Contacts of the helix formed by residues 150 - 173 (chain A) in PDB entry 6YBO
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 ASP 150 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147A GLY 5.1 0.8 + - - -
148A ALA 4.3 0.2 - - - -
149A LYS* 1.3 70.9 - - - +
151A VAL* 1.3 59.0 + - - +
152A ARG* 3.1 21.0 + - - +
153A ASP* 3.0 40.2 + - + +
154A ALA* 2.9 27.8 + - - +
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Residues in contact with VAL 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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149A LYS* 3.4 16.8 + - + +
150A ASP* 1.3 71.4 + - - +
152A ARG* 1.3 62.1 + - + +
154A ALA* 3.7 5.5 - - - +
155A LEU* 2.8 45.3 + - + +
192A LEU* 4.1 29.2 - - + -
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Residues in contact with ARG 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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150A ASP* 3.1 14.6 + - - +
151A VAL* 1.3 78.7 - - + +
153A ASP* 1.3 65.0 + - - +
155A LEU* 3.2 11.1 + - + +
156A ASP* 3.0 27.2 + - - +
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Residues in contact with ASP 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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150A ASP* 3.0 35.7 + - + +
152A ARG* 1.3 76.8 - - - +
154A ALA* 1.3 62.7 + - - +
156A ASP* 3.2 16.9 + - - +
157A ARG* 3.0 37.3 + - + +
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Residues in contact with ALA 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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105A THR* 3.4 20.8 - - - +
149A LYS* 4.1 18.6 - - + -
150A ASP 2.9 17.1 + - - +
151A VAL* 3.7 8.3 - - - +
152A ARG 3.3 0.2 - - - -
153A ASP* 1.3 77.5 - - - +
155A LEU* 1.3 57.6 + - - +
157A ARG* 3.2 5.8 + - - +
158A MET* 2.8 24.1 + - - +
192A LEU* 3.7 25.4 - - + -
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Residues in contact with LEU 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 VAL* 2.8 37.5 + - + +
152A ARG* 3.7 9.0 - - + +
154A ALA* 1.3 72.8 - - + +
156A ASP* 1.3 62.0 + - - +
158A MET* 3.7 7.1 - - + +
159A LYS* 2.9 31.5 + - - +
192A LEU* 5.2 11.7 - - + -
193A LEU* 4.1 28.0 - - + +
202A PHE* 4.0 18.5 - - + -
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Residues in contact with ASP 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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152A ARG* 3.0 17.3 + - - +
153A ASP* 3.2 19.3 + - - +
155A LEU* 1.3 77.5 - - - +
157A ARG* 1.3 78.0 + - - +
159A LYS* 3.7 8.9 - - - +
160A GLU* 2.9 28.6 + - - +
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Residues in contact with ARG 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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104A PHE 3.7 19.4 - - - +
105A THR* 4.5 4.3 - - + -
106A ALA 5.8 0.2 - - - +
112A ARG* 3.5 39.3 - - - +
153A ASP* 3.0 33.5 + - + +
154A ALA* 3.2 9.8 + - - +
156A ASP* 1.3 94.8 + - - +
158A MET* 1.3 65.0 + - - +
160A GLU* 2.9 31.8 + - - +
161A ALA* 3.0 24.8 + - - +
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Residues in contact with MET 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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104A PHE* 4.3 14.8 - - - -
105A THR* 3.9 22.4 - - + +
138A GLY* 5.8 2.7 - - - -
141A GLU* 4.0 23.6 - - + -
154A ALA 2.8 16.7 + - - +
155A LEU* 3.7 10.3 - - + +
157A ARG* 1.3 77.0 - - - +
159A LYS* 1.3 62.1 + - - +
161A ALA* 3.3 5.6 + - - +
162A PHE* 3.0 48.7 + - + -
192A LEU* 4.2 20.9 - - + +
193A LEU* 4.5 15.5 - - + -
202A PHE* 3.5 22.9 - - + -
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Residues in contact with LYS 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 LEU 2.9 17.2 + - - +
156A ASP* 3.7 10.1 - - - +
158A MET* 1.3 75.9 - - - +
160A GLU* 1.3 57.3 + - - +
162A PHE* 3.3 1.0 + - - +
163A ASP* 2.8 57.9 + - - +
202A PHE* 3.6 15.1 - - + -
205A ARG* 2.8 32.1 + - + +
206A LEU* 3.9 11.7 - - + -
207A GLU* 2.8 27.6 + - - +
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Residues in contact with GLU 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 LEU* 6.2 0.2 - - + -
156A ASP 2.9 17.3 + - - +
157A ARG* 2.9 38.7 + - - +
158A MET 3.3 0.2 - - - -
159A LYS* 1.3 78.3 - - - +
161A ALA* 1.3 62.7 + - - +
163A ASP* 3.8 5.4 - - - +
164A LEU* 3.0 45.9 + - + +
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Residues in contact with ALA 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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104A PHE* 3.6 36.8 - - + +
116A LEU* 3.8 25.0 - - + +
157A ARG 3.0 17.0 + - - +
158A MET 3.6 4.5 - - - +
160A GLU* 1.3 76.9 - - - +
162A PHE* 1.3 61.6 + - - +
164A LEU* 3.2 4.4 + - - +
165A LEU* 3.0 27.9 + - - +
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Residues in contact with PHE 162 (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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104A PHE* 4.2 16.8 - + - -
136A ALA* 3.8 30.5 - - + -
