Contacts of the helix formed by residues 153 - 169 (chain A) in PDB entry 6HBU
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 THR 153 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150A THR 5.2 0.4 - - - -
151A THR 3.7 2.8 + - - -
152A MET* 1.3 77.9 - - - +
154A ASN* 1.3 69.7 + - - +
155A HIS* 3.6 12.4 + - + +
156A GLU* 3.4 38.7 + - + +
157A LYS* 3.1 23.9 + - - +
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Residues in contact with ASN 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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145A ALA* 6.3 0.4 - - - +
153A THR* 1.3 81.4 + - - +
155A HIS* 1.3 57.2 + - - +
157A LYS* 4.0 15.2 - - - +
158A ASN* 2.9 37.7 + - - +
379A TRP* 4.6 23.1 - - - -
382A LYS* 5.6 2.1 + - - -
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Residues in contact with HIS 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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153A THR* 3.2 12.7 + - + +
154A ASN* 1.3 77.3 - - - +
156A GLU* 1.3 64.5 + - + +
158A ASN* 3.4 7.8 + - - +
159A GLU* 2.8 59.3 + - + +
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Residues in contact with GLU 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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151A THR 4.9 1.4 - - - +
152A MET* 3.8 22.9 - - + +
153A THR* 3.4 31.2 + - + +
155A HIS* 1.3 80.4 - - + +
157A LYS* 1.3 63.8 + - - +
159A GLU* 3.6 17.3 + - - +
160A ARG* 3.4 25.1 + - - +
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Residues in contact with LYS 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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144A ALA* 3.3 38.3 + - + +
145A ALA* 3.5 19.2 + - + +
148A LEU* 3.5 25.2 + - + +
149A ALA 3.6 22.2 + - - -
150A THR* 4.7 5.3 - - - +
152A MET* 3.8 27.3 + - + -
153A THR 3.1 16.9 + - - +
154A ASN* 4.1 15.0 - - - +
155A HIS 3.3 0.2 - - - -
156A GLU* 1.3 77.9 - - - +
158A ASN* 1.3 57.8 + - - +
160A ARG* 3.2 6.0 + - - +
161A ILE* 3.0 33.7 + - + +
375A HIS* 4.4 7.9 + - - -
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Residues in contact with ASN 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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137A ARG* 5.2 1.7 + - - +
141A GLN* 3.6 35.4 + - - +
154A ASN* 2.9 35.6 + - - +
155A HIS* 3.4 9.0 + - - +
157A LYS* 1.3 74.0 - - - +
159A GLU* 1.3 59.7 + - - +
161A ILE* 3.6 11.2 - - - +
162A ASN* 2.8 39.3 + - - +
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Residues in contact with GLU 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 HIS* 2.8 52.3 + - + +
156A GLU* 3.8 17.2 - - - +
157A LYS 3.2 0.6 - - - -
158A ASN* 1.3 79.1 - - - +
160A ARG* 1.3 58.2 + - + +
162A ASN* 3.6 9.3 + - - +
163A ARG* 3.2 40.5 + - - +
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Residues in contact with ARG 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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148A LEU* 4.7 8.2 - - + +
152A MET* 3.7 30.2 - - - +
156A GLU 3.4 6.7 + - - +
157A LYS* 3.2 8.8 + - - +
159A GLU* 1.3 76.2 - - + +
161A ILE* 1.3 64.9 + - + +
163A ARG* 3.5 28.7 - - - +
164A VAL* 3.3 29.6 + - + +
200A LEU 5.1 2.0 + - - -
201A ILE* 3.8 23.5 + - + +
203A ASP* 3.2 35.4 + - - +
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Residues in contact with ILE 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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137A ARG* 4.5 16.2 - - + +
140A LEU* 3.5 45.9 - - + +
141A GLN* 3.7 14.4 - - + +
144A ALA* 3.8 15.9 - - + -
157A LYS* 3.0 18.8 + - + +
158A ASN* 3.6 23.6 - - + +
159A GLU 3.3 0.4 - - - -
160A ARG* 1.3 75.7 - - + +
162A ASN* 1.3 63.1 + - - +
