Contacts of the helix formed by residues 217 - 234 (chain A) in PDB entry 1J3H
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 LYS 217 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158A HIS* 3.3 66.5 + - + +
161A ASP* 5.0 10.6 + - - +
162A LEU 5.4 0.2 - - - +
163A ILE* 3.3 27.2 - - + +
191A VAL 5.9 2.2 - - - -
192A LYS 5.5 6.1 - - - -
216A ASN* 1.3 86.6 - - + +
218A ALA* 1.3 62.2 - - - +
219A VAL 3.1 1.3 - - - -
220A ASP* 3.1 13.3 + - - +
221A TRP* 4.0 6.0 + - + +
282A GLY 5.6 4.7 - - - +
283A ASN* 4.4 7.0 - - - +
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Residues in contact with ALA 218 (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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208A GLU* 4.6 1.6 - - - +
216A ASN* 2.8 19.0 + - - +
217A LYS* 1.3 77.9 - - - +
219A VAL* 1.3 64.9 + - - +
220A ASP 3.1 0.2 - - - -
221A TRP* 3.1 15.9 + - + +
222A TRP 3.1 18.0 + - - -
277A LEU* 5.7 3.6 - - + -
280A ARG* 3.5 24.3 + - + +
283A ASN* 3.5 31.2 - - + +
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Residues in contact with VAL 219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A ILE* 5.2 2.2 - - + -
165A ARG* 4.4 22.2 - - + -
204A TYR 4.9 3.0 - - - +
206A ALA* 4.4 7.2 - - + +
208A GLU* 3.9 13.9 - - - +
209A ILE* 3.6 28.7 - - + -
215A TYR* 3.5 38.8 - - + -
216A ASN 3.0 10.3 + - - +
218A ALA* 1.3 78.8 - - - +
220A ASP* 1.3 60.1 + - - +
222A TRP* 3.4 7.8 + - - +
223A ALA* 3.0 27.6 + - + +
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Residues in contact with ASP 220 (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 PHE* 3.3 35.9 - - + -
158A HIS* 3.0 21.9 - - - +
163A ILE* 3.8 6.9 - - - +
164A TYR* 2.9 30.3 + - - +
165A ARG* 2.8 31.6 + - - +
166A ASP 4.4 1.2 + - - -
167A LEU* 5.1 1.7 + - - +
217A LYS 3.1 10.1 + - - +
219A VAL* 1.3 77.3 - - - +
221A TRP* 1.3 59.0 + - - +
223A ALA* 3.5 5.4 + - - +
224A LEU* 3.0 22.0 + - - +
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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
----------------------------------------------------------
151A VAL* 3.9 31.4 - - + -
154A PHE* 3.8 31.6 - + + -
158A HIS* 3.6 22.5 - + - -
217A LYS* 4.0 15.4 - - + +
218A ALA* 3.1 13.9 + - - +
220A ASP* 1.3 75.2 - - - +
222A TRP* 1.3 69.2 + - - +
224A LEU* 3.2 37.9 + - + +
225A GLY* 3.1 14.6 + - - -
272A LEU* 4.1 18.0 - - + +
280A ARG* 4.5 4.9 - - - -
281A PHE 3.7 17.0 - - - +
282A GLY* 3.8 33.5 + - - -
288A VAL* 4.2 25.4 - - + +
291A ILE* 4.7 8.1 - - + -
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Residues in contact with TRP 222 (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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203A GLU 5.0 0.4 + - - -
204A TYR 3.4 17.5 + - - -
205A LEU 3.4 14.4 + - - -
206A ALA* 3.3 20.9 - - + -
207A PRO* 3.6 24.5 - - + -
218A ALA 3.1 11.4 + - - +
219A VAL 3.6 7.4 - - - +
221A TRP* 1.3 76.3 - - - +
223A ALA* 1.3 56.1 + - - +
225A GLY* 2.7 25.1 + - - -
226A VAL* 3.2 23.2 + - + +
238A PHE* 3.4 35.6 - + - -
250A ILE* 3.9 11.4 - - - -
253A GLY* 5.4 5.8 - - - -
