Contacts of the helix formed by residues 146 - 165 (chain A) in PDB entry 1HXD
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 ALA 146 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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139A LEU* 4.2 5.2 - - + +
143A PRO 4.5 9.2 + - - +
145A ALA* 1.3 82.6 - - - +
147A ILE* 1.4 58.9 + - - +
149A LEU* 2.4 45.0 + - + +
150A SER* 2.7 17.8 + - - +
189A VAL* 5.7 5.2 - - + -
191A LEU* 5.1 17.7 - - + -
201A ILE* 5.6 5.6 - - + -
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Residues in contact with ILE 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A ALA* 2.5 27.6 + - - +
146A ALA* 1.4 78.4 - - - +
148A GLY* 1.3 72.1 + - - +
150A SER* 2.9 14.6 + - - -
151A LEU* 3.3 11.7 + - + +
173A TRP* 4.5 12.3 - - + -
174A PRO* 5.5 8.1 - - + -
253A PHE* 6.1 0.2 - - + -
258A LEU* 5.6 0.4 - - + -
295A GLN* 3.9 20.4 - - + +
296A GLY* 3.8 24.0 - - - +
310A MET* 4.3 30.5 - - + +
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Residues in contact with GLY 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A ILE* 1.3 87.6 - - - +
149A LEU* 1.4 63.1 + - - +
151A LEU* 3.6 11.6 - - - +
152A VAL* 2.8 30.3 + - - +
253A PHE* 3.7 7.3 - - - -
258A LEU* 3.2 32.7 - - - +
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Residues in contact with LEU 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A TRP* 5.2 6.3 - - + -
139A LEU* 5.1 4.9 - - + -
146A ALA* 2.4 35.5 + - - +
148A GLY* 1.4 67.8 - - - +
150A SER* 1.3 76.6 + - - +
152A VAL* 2.8 26.7 - - - +
153A ILE* 2.8 32.6 + - + +
189A VAL* 3.8 22.0 - - + -
201A ILE* 4.3 19.5 - - + -
203A ILE* 4.0 14.1 - - + -
250A LEU* 3.6 23.6 - - + -
253A PHE* 3.5 25.7 - - + -
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Residues in contact with SER 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A ALA* 2.7 16.5 + - - +
147A ILE* 2.9 5.7 + - - -
149A LEU* 1.3 76.9 - - - +
151A LEU* 1.3 66.9 + - - -
152A VAL 3.1 1.6 - - - -
153A ILE* 3.1 11.7 + - - +
154A GLY* 2.9 21.1 + - - -
174A PRO* 4.1 20.5 - - - +
175A ASN* 4.2 7.6 - - - -
187A ILE* 5.0 3.4 - - - +
189A VAL* 3.8 20.2 - - - +
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Residues in contact with LEU 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A ILE* 3.6 13.9 - - + +
148A GLY* 3.3 8.5 + - - +
150A SER* 1.3 75.1 - - - +
152A VAL* 1.3 53.3 + - - +
154A GLY* 3.2 0.7 + - - -
155A ILE* 2.7 47.1 + - + +
173A TRP* 3.2 34.8 - - + +
174A PRO* 4.2 17.5 - - + +
258A LEU* 3.8 16.4 - - + -
265A TRP* 3.9 23.7 - - + -
292A ILE* 4.1 10.8 - - + -
296A GLY* 3.1 35.9 - - - +
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Residues in contact with VAL 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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148A GLY 2.8 22.8 + - - +
149A LEU* 2.8 13.5 - - - +
151A LEU* 1.3 78.0 - - - +
153A ILE* 1.3 57.0 - - + +
155A ILE* 3.2 8.0 - - - +
156A VAL* 2.9 36.5 + - + +
246A LEU* 5.4 0.7 - - + -
249A ALA* 4.0 33.4 - - + +
250A LEU* 4.8 11.0 - - + -
253A PHE* 4.0 13.2 - - + -
258A LEU* 4.1 4.0 - - + -
261A TYR* 3.8 36.8 - - + -
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Residues in contact with ILE 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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149A LEU* 2.8 62.4 + - + +
150A SER* 3.1 8.3 + - - +
152A VAL* 1.3 75.4 - - + +
154A GLY* 1.3 66.7 + - - +
155A ILE 3.3 0.2 + - - -
156A VAL* 3.3 2.3 + - - +
157A MET* 3.0 47.2 + - + +
187A ILE* 4.2 15.3 - - + -
189A VAL* 4.9 0.2 - - + -
203A ILE* 4.2 29.4 - - + -
205A ALA* 5.5 2.0 - - + -
246A LEU* 4.1 26.2 - - + -
250A LEU* 4.5 9.2 - - + -
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Residues in contact with GLY 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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150A SER 2.9 16.9 + - - -
151A LEU* 3.7 1.8 - - - -
153A ILE* 1.3 71.8 - - - +
155A ILE* 1.3 63.8 + - - +
157A MET* 3.1 5.2 + - - +
158A ALA* 2.8 23.9 + - - +
171A VAL* 3.8 11.5 - - - +
176A ASP 5.8 0.7 - - - -
177A LEU* 3.9 9.2 - - - +
187A ILE* 3.9 19.7 - - - +
265A TRP* 5.8 1.8 - - - -
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Residues in contact with ILE 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 LEU* 2.7 38.7 + - + +
152A VAL* 3.2 5.4 - - - +
154A GLY* 1.3 70.4 - - - +
156A VAL* 1.3 67.4 + - + +
158A ALA* 3.0 6.1 + - - +
159A GLU* 3.0 44.4 + - - +
171A VAL* 4.1 10.5 - - + +
261A TYR* 3.6 36.3 - - + -
264A ARG* 4.3 15.3 - - + +
265A TRP* 3.8 40.8 - - + +
268A LEU* 4.0 6.4 - - + +