164A VAL* 3.3 2.4 + - - +
165A ILE* 3.1 36.1 + - + +
201A ILE* 4.3 13.2 - - + -
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Residues in contact with ASN 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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137A ARG* 2.4 39.0 + - - +
158A ASN* 2.8 25.6 + - - +
159A GLU* 3.8 9.8 - - - +
160A ARG 3.4 0.2 - - - -
161A ILE* 1.3 75.9 - - - +
163A ARG* 1.3 62.3 + - - +
165A ILE* 3.6 5.5 + - - +
166A GLN* 3.2 31.0 + - + +
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Residues in contact with ARG 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 GLU* 3.2 27.0 + - - +
160A ARG* 3.5 44.1 - - - +
161A ILE 3.2 0.4 - - - -
162A ASN* 1.3 77.5 - - - +
164A VAL* 1.3 59.4 + - + +
166A GLN* 3.4 6.7 + - + +
167A GLU* 3.0 51.7 + - + +
307B LEU* 6.1 1.1 - - + -
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Residues in contact with VAL 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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140A LEU* 4.3 7.0 - - + -
160A ARG* 3.3 18.7 + - + +
161A ILE 3.3 4.4 + - - +
163A ARG* 1.3 76.1 - - + +
165A ILE* 1.3 60.7 + - + +
167A GLU* 4.4 9.2 - - - +
168A LEU* 3.0 51.3 + - + +
170A LEU* 5.5 0.9 - - + -
197A GLY* 4.0 20.6 - - - +
200A LEU* 3.9 23.8 - - + +
201A ILE* 3.7 20.9 - - + -
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Residues in contact with ILE 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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136A VAL* 5.2 2.7 - - + +
137A ARG* 3.9 44.9 - - + +
140A LEU* 4.9 9.4 - - + -
161A ILE* 3.1 29.3 + - + +
162A ASN* 3.9 5.6 - - - +
164A VAL* 1.3 77.5 - - + +
166A GLN* 1.3 60.6 + - - +
169A GLY* 3.2 2.8 + - - -
170A LEU* 2.9 64.3 + - + +
171A ASP* 3.4 18.9 - - - +
174A ALA* 3.9 15.9 - - + -
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Residues in contact with GLN 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 ASN* 3.2 20.8 + - + +
163A ARG* 3.7 7.2 - - - +
164A VAL 3.3 0.2 - - - -
165A ILE* 1.3 78.1 - - - +
167A GLU* 1.3 60.3 + - - +
169A GLY 3.4 2.1 + - - -
171A ASP* 2.7 39.4 + - - +
303B THR* 3.2 43.2 + - - +
307B LEU* 3.9 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 ARG* 3.0 43.6 + - + +
164A VAL* 4.1 11.2 - - - +
166A GLN* 1.3 77.1 - - - +
168A LEU* 1.3 61.5 + - - +
200A LEU* 5.2 2.9 - - - +
223A ALA 4.9 1.0 - - - +
224A VAL* 6.1 0.5 - - - +
227A LEU* 3.6 24.6 - - + +
230A ARG* 3.2 31.2 + - - -
304B ALA* 3.6 7.6 - - - +
307B LEU* 3.8 25.8 - - + +
308B ASN* 3.4 24.4 + - - +
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Residues in contact with LEU 168 (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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164A VAL* 3.0 27.4 + - + +
167A GLU* 1.3 76.9 - - - +
169A GLY* 1.3 52.1 + - - +
170A LEU* 4.0 17.0 - - + +
193A ARG* 2.7 67.5 + - + +
196A ILE* 4.2 17.7 - - + -
197A GLY* 3.6 21.5 - - - +
200A LEU* 5.0 2.2 - - + -
220A THR* 4.6 0.9 - - - +
224A VAL* 4.3 20.1 - - + +
227A LEU* 3.9 23.8 - - + -
304B ALA* 3.9 7.0 - - - +
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Residues in contact with GLY 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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165A ILE 3.2 5.3 + - - -
166A GLN 3.4 4.6 + - - -
167A GLU 3.5 0.2 - - - -
168A LEU* 1.3 78.9 - - - +
170A LEU* 1.3 59.3 + - - +
171A ASP 3.5 3.4 + - - -
172A LYS 5.3 0.2 + - - -
173A VAL* 5.4 1.0 - - - +
190A GLU* 5.7 0.3 - - - +
193A ARG* 3.3 21.8 + - - -
302B SER* 4.9 4.0 - - - -
303B THR* 3.8 22.0 - - - -
304B ALA* 3.9 7.6 - - - +
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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