158A MET* 3.0 51.2 + - + +
161A ALA* 1.3 76.7 - - - +
163A ASP* 1.3 59.6 + - - +
165A LEU* 3.3 17.0 + - + +
166A GLY 3.0 9.7 + - - -
178A PHE* 5.2 9.6 - + + -
180A ILE* 3.9 28.0 - - + -
193A LEU* 5.5 1.3 - - + -
202A PHE* 3.9 14.1 - + - -
206A LEU* 4.1 14.8 - - + -
212A TYR* 2.6 49.5 + + + -
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Residues in contact with ASP 163 (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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159A LYS* 2.8 54.6 + - - +
160A GLU* 3.8 6.0 - - - +
162A PHE* 1.3 73.3 - - - +
164A LEU* 1.3 56.8 + - + +
166A GLY* 3.2 1.9 + - - -
167A GLU* 2.9 28.3 + - - +
206A LEU* 3.7 7.8 - - - +
207A GLU* 2.9 30.0 + - + +
208A ARG* 4.8 3.5 + - - -
403A NA 2.7 26.8 - - - -
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Residues in contact with LEU 164 (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 LEU* 3.8 30.1 - - + -
120A ILE* 5.7 3.5 - - + +
160A GLU* 3.0 40.9 + - + +
161A ALA 3.6 4.5 - - - +
163A ASP* 1.3 75.2 - - - +
165A LEU* 1.3 58.3 + - + +
167A GLU* 3.2 22.7 + - - +
168A TYR* 2.9 28.2 + - - +
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Residues in contact with LEU 165 (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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104A PHE* 3.9 29.2 - - + -
116A LEU* 3.9 14.6 - - + -
119A THR* 4.0 21.5 - - + -
120A ILE* 3.8 28.9 - - + -
123A ILE* 4.0 6.5 - - + +
161A ALA 3.0 18.7 + - - +
162A PHE* 3.7 20.9 - - + +
163A ASP 3.3 0.2 - - - -
164A LEU* 1.3 76.1 - - - +
166A GLY* 1.3 58.5 + - - +
168A TYR* 3.2 5.0 + - - +
169A VAL* 3.0 32.4 + - - +
178A PHE* 3.7 24.7 - - + -
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Residues in contact with GLY 166 (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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162A PHE 3.0 11.3 + - - -
163A ASP 3.6 1.8 - - - -
165A LEU* 1.3 74.1 - - - +
167A GLU* 1.3 63.0 + - - +
169A VAL* 3.5 5.0 + - - +
170A THR* 2.8 31.6 + - - -
178A PHE* 4.2 2.4 - - - -
208A ARG* 4.3 6.7 - - - -
211A LEU* 3.9 15.0 - - - -
212A TYR* 3.3 17.6 + - - -
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Residues in contact with GLU 167 (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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163A ASP 2.9 13.6 + - - +
164A LEU* 3.5 26.2 - - - +
166A GLY* 1.3 75.3 - - - +
168A TYR* 1.3 58.3 + - - +
170A THR* 3.8 3.0 - - - -
171A SER* 2.9 36.3 + - - -
208A ARG* 3.9 20.1 - - - +
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Residues in contact with TYR 168 (chain A).
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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120A ILE* 3.5 46.8 - - + +
123A ILE* 4.5 8.1 - - + -
124A ASP* 2.6 37.4 + - - -
164A LEU 2.9 13.8 + - - +
165A LEU* 3.2 10.9 + - - +
167A GLU* 1.3 76.6 - - - +
169A VAL* 1.3 73.3 + - + +
171A SER* 2.8 23.2 + - - -
172A GLN* 3.0 43.0 + - + +
174A TYR* 3.9 11.7 - + - -
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Residues in contact with VAL 169 (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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123A ILE* 4.0 17.9 - - + -
165A LEU 3.0 15.9 + - - +
166A GLY* 3.5 11.7 - - - +
168A TYR* 1.3 80.1 - - + +
170A THR* 1.3 66.3 + - - +
172A GLN* 3.4 1.0 + - - -
173A GLY 3.1 3.5 + - - -
174A TYR* 3.1 46.9 + - + +
176A ILE* 3.9 26.7 - - + +
178A PHE* 3.7 29.8 - - + -
211A LEU* 4.2 12.6 - - + -
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Residues in contact with THR 170 (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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166A GLY 2.8 22.4 + - - -
167A GLU* 3.8 3.6 - - - -
169A VAL* 1.3 78.9 - - - +
171A SER* 1.3 63.6 + - - +
173A GLY* 3.2 12.5 + - - -
174A TYR 5.6 0.4 - - - -
208A ARG* 3.7 34.7 + - - +
211A LEU* 4.0 9.2 - - - +
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Residues in contact with SER 171 (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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167A GLU* 2.9 21.0 + - - -
168A TYR* 2.8 21.5 + - - -
170A THR* 1.3 78.5 - - - +
172A GLN* 1.3 72.4 + - - +
173A GLY 3.6 0.2 + - - -
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Residues in contact with GLN 172 (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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168A TYR* 3.0 55.1 + - + +
170A THR 3.2 0.2 - - - -
171A SER* 1.3 89.0 + - - +
173A GLY* 1.3 62.8 + - - +
174A TYR* 3.6 36.7 + - + -
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Residues in contact with GLY 173 (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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169A VAL 3.1 5.5 + - - -
170A THR* 3.2 12.3 + - - -
171A SER 3.3 1.0 + - - -
172A GLN* 1.3 77.9 - - - +
174A TYR* 1.3 64.6 + - - +
175A ASP* 3.9 1.0 + - - +
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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