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Residues in contact with VAL 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 VAL* 2.9 21.3 + - + +
153A ILE 3.5 4.9 - - - +
155A ILE* 1.3 81.9 - - + +
157A MET* 1.3 66.2 + - + +
159A GLU* 2.8 24.7 + - + +
160A VAL* 2.8 18.2 + - + +
242A LEU* 5.2 1.8 - - + +
245A GLU* 4.0 28.5 - - + +
246A LEU* 3.8 25.4 - - + -
249A ALA* 3.8 26.9 - - + -
261A TYR* 4.9 4.5 - - + -
264A ARG* 5.1 2.9 - - - +
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Residues in contact with MET 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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133A LEU* 4.6 2.9 - - + -
153A ILE* 3.0 30.1 + - + +
154A GLY* 3.6 5.2 - - - +
156A VAL* 1.3 78.6 - - + +
158A ALA* 1.3 64.5 + - - +
160A VAL* 3.2 6.7 + - - +
161A LEU* 3.0 31.0 + - + +
177A LEU* 3.8 21.3 - - + -
185A ALA* 5.5 1.3 - - - -
187A ILE* 4.8 8.3 - - - -
205A ALA* 3.9 30.5 - - + -
207A ILE* 4.6 11.2 - - + -
242A LEU* 3.5 37.2 - - + -
246A LEU* 4.5 15.9 - - + -
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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 GLY 2.8 13.6 + - - +
155A ILE 3.5 8.1 - - - +
157A MET* 1.3 76.3 - - - +
159A GLU* 1.3 57.2 + - - +
161A LEU* 3.2 2.4 + - - +
162A ARG* 2.7 36.1 + - - +
169A VAL* 3.9 30.9 - - + +
171A VAL* 3.6 21.5 - - + -
177A LEU* 4.4 1.7 - - + +
268A LEU* 3.9 13.5 - - + -
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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 ILE* 3.2 33.9 - - - +
156A VAL* 2.8 12.7 + - + +
158A ALA* 1.3 77.4 - - - +
160A VAL* 1.3 64.5 + - + +
162A ARG* 3.7 6.6 - - - +
163A LYS* 2.9 34.8 + - - +
245A GLU* 5.4 5.0 - - - +
264A ARG* 3.1 41.6 + - - +
268A LEU* 4.1 12.8 - - + +
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Residues in contact with VAL 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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156A VAL* 2.8 17.6 + - + +
157A MET 3.2 6.0 + - - +
159A GLU* 1.3 78.4 - - + +
161A LEU* 1.3 64.9 + - + +
163A LYS* 3.3 6.5 + - - +
164A LEU* 2.8 48.8 + - + +
238A LEU* 4.1 8.1 - - + -
241A MET* 4.0 19.3 - - + +
242A LEU* 4.0 26.0 - - + -
245A GLU* 3.9 39.3 - - + +
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Residues in contact with LEU 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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157A MET* 3.0 18.8 + - + +
158A ALA 3.6 2.9 - - - +
160A VAL* 1.3 77.9 - - + +
162A ARG* 1.3 65.1 + - - +
164A LEU* 2.7 19.1 + - - +
165A GLY 3.2 9.9 + - - -
166A ALA* 3.5 13.0 + - + +
169A VAL* 3.8 19.1 - - + -
177A LEU* 3.3 35.0 - - + -
184A LEU* 4.3 9.6 - - + -
207A ILE* 4.9 12.8 - - + -
226A LEU* 4.5 18.2 - - + -
233A LEU* 4.4 20.1 - - + +
238A LEU* 4.5 17.9 - - + -
242A LEU* 6.0 1.8 - - + -
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Residues in contact with ARG 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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158A ALA 2.7 26.1 + - - +
159A GLU* 3.8 6.3 - - - +
161A LEU* 1.3 71.8 - - - +
163A LYS* 1.3 58.5 + - - +
165A GLY 3.0 19.6 + - - +
166A ALA 2.9 14.5 - - - +
167A ASP* 3.3 27.2 + - - +
168A LYS* 4.2 7.5 + - - +
169A VAL* 2.8 30.9 + - + +
170A ARG* 3.1 30.9 - - - +
267A LYS* 4.0 11.4 + - - +
268A LEU* 2.9 27.0 - - - +
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Residues in contact with LYS 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* 2.9 24.1 + - - +
160A VAL* 3.5 13.5 - - - +
161A LEU 3.0 0.2 - - - -
162A ARG* 1.3 73.2 - - - +
164A LEU* 1.3 62.2 + - + +
165A GLY 3.3 1.1 - - - -
241A MET* 3.6 29.7 - - + +
245A GLU* 3.3 29.9 + - - +
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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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160A VAL* 2.8 45.7 + - + +
161A LEU* 2.7 9.7 + - - +
163A LYS* 1.3 75.8 - - - +
165A GLY* 1.3 57.6 + - - +
233A LEU* 3.9 33.4 - - + +
234A ASP 5.9 1.8 - - - +
237A THR* 3.9 17.9 - - + -
238A LEU* 4.6 12.3 - - + +
241A MET* 3.4 37.2 - - + -
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Residues in contact with GLY 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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161A LEU 3.2 1.4 + - - -
162A ARG 3.0 9.6 - - - +
163A LYS 3.3 2.0 - - - -
164A LEU* 1.3 80.5 - - - +
166A ALA* 1.3 55.6 + - - +
167A ASP* 2.5 29.8 + - - +
231A ILE* 5.0 2.0 - - - -
233A LEU* 4.7 4.5 - - - -
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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
------------------------------------------------------------
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