - +
158A ALA 3.8 0.3 - - - -
159A ASP* 2.8 52.7 + - - +
185A THR* 6.0 0.2 - - - +
186A LEU* 3.4 14.2 - - - +
189A HIS* 3.8 18.1 + - + -
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Residues in contact with LYS 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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115A THR* 3.8 21.3 - - + +
116A GLN* 4.6 12.9 + - - +
119A VAL* 4.3 4.8 - - + +
152A HIS* 3.0 31.5 + - + +
153A HIS 3.7 4.0 - - - +
155A THR* 1.3 76.5 - - - +
157A VAL* 1.3 62.5 + - - +
159A ASP* 3.2 11.5 + - + +
160A LEU* 3.0 56.5 + - + +
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Residues in contact with VAL 157 (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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115A THR* 4.3 7.2 - - + +
118A THR* 3.6 33.4 - - + +
119A VAL* 4.1 18.1 - - + +
122A THR* 4.0 24.9 - - + +
135A VAL* 4.3 9.9 - - + -
153A HIS* 3.1 23.6 + - + +
154A TYR* 3.9 6.1 - - + +
155A THR 3.4 0.2 - - - -
156A LYS* 1.3 75.3 - - - +
158A ALA* 1.3 58.0 + - - +
160A LEU 3.2 2.3 + - - -
161A SER* 2.9 32.7 + - - -
165A VAL* 4.2 16.6 - - + -
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Residues in contact with ALA 158 (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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154A TYR 2.8 19.4 + - - +
157A VAL* 1.3 76.4 - - - +
159A ASP* 1.3 62.8 + - - +
160A LEU 3.4 0.5 + - - -
161A SER 3.6 2.1 + - - +
165A VAL* 3.9 17.0 - - + +
189A HIS* 3.5 24.8 - - + +
191A ASN* 2.9 28.6 + - + +
192A ILE* 3.5 25.8 - - + -
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Residues in contact with ASP 159 (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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155A THR* 2.8 37.1 + - - +
156A LYS* 3.4 12.9 - - + +
158A ALA* 1.3 74.3 - - - +
160A LEU* 1.3 68.1 + - + +
161A SER 3.8 2.3 + - - +
189A HIS* 2.7 31.7 + - - -
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Residues in contact with LEU 160 (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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116A GLN* 5.7 2.0 - - - +
119A VAL* 3.9 31.2 - - + -
123A VAL* 3.9 11.4 - - - +
156A LYS* 3.0 51.9 + - + +
157A VAL 3.6 1.6 - - - +
159A ASP* 1.3 85.0 - - + +
161A SER* 1.3 62.1 + - - +
162A PRO* 3.7 7.1 - - - +
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Residues in contact with SER 161 (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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122A THR* 3.1 31.5 - - - +
123A VAL* 5.0 0.9 - - - -
157A VAL 2.9 16.1 + - - -
158A ALA 3.6 1.4 + - - +
159A ASP 3.5 3.1 - - - +
160A LEU* 1.3 78.2 - - - +
162A PRO* 1.4 63.3 - - - +
163A ILE* 2.6 31.2 + - - +
165A VAL* 4.0 7.8 - - - +
191A ASN* 3.2 21.8 + - - -
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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