Contacts of the helix formed by residues 216 - 234 (chain B) in PDB entry 3JW8
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 216 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96B GLU* 4.0 14.5 + - - -
97B ARG* 3.9 20.4 - - - -
98B MSE 4.5 5.4 + - + +
99B VAL* 3.7 11.7 - - + -
182B PRO 3.9 9.0 - - - +
183B ASN* 3.5 46.1 + - - +
184B LEU 3.3 5.8 - - - -
185B SER* 5.1 2.2 - - - -
186B LEU* 4.5 1.1 - - - -
213B ALA* 6.1 5.7 - - - +
214B GLY 3.4 8.8 + - - +
215B LEU* 1.3 77.5 - - - +
217B VAL* 1.3 61.5 + - - +
218B CYS* 4.2 7.2 - - - -
219B PHE* 3.0 10.0 + - + +
220B GLY 2.9 25.1 + - - -
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Residues in contact with VAL 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B ALA* 3.6 29.7 - - + +
177B LEU* 4.0 18.2 - - + -
178B ASN* 3.7 22.0 - - + +
181B LEU 3.9 4.0 - - - +
182B PRO 3.5 8.2 + - - +
184B LEU* 3.0 34.6 + - + +
186B LEU* 3.7 29.7 - - + +
215B LEU 3.8 0.6 + - - -
216B LYS* 1.3 70.5 - - - +
218B CYS* 1.4 62.8 + - - +
220B GLY* 3.3 1.7 + - - -
221B ILE* 3.1 24.6 + - + +
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Residues in contact with CYS 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B VAL* 3.6 33.0 - - - -
100B VAL 5.8 2.9 - - - +
178B ASN* 3.4 26.2 - - - +
182B PRO* 3.0 25.3 + - + +
183B ASN* 3.9 8.5 - - - -
216B LYS* 4.2 3.6 - - - -
217B VAL* 1.4 76.1 - - - +
219B PHE* 1.3 68.6 + - - +
221B ILE* 3.5 7.6 + - - +
222B GLN* 3.3 24.6 + - - +
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Residues in contact with PHE 219 (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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61B ALA* 4.5 3.6 - - + -
90B HIS* 4.4 8.7 - + - -
98B MSE 3.1 56.8 - - + +
99B VAL* 3.8 9.9 - - - -
100B VAL* 3.9 18.8 - - + +
106B PHE* 3.8 24.7 - + - -
133B MSE 3.7 30.3 - - - -
215B LEU* 3.6 21.8 - - + -
216B LYS* 3.0 13.4 + - + +
218B CYS* 1.3 80.2 - - - +
220B GLY* 1.4 58.9 - - - +
222B GLN* 3.1 8.2 + - + +
223B LEU* 2.9 39.4 + - + +
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Residues in contact with GLY 220 (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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186B LEU* 4.7 2.9 - - - -
215B LEU* 3.9 12.0 - - - +
216B LYS 2.9 14.0 + - - -
217B VAL 3.3 4.0 + - - -
219B PHE* 1.4 73.2 - - - +
221B ILE* 1.4 61.8 + - - +
223B LEU* 3.3 7.1 + - - +
224B LEU* 3.0 27.0 + - - +
812B MPD 3.7 26.1 - - - +
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Residues in contact with ILE 221 (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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174B ALA* 3.6 32.5 - - + +
175B LYS* 3.9 33.2 - - + +
178B ASN* 3.5 38.6 - - + -
217B VAL* 3.1 14.0 + - + +
218B CYS* 3.6 8.1 - - - +
220B GLY* 1.4 76.7 - - - +
222B GLN* 1.4 63.4 + - - +
224B LEU* 3.2 14.3 + - + +
225B ASN* 2.9 37.2 + - - +
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Residues in contact with GLN 222 (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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100B VAL* 3.6 35.9 + - + +
101B SER 3.6 13.5 + - - -
102B ASP* 3.4 14.8 + - - +
103B PHE* 3.0 34.5 + - + +
218B CYS 3.3 12.1 + - - +
219B PHE* 3.1 14.1 + - + +
221B ILE* 1.4 83.1 - - - +
223B LEU* 1.3 58.4 + - - +
225B ASN* 2.9 32.1 + - - +
226B ALA 2.9 23.4 + - - -
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Residues in contact with LEU 223 (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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61B ALA* 5.4 0.4 - - + -
103B PHE* 4.0 10.3 - - + -
133B MSE 3.9 35.9 - - + -
158B LEU* 4.0 10.6 - - + +
215B LEU* 3.9 23.6 - - + -
219B PHE* 2.9 25.0 + - + +
220B GLY 3.5 7.9 - - - +
221B ILE 3.2 0.2 - - - -
222B GLN* 1.3 75.6 - - - +
224B LEU* 1.4 58.8 + - - +
226B ALA* 3.3 5.9 + - - +
227B VAL* 3.1 31.5 + - - +
812B MPD 3.7 14.1 - - + -
830B MRD 3.8 41.1 - - + +
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Residues in contact with LEU 224 (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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161B ALA* 4.1 8.1 - - + -
165B SER 4.1 14.1 - - - +
166B ALA* 4.0 26.2 - - + -
170B LYS 5.8 0.4 - - - +
171B VAL* 4.4 20.2 - - + -
174B ALA* 5.2 13.9 - - + -
220B GLY 3.0 18.8 + - - +
221B ILE* 3.2 16.6 + - + +
223B LEU* 1.4 71.5 - - - +
225B ASN* 1.4 66.2 + - - +
227B VAL* 3.1 19.9 - - + +
228B SER* 3.1 12.5 + - - -
812B MPD 3.8 32.1 - - + +