272A LEU 4.0 9.9 - - - -
273A LEU* 3.6 42.7 - - + +
274A GLN 3.7 12.3 - - - -
275A VAL* 3.9 3.4 - - + -
280A ARG* 3.6 27.2 - - - +
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Residues in contact with ALA 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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167A LEU* 3.8 33.1 - - + +
204A TYR* 3.9 17.3 - - + +
219A VAL* 3.0 15.7 + - + +
220A ASP* 3.7 7.6 - - - +
222A TRP* 1.3 84.7 - - - +
224A LEU* 1.3 52.4 + - - +
226A VAL* 3.0 8.3 + - - +
227A LEU* 2.7 35.0 + - - +
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Residues in contact with LEU 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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147A ALA* 4.5 7.6 - - + -
150A ILE* 3.8 32.5 - - + -
151A VAL* 4.1 15.0 - - + -
154A PHE* 4.7 0.4 - - + -
167A LEU* 3.6 12.5 - - + +
220A ASP 3.0 15.5 + - - +
221A TRP* 3.3 39.3 - - + +
222A TRP 3.2 0.2 - - - -
223A ALA* 1.3 76.0 - - - +
225A GLY* 1.3 57.6 + - - +
227A LEU* 3.3 3.3 + - + -
228A ILE* 2.8 46.6 + - + +
231A MET* 5.8 0.7 - - + -
272A LEU* 4.0 20.9 - - + -
291A ILE* 4.7 3.6 - - + -
297A PHE* 5.9 1.8 - - + -
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Residues in contact with GLY 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 3.1 5.1 + - - -
222A TRP 2.7 11.7 + - - -
224A LEU* 1.3 74.7 - - - +
226A VAL* 1.3 65.2 + - - -
228A ILE 3.0 1.9 + - - -
229A TYR* 2.8 26.0 + - - +
269A LEU* 3.6 10.3 - - - +
272A LEU* 4.1 22.8 - - - +
273A LEU* 4.0 13.5 - - - -
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Residues in contact with VAL 226 (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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203A GLU 3.3 26.0 - - - +
204A TYR* 3.3 27.6 - - + -
222A TRP* 3.2 34.2 + - + +
223A ALA* 3.0 7.5 + - - +
225A GLY* 1.3 72.4 - - - +
227A LEU* 1.3 57.0 + - - +
229A TYR* 3.6 1.9 - - - +
230A GLU* 3.0 27.9 + - - +
236A PRO* 4.8 4.5 - - + -
237A PRO* 3.8 29.4 - - + +
238A PHE* 4.8 2.7 - - + -
273A LEU* 3.6 11.0 - - + +
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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
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128A MET* 5.3 1.3 - - - -
132A LEU* 6.5 0.4 - - + -
150A ILE* 4.5 9.0 - - + -
167A LEU* 3.8 26.7 - - + -
168A LYS* 4.4 2.0 - - - -
169A PRO* 3.5 37.9 - - + -
172A LEU* 3.4 30.3 - - + -
204A TYR* 4.4 5.4 - - + -
223A ALA 2.7 19.3 + - - +
224A LEU* 3.6 6.7 - - + +
226A VAL* 1.3 72.3 - - - +
228A ILE* 1.3 63.6 + - - +
230A GLU* 3.3 7.0 + - + +
231A MET* 3.0 44.4 + - + +
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Residues in contact with ILE 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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143A ALA* 4.7 3.0 - - + +
147A ALA* 3.6 22.0 - - + -
224A LEU* 2.8 44.7 + - + +
225A GLY 3.7 2.9 - - - +
227A LEU* 1.3 68.8 - - - +
229A TYR* 1.3 68.9 + - - +
231A MET* 3.5 11.2 + - + +
232A ALA* 3.3 19.4 + - - +
265A LEU* 3.7 20.6 - - + -
268A LEU* 5.3 4.3 - - + -
269A LEU* 3.7 19.3 - - + -
