Contacts of the helix formed by residues 146 - 164 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143B PRO 6.2 0.7 - - - -
144B ALA* 4.0 3.3 - - - +
145B ALA* 1.3 78.8 - - - +
147B ILE* 1.4 74.5 + - + +
148B GLY 2.8 3.8 - - - -
149B LEU* 2.6 42.4 + - - +
150B SER* 3.2 3.7 + - - -
189B VAL* 5.8 4.9 - - - +
191B LEU* 4.6 18.6 - - + -
201B ILE* 6.2 3.3 - - - +
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Residues in contact with ILE 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B ALA 2.9 2.5 + - - +
146B ALA* 1.4 91.4 - - + +
148B GLY* 1.3 66.1 + - - +
150B SER* 3.7 8.8 + - - -
151B LEU* 3.4 17.7 + - + +
173B TRP* 4.7 9.2 - - + +
174B PRO* 4.9 11.7 - - + -
191B LEU* 5.8 3.1 - - + -
295B GLN 4.9 1.6 - - - +
296B GLY 3.9 20.9 - - - +
310B MET* 4.0 29.2 - - + -
311B GLY* 4.5 21.8 - - - +
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Residues in contact with GLY 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B ALA 2.8 10.5 + - - -
146B ALA 2.8 3.4 + - - -
147B ILE* 1.3 75.9 - - - +
149B LEU* 1.3 63.6 + - - +
151B LEU* 2.8 26.2 + - - +
152B VAL* 3.1 4.5 + - - +
253B PHE* 3.6 22.0 - - - -
258B LEU* 4.3 20.5 - - - +
295B GLN 5.0 2.0 + - - -
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Residues in contact with LEU 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B TRP* 6.0 1.6 - - + -
139B LEU* 4.4 7.4 - - + -
145B ALA* 3.8 12.3 - - + -
146B ALA* 2.6 17.2 + - - +
148B GLY* 1.3 68.5 - - - -
150B SER* 1.3 61.2 - - - +
152B VAL* 2.5 36.1 + - + +
153B ILE* 2.8 18.4 + - + +
189B VAL* 5.2 7.4 - - + -
201B ILE* 5.0 19.1 - - + -
203B ILE* 4.8 9.4 - - + -
250B LEU* 3.4 33.9 - - + -
253B PHE* 3.0 36.5 - - + -
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Residues in contact with SER 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B ALA 3.2 4.6 + - - -
147B ILE* 3.7 11.2 + - - -
148B GLY 3.2 0.2 + - - -
149B LEU* 1.3 79.7 - - - +
151B LEU* 1.3 64.9 + - - +
153B ILE* 3.0 25.1 - - - +
154B GLY* 3.1 5.0 + - - -
174B PRO* 2.6 45.7 + - - +
175B ASN* 4.2 15.0 - - - -
187B ILE* 4.1 4.4 - - - +
189B VAL* 4.4 15.9 - - - -
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Residues in contact with LEU 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B ILE* 3.4 12.6 - - + +
148B GLY 2.8 12.5 + - - +
150B SER* 1.3 77.4 + - - +
152B VAL* 1.3 70.7 + - + +
153B ILE 2.9 1.4 + - - -
154B GLY* 3.0 3.6 + - - -
155B ILE* 3.0 30.0 + - + +
173B TRP* 4.1 13.9 - - + +
174B PRO* 3.9 23.6 - - + -
258B LEU* 4.7 13.9 - - + -
265B TRP* 3.7 39.7 - - + -
292B ILE* 4.4 13.0 - - + -
296B GLY* 3.9 29.6 - - - +
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Residues in contact with VAL 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B GLY 3.1 5.4 + - - +
149B LEU* 2.5 18.6 + - - +
151B LEU* 1.3 75.9 - - + +
153B ILE* 1.3 66.4 + - + +
155B ILE* 3.3 8.7 - - - +
156B VAL* 2.9 25.2 + - + +
246B LEU* 5.7 0.2 - - + -
249B ALA* 3.9 28.5 - - + +
250B LEU* 4.0 18.4 - - + -
253B PHE* 3.6 30.3 - - + -
258B LEU* 5.6 2.7 - - + -
261B TYR* 3.6 31.0 - - + +
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Residues in contact with ILE 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B LEU* 2.9 38.8 - - + +
150B SER* 3.0 13.9 - - - +
151B LEU 2.9 0.6 + - - -
152B VAL* 1.3 80.6 - - - +
154B GLY* 1.3 66.8 + - - +
156B VAL* 2.8 10.2 + - - +
157B MET* 3.0 27.7 + - - +
187B ILE* 4.0 23.3 - - + -
189B VAL* 4.8 3.8 - - + -
203B ILE* 4.2 27.8 - - + -
205B ALA* 5.7 1.1 - - + -
246B LEU* 4.2 21.9 - - + +
250B LEU* 4.2 13.0 - - + -
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Residues in contact with GLY 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B SER 3.1 5.0 + - - -
151B LEU* 3.0 7.5 + - - -
153B ILE* 1.3 76.2 - - - +
155B ILE* 1.3 52.7 + - - +
157B MET* 3.8 5.8 - - - -
158B ALA* 2.7 38.5 + - - +
171B VAL* 4.1 9.6 - - - -
176B ASP 5.3 0.9 - - - -
177B LEU* 3.7 10.7 - - - +
187B ILE* 3.6 20.2 - - - +
265B TRP* 6.1 1.3 - - - -
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Residues in contact with ILE 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B LEU* 3.0 25.9 + - + +
152B VAL* 3.3 6.5 - - - +
153B ILE 2.8 0.2 + - - -
154B GLY* 1.3 76.4 - - - +
156B VAL* 1.3 66.9 - - + +