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Residues in contact with ASN 225 (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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102B ASP* 4.2 1.6 + - - -
175B LYS* 5.1 5.4 + - - +
221B ILE* 2.9 23.3 + - - +
222B GLN* 2.9 41.2 + - - +
224B LEU* 1.4 73.5 - - - +
226B ALA* 1.4 65.6 + - - +
228B SER* 3.2 6.9 + - - -
229B ARG* 2.9 59.0 + - - +
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Residues in contact with ALA 226 (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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103B PHE* 3.6 47.5 - - + -
136B ALA* 4.5 5.8 - - + -
140B LEU* 4.3 1.3 - - + +
158B LEU* 4.5 10.1 - - + -
222B GLN 2.9 8.7 + - - +
223B LEU* 3.3 10.5 + - - +
225B ASN* 1.4 75.3 - - - +
227B VAL* 1.3 53.8 + - - +
229B ARG* 3.2 7.5 + - - +
230B VAL* 2.7 39.1 + - - +
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Residues in contact with VAL 227 (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 LEU* 3.7 34.5 - - + -
159B VAL 3.8 16.8 - - - +
160B LEU* 3.8 13.7 - - - -
161B ALA* 4.0 25.1 - - + +
166B ALA* 5.9 0.4 - - + -
223B LEU 3.1 16.2 + - - +
224B LEU* 3.1 26.2 - - + +
226B ALA* 1.3 76.6 - - - +
228B SER* 1.3 58.5 + - - +
230B VAL* 3.4 4.3 + - - +
231B GLU* 3.0 29.6 + - - +
812B MPD 4.3 4.0 - - + -
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Residues in contact with SER 228 (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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224B LEU 3.1 17.9 + - - -
225B ASN* 3.6 8.1 - - - -
227B VAL* 1.3 77.1 - - - +
229B ARG* 1.4 60.8 + - - +
231B GLU* 3.5 10.0 + - - +
232B ARG* 2.3 69.1 + - - +
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Residues in contact with ARG 229 (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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102B ASP* 2.8 43.2 + - - -
103B PHE* 3.8 8.5 - - - +
104B HIS* 3.5 20.6 - - - +
140B LEU* 3.6 26.2 - - + +
225B ASN* 2.9 44.1 + - - +
226B ALA* 3.6 3.8 - - - +
228B SER* 1.4 73.4 - - - +
230B VAL* 1.4 66.3 + - - +
231B GLU 3.4 0.2 + - - -
232B ARG* 3.4 25.1 + - - +
233B ALA* 3.0 23.0 + - - +
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Residues in contact with VAL 230 (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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136B ALA* 3.9 33.7 - - + +
139B ILE* 4.3 15.3 - - + -
140B LEU* 3.9 18.2 - - + -
158B LEU 4.2 2.7 - - - +
159B VAL* 4.1 28.0 - - + +
226B ALA 2.7 23.5 + - - +
227B VAL* 3.4 5.4 + - - +
229B ARG* 1.4 74.1 - - - +
231B GLU* 1.3 63.2 + - - +
233B ALA* 3.1 4.9 + - - +
234B LEU* 3.0 43.2 + - + +
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Residues in contact with GLU 231 (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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159B VAL 5.0 2.9 + - - +
227B VAL 3.0 17.2 + - - +
228B SER* 3.6 10.7 - - - +
229B ARG 3.3 0.2 - - - -
230B VAL* 1.3 78.2 - - - +
232B ARG* 1.4 65.9 + - - +
234B LEU* 3.6 12.1 + - + +
235B PRO* 3.5 16.8 - - - +
259B LEU* 5.9 6.3 - - + -
263B LEU* 5.5 6.4 - - + +
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Residues in contact with ARG 232 (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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228B SER* 2.3 49.3 + - - +
229B ARG* 3.7 31.6 - - - +
230B VAL 3.3 0.4 - - - -
231B GLU* 1.4 81.7 + - + +
233B ALA* 1.3 60.6 + - - +
235B PRO* 3.6 10.5 - - - +
236B LYS* 3.8 23.0 - - - +
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Residues in contact with ALA 233 (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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139B ILE* 4.5 7.4 - - + -
140B LEU* 4.2 11.7 - - + -
143B ALA* 3.7 28.3 - - + +
229B ARG 3.0 17.3 + - - +
230B VAL* 3.1 5.4 + - - +
232B ARG* 1.3 77.3 - - - +
234B LEU* 1.3 64.8 + - - +
236B LYS* 3.1 20.9 + - - +
237B LEU* 3.2 12.9 + - - +
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Residues in contact with LEU 234 (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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139B ILE* 4.4 5.6 - - + -
159B VAL* 4.5 10.3 - - + -
230B VAL* 3.0 36.6 + - + +
231B GLU* 4.0 8.7 - - + +
233B ALA* 1.3 73.2 - - - +
235B PRO* 1.4 65.5 - - + +
236B LYS 2.9 5.9 + - - -
237B LEU* 2.9 27.5 + - + +
259B LEU* 4.4 13.9 - - + -
260B LEU* 3.4 45.3 - - + -
263B LEU* 3.9 31.2 - - + -
264B ALA* 3.4 13.0 - - - +
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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