272A LEU* 5.1 4.9 - - + -
296A TRP* 4.3 18.4 - - + -
297A PHE* 5.7 0.4 - - + -
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Residues in contact with TYR 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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225A GLY 2.8 16.1 + - - +
226A VAL 3.6 3.6 - - - +
228A ILE* 1.3 81.2 - - - +
230A GLU* 1.3 55.3 + - - +
232A ALA* 3.7 0.2 - - - -
233A ALA* 2.8 44.9 + - + +
235A TYR* 3.3 31.7 - + - -
236A PRO 3.9 1.1 - - - -
237A PRO* 3.4 42.3 + - + +
255A VAL* 5.2 3.4 - - + -
256A ARG 2.8 23.6 + - - -
257A PHE* 3.7 26.0 - + - -
258A PRO* 3.5 13.0 - - + +
261A PHE* 3.7 8.3 - + - -
269A LEU* 3.5 30.5 - - + +
273A LEU* 4.7 4.7 - - + -
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Residues in contact with GLU 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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129A PHE* 5.7 2.8 - - - -
132A LEU* 3.7 23.7 - - + +
169A PRO* 4.1 13.4 - - - +
204A TYR* 2.8 38.1 + - - -
226A VAL 3.0 12.9 + - - +
227A LEU* 3.3 6.8 + - + +
229A TYR* 1.3 79.6 - - - +
231A MET* 1.3 57.1 + - + +
234A GLY* 2.8 29.0 + - - +
235A TYR* 3.5 17.0 - - - +
236A PRO* 3.7 32.4 - - + +
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Residues in contact with MET 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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128A MET* 3.8 23.6 - - - +
132A LEU* 4.2 13.7 - - + +
137A ARG* 3.7 4.9 - - - -
138A PHE* 2.8 35.9 + - + +
143A ALA* 3.8 29.8 - - + +
146A TYR* 3.7 37.5 - - + -
147A ALA* 4.1 11.7 - - + +
150A ILE* 5.9 0.9 - - + -
172A LEU* 6.1 0.2 - - + -
224A LEU* 5.8 0.4 - - + -
227A LEU* 3.0 41.5 + - + +
228A ILE* 3.8 16.4 - - + +
229A TYR 3.2 0.2 - - - -
230A GLU* 1.3 78.8 - - - +
232A ALA* 1.3 59.3 + - - +
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Residues in contact with ALA 232 (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* 3.2 26.4 - - - +
138A PHE 3.7 14.5 - - - +
140A GLU* 4.8 8.5 - - + -
143A ALA* 4.4 10.7 - - + +
228A ILE* 3.3 12.0 + - + +
229A TYR 3.1 1.6 + - - -
231A MET* 1.3 78.4 - - - +
233A ALA* 1.3 59.3 + - - +
260A HIS* 3.4 7.8 + - - +
261A PHE* 3.7 18.4 - - + -
265A LEU* 3.9 16.8 - - + -
296A TRP* 6.0 0.4 - - + -
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Residues in contact with ALA 233 (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* 2.7 31.9 + - - +
229A TYR* 2.8 41.7 + - + +
232A ALA* 1.3 78.7 - - - +
234A GLY* 1.3 58.4 + - - +
235A TYR* 3.3 21.1 - - + +
258A PRO* 3.9 9.0 - - + -
261A PHE* 3.6 15.0 - - + -
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Residues in contact with GLY 234 (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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132A LEU* 5.0 6.8 - - - +
136A GLY 3.3 26.9 - - - +
137A ARG* 4.0 3.6 - - - -
230A GLU* 2.8 21.6 + - - +
232A ALA 3.7 1.2 - - - -
233A ALA* 1.3 72.3 - - - +
235A TYR* 1.3 67.4 + - - +
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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