Contacts of the helix formed by residues 216 - 233 (chain A) in PDB entry 3D5V
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 PHE 216 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A HIS* 3.2 71.2 - + + +
157A ARG* 3.8 35.4 - - - -
158A VAL 4.2 0.4 - - - -
159A ILE* 3.7 20.2 - - + -
187A ILE* 3.7 33.2 - - + -
215A SER* 1.3 102.8 + - - +
217A GLU* 1.3 62.3 + - - +
218A VAL 3.2 1.6 - - - -
219A ASP* 3.2 12.4 + - - +
220A ILE* 3.8 3.4 + - + +
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Residues in contact with GLU 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214A HIS* 4.8 1.2 - - - -
215A SER* 3.2 37.4 + - - +
216A PHE* 1.3 78.6 - - - +
218A VAL* 1.3 59.0 + - + +
219A ASP 3.3 0.2 - - - -
220A ILE* 3.5 15.5 + - + +
221A TRP 3.1 16.5 + - - -
276A PRO* 3.5 45.0 - - + +
277A THR* 5.5 1.4 - - - -
279A ARG* 2.8 30.4 + - + +
280A PRO 5.9 0.2 - - - +
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Residues in contact with VAL 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A ILE* 3.8 13.7 - - + -
161A ARG* 3.9 21.5 - - + +
214A HIS* 3.7 31.6 - - + -
215A SER 3.3 17.9 - - - +
217A GLU* 1.3 78.3 - - + +
219A ASP* 1.3 66.2 + - - +
221A TRP* 3.4 8.4 - - + +
222A SER* 3.1 29.2 + - - -
279A ARG* 4.2 8.5 - - - +
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Residues in contact with ASP 219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A VAL* 4.3 4.6 - - + +
153A LEU* 5.2 0.7 - - - +
154A HIS* 3.0 34.9 + - + +
159A ILE* 3.5 8.2 - - - +
160A HIS* 2.9 26.8 + - - +
161A ARG* 2.8 30.4 + - - -
163A LEU* 3.7 21.8 - - + +
216A PHE 3.2 2.6 + - - +
218A VAL* 1.3 76.5 - - - +
220A ILE* 1.3 58.5 + - - +
222A SER* 3.3 5.8 + - - -
223A LEU* 3.0 33.6 + - - +
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Residues in contact with ILE 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A HIS* 4.2 11.2 - - + -
216A PHE* 3.9 3.4 - - + +
217A GLU* 3.6 23.8 - - + +
218A VAL 3.3 0.2 - - - -
219A ASP* 1.3 74.5 - - - +
221A TRP* 1.3 62.8 + - - +
223A LEU* 3.3 10.8 + - + +
224A GLY 3.1 17.8 + - - -
271A MET* 3.8 20.6 - - + +
279A ARG* 4.4 4.7 - - + -
280A PRO* 3.3 37.7 - - + +
281A SER* 5.0 0.9 - - - -
282A VAL* 3.8 39.3 - - + +
285A LEU* 4.2 14.6 - - + -
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Residues in contact with TRP 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A GLU 3.1 6.1 + - - -
218A VAL* 3.4 11.7 - - + +
220A ILE* 1.3 75.9 - - - +
222A SER* 1.3 75.3 + - - +
224A GLY 3.1 9.2 + - - -
225A CYS* 3.2 22.7 + - - -
237A PHE* 3.4 40.2 - + - -
249A ILE* 3.7 34.3 - - + +
252A ASN* 3.4 11.4 - - - -
271A MET 3.5 12.3 + - - -
272A LEU* 3.2 50.8 - - + +
273A HIS 4.7 0.4 - - - -
274A ALA* 5.6 0.7 - - - -
279A ARG* 3.6 37.9 - - - +
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Residues in contact with SER 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A ARG 5.1 5.0 + - - -
162A ASP* 5.5 0.2 - - - -
163A LEU* 3.4 39.3 + - - +
218A VAL 3.1 12.5 + - - -
219A ASP* 3.3 10.8 + - - -
221A TRP* 1.3 86.1 - - - +
223A LEU* 1.3 58.3 + - - +
225A CYS* 3.2 9.7 + - - +
226A ILE* 3.0 32.4 + - - +
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Residues in contact with LEU 223 (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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143A MET* 3.4 24.7 - - + +
146A THR* 3.6 32.1 - - + -
147A ILE* 4.2 8.1 - - + -
150A VAL* 4.0 30.1 - - + -
163A LEU* 4.1 6.5 - - + -
219A ASP 3.0 18.4 + - - +
220A ILE* 3.6 10.3 - - + +
221A TRP 3.3 0.2 - - - -
222A SER* 1.3 75.0 - - - +
224A GLY* 1.3 58.0 + - - +
226A ILE* 4.2 13.0 - - + -
227A LEU* 3.0 24.6 + - - +
271A MET* 3.5 15.0 - - + -
285A LEU* 4.1 21.8 - - + -
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Residues in contact with GLY 224 (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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220A ILE 3.1 10.5 + - - -
221A TRP 3.1 5.5 + - - -
223A LEU* 1.3 77.4 - - - +
225A CYS* 1.3 55.6 + - - +
227A LEU* 3.7 2.3 + - - +
228A TYR* 3.1 28.2 + - - +
268A ILE* 4.1 9.1 - - - +
271A MET* 3.6 27.3 - - - +
272A LEU* 3.8 13.0 - - - +
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Residues in contact with CYS 225 (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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221A TRP* 3.2 36.4 + - - -