158B ALA* 3.8 1.9 - - - +
159B GLU* 2.9 49.4 + - - +
171B VAL* 4.3 8.6 - - + +
261B TYR* 3.7 40.6 - - + +
264B ARG* 4.3 17.9 - - + +
265B TRP* 4.1 33.6 - - + +
268B LEU* 4.2 6.0 - - + +
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Residues in contact with VAL 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B VAL* 2.9 17.7 - - + +
153B ILE 2.8 7.1 + - - +
155B ILE* 1.3 87.6 - - + +
157B MET* 1.3 60.7 + - - +
159B GLU* 3.0 14.7 + - + +
160B VAL* 2.7 32.8 + - + +
242B LEU* 5.8 0.9 - - + -
245B GLU* 4.1 34.1 - - + +
246B LEU* 4.1 12.6 - - + -
249B ALA* 3.9 22.9 - - + -
261B TYR* 4.7 6.7 - - + -
264B ARG* 5.2 1.1 - - - +
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Residues in contact with MET 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B ILE* 3.0 34.0 + - + +
154B GLY* 3.8 4.5 - - - +
156B VAL* 1.3 75.2 - - - +
158B ALA* 1.3 54.1 - - - +
160B VAL* 3.0 2.1 + - - +
161B LEU* 2.8 41.1 + - + +
177B LEU* 3.8 24.7 - - + -
185B ALA* 4.2 12.6 - - + -
186B GLY 5.4 0.2 - - - +
187B ILE* 4.1 21.3 - - + -
205B ALA* 4.1 26.2 - - + -
207B ILE* 4.4 12.3 - - + -
242B LEU* 4.2 29.8 - - + +
246B LEU* 5.1 7.6 - - + +
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Residues in contact with ALA 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B GLY 2.7 18.0 + - - +
155B ILE 3.8 4.3 - - - +
157B MET* 1.3 75.9 - - - +
159B GLU* 1.3 58.5 + - - +
161B LEU* 3.0 3.5 + - - +
162B ARG* 2.8 36.6 + - - +
169B VAL* 4.1 27.1 - - + +
171B VAL* 4.2 16.8 - - + -
177B LEU* 4.1 3.8 - - + +
268B LEU* 4.4 15.5 - - + -
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Residues in contact with GLU 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B ILE* 2.9 38.9 + - + +
156B VAL* 3.0 17.7 + - + +
158B ALA* 1.3 79.4 - - - +
160B VAL* 1.3 58.0 + - + +
162B ARG* 3.9 8.6 - - - +
163B LYS* 2.9 40.3 + - + +
264B ARG* 3.6 39.0 + - - +
268B LEU* 4.5 10.0 - - + +
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Residues in contact with VAL 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B VAL* 2.7 35.1 + - + +
157B MET* 3.7 7.6 - - - +
159B GLU* 1.3 72.5 - - + +
161B LEU* 1.3 69.8 + - + +
163B LYS* 3.3 8.7 + - + +
164B LEU* 2.8 30.8 + - + +
238B LEU* 4.4 8.1 - - + -
241B MET* 3.5 40.6 - - + +
242B LEU* 4.5 12.8 - - + -
245B GLU* 4.3 21.5 - - + +
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Residues in contact with LEU 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157B MET* 2.8 17.5 + - + +
158B ALA 3.6 3.4 - - - +
160B VAL* 1.3 78.1 - - - +
162B ARG* 1.4 61.1 + - - +
164B LEU* 3.1 12.3 + - - +
165B GLY 3.2 1.0 + - - -
166B ALA* 2.8 26.2 + - + +
169B VAL* 4.1 20.2 - - + -
177B LEU* 3.5 32.3 - - + -
184B LEU* 4.2 14.4 - - + -
207B ILE* 4.8 13.7 - - + -
226B LEU* 4.6 9.4 - - + -
233B LEU* 4.1 17.5 - - + -
238B LEU* 3.5 33.9 - - + -
242B LEU* 6.4 0.4 - - + -
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Residues in contact with ARG 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158B ALA 2.8 20.9 + - - +
159B GLU* 4.0 6.7 - - - +
161B LEU* 1.4 75.0 - - - +
163B LYS* 1.3 64.1 + - + +
165B GLY* 2.8 15.8 + - - -
166B ALA 3.4 22.3 + - - +
167B ASP* 2.7 36.6 + - + +
168B LYS* 3.9 9.5 - - - +
169B VAL* 3.0 27.5 + - + +
170B ARG* 3.6 29.1 - - - +
267B LYS* 4.8 18.3 + - - +
268B LEU* 3.5 23.7 - - - +
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Residues in contact with LYS 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B GLU* 2.9 26.9 + - + +
160B VAL* 3.7 9.2 - - + +
162B ARG* 1.3 77.5 - - + +
164B LEU* 1.3 60.9 + - + +
165B GLY* 2.9 5.9 + - - -
241B MET* 5.4 12.3 - - + -
245B GLU* 5.2 10.5 - - - +
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Residues in contact with LEU 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B VAL* 2.8 24.8 + - + +
161B LEU 3.1 6.9 + - - +
163B LYS* 1.3 75.2 - - - +
165B GLY* 1.3 57.0 + - - +
233B LEU* 3.4 38.2 - - + +
234B ASP 5.5 0.2 - - - +
237B THR* 4.7 11.4 - - + -
238B LEU* 3.7 48.9 - - + +
241B MET* 3.4 34.3 - - + -
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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
------------------------------------------------------------
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