222A SER* 3.2 10.6 + - - +
224A GLY* 1.3 73.9 - - - +
226A ILE* 1.3 56.8 + - + +
228A TYR* 3.5 2.1 + - - +
229A THR* 2.6 39.3 + - - +
236A PRO* 3.8 26.3 - - + +
237A PHE* 4.2 7.2 - - - -
272A LEU* 3.7 13.5 - - - -
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Residues in contact with ILE 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A LEU* 5.4 0.4 - - + -
143A MET* 3.8 17.9 - - - -
163A LEU* 4.1 10.1 - - + +
164A LYS* 4.0 30.1 - - - +
165A LEU* 3.9 26.9 - - + +
168A LEU* 3.9 29.2 - - + -
222A SER 3.0 22.2 + - - +
223A LEU* 3.7 18.2 - - + +
224A GLY 3.4 0.2 - - - -
225A CYS* 1.3 76.6 - - + +
227A LEU* 1.3 57.1 - - - +
229A THR* 3.2 6.2 + - - -
230A LEU* 2.9 35.8 + - + +
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Residues in contact with LEU 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A ALA* 4.4 4.9 - - + -
143A MET* 3.7 33.2 - - + -
223A LEU 3.0 17.9 + - - +
224A GLY 4.0 3.8 - - - +
226A ILE* 1.3 72.9 - - - +
228A TYR* 1.3 66.7 + - - +
230A LEU* 3.6 2.7 + - - +
231A LEU* 3.2 41.6 + - + +
264A ALA 4.7 2.2 - - - +
267A LEU* 3.9 27.6 - - + -
268A ILE* 3.8 24.7 - - + -
271A MET* 4.0 12.1 - - - -
290A PHE* 3.9 18.2 - - + -
291A PHE* 5.9 0.7 - - + -
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Residues in contact with TYR 228 (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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224A GLY 3.1 19.5 + - - +
225A CYS 3.6 4.3 - - - +
226A ILE 3.3 0.2 - - - -
227A LEU* 1.3 76.4 - - - +
229A THR* 1.3 55.4 + - - +
231A LEU 3.2 1.4 + - - -
232A VAL* 2.8 65.6 + - + +
234A LYS* 3.2 26.6 - - + +
235A PRO 3.9 1.3 - - - -
236A PRO* 3.5 41.5 + - + +
254A TYR* 4.3 4.7 - + - -
255A SER 2.7 31.9 + - - -
256A VAL* 3.7 29.4 - - + -
257A PRO* 4.4 0.9 - - - +
268A ILE* 4.0 20.8 - - + +
272A LEU* 5.0 0.2 - - + -
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Residues in contact with THR 229 (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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128A HIS* 3.5 34.8 - - + +
133A ALA* 4.9 0.2 - - - -
165A LEU* 3.8 21.0 - - + +
225A CYS* 2.6 24.6 + - - +
226A ILE* 3.7 4.9 - - - -
228A TYR* 1.3 75.8 - - - +
230A LEU* 1.3 58.5 + - - +
233A GLY* 2.9 26.5 + - - -
234A LYS 3.5 20.2 - - - -
235A PRO* 3.5 22.6 - - + +
236A PRO* 3.7 1.0 - - - +
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Residues in contact with LEU 230 (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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124A LEU* 4.7 13.7 - - + +
127A LEU* 5.1 5.4 - - + -
128A HIS* 5.4 6.5 - - + -
132A LYS 4.2 1.5 - - - +
133A ALA* 3.4 3.3 - - - -
134A VAL* 2.8 58.2 + - + +
139A ALA* 4.3 12.1 - - + -
142A PHE* 4.3 24.5 - - + -
143A MET* 4.1 19.3 - - + -
165A LEU* 4.0 22.0 - - + -
226A ILE* 2.9 34.3 + - + +
227A LEU* 3.9 4.5 - - - +
229A THR* 1.3 76.8 - - - +
231A LEU* 1.3 57.1 + - - +
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Residues in contact with LEU 231 (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 ALA* 3.5 11.4 - - - +
134A VAL 4.4 9.0 - - - +
136A GLU* 3.9 30.3 - - + +
139A ALA* 3.7 25.6 - - + -
227A LEU* 3.2 35.1 + - + +
228A TYR* 4.1 1.6 - - - +
230A LEU* 1.3 79.2 - - - +
232A VAL* 1.3 63.9 + - + +
260A ILE* 3.7 26.7 - - + +
264A ALA* 3.8 27.6 - - + -
268A ILE* 4.5 7.6 - - + -
290A PHE* 4.3 4.0 - - + -
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Residues in contact with VAL 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A ALA* 3.6 8.5 - - - +
228A TYR* 2.8 67.3 + - + +
231A LEU* 1.3 77.2 - - + +
233A GLY* 1.3 56.7 + - - +
234A LYS* 3.8 22.0 + - + +
256A VAL* 4.7 3.4 - - + -
257A PRO* 4.1 26.7 - - + -
259A HIS* 6.4 0.7 - - + -
260A ILE* 4.5 12.6 - - + -
268A ILE* 5.7 0.9 - - + -
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Residues in contact with GLY 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A HIS* 3.1 17.4 + - - -
132A LYS* 4.0 17.6 - - - +
133A ALA* 3.4 24.7 - - - +
229A THR 2.9 17.6 + - - -
231A LEU 3.6 1.2 - - - -
232A VAL* 1.3 76.8 - - - +
234A LYS* 1.3 61.5 + - - +
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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
------------------------------------------------------------
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