Contacts of the helix formed by residues 220 - 234 (chain B) in PDB entry 5JJA
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 GLY 220 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171B PHE* 3.3 19.8 + - - -
179B ARG* 3.9 2.2 - - - -
218B HIS* 3.2 12.8 + - - -
219B ASN* 1.3 79.0 - - - +
221B ILE* 1.3 65.1 + - - +
222B ALA 3.3 2.2 - - - -
223B GLU* 3.3 17.2 + - - +
224B LEU* 3.1 26.9 + - - +
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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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207B ILE* 4.8 1.8 - - + -
208B PHE* 3.9 32.8 - - + -
211B PHE* 3.9 32.1 - - + -
218B HIS* 3.7 40.1 + - + +
219B ASN 3.8 1.4 - - - -
220B GLY* 1.3 75.2 - - - +
222B ALA* 1.3 64.1 + - - +
224B LEU* 3.2 3.6 + - - +
225B LEU* 2.9 34.2 + - + +
254B LEU* 4.6 7.4 - - + -
263B TYR* 3.7 33.7 - - + -
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Residues in contact with ALA 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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219B ASN 5.5 0.2 + - - -
220B GLY 3.3 0.4 - - - -
221B ILE* 1.3 78.5 - - - +
223B GLU* 1.3 66.8 + - - +
225B LEU* 3.3 1.8 + - - +
226B GLU* 3.0 25.7 + - - +
262B VAL* 4.3 12.2 - - + +
263B TYR* 3.8 25.3 - - + +
266B GLN* 3.5 32.7 - - - +
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Residues in contact with GLU 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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171B PHE* 4.2 18.2 - - + -
176B PRO* 5.0 2.9 - - - +
179B ARG* 3.1 54.3 + - + +
180B ASP* 4.8 1.0 + - - +
183B LYS* 4.1 20.4 - - + +
219B ASN 3.9 1.2 - - - +
220B GLY* 3.3 23.0 - - - +
221B ILE 3.3 0.6 - - - -
222B ALA* 1.3 81.4 - - - +
224B LEU* 1.3 63.6 + - - +
226B GLU* 3.2 12.0 + - - +
227B ILE* 3.2 24.9 + - - +
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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
----------------------------------------------------------
168B LEU* 4.1 16.8 - - + -
171B PHE* 3.6 35.2 - - + -
186B LEU* 4.5 2.7 - - + -
204B ILE* 4.3 20.3 - - + +
207B ILE* 4.1 25.1 - - + -
208B PHE* 3.9 28.7 - - + -
218B HIS* 4.2 12.8 - - + -
220B GLY 3.1 19.3 + - - +
221B ILE* 3.6 6.5 - - + +
223B GLU* 1.3 77.0 - - - +
225B LEU* 1.3 57.1 + - - +
227B ILE* 3.2 8.6 + - + +
228B LEU* 3.0 28.8 + - - +
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Residues in contact with LEU 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B PHE* 3.7 27.6 - - + -
221B ILE* 2.9 24.3 + - + +
222B ALA 3.7 3.8 - - - +
224B LEU* 1.3 72.8 - - - +
226B GLU* 1.3 62.0 + - - +
228B LEU* 3.2 4.8 + - + -
229B GLY* 2.8 25.8 + - - -
251B LEU* 3.8 22.7 - - + -
254B LEU* 4.0 6.3 - - + -
263B TYR* 3.7 34.5 - - + +
266B GLN* 3.8 12.7 - - + +
267B LEU* 3.8 22.4 - - + +
270B CYS* 3.3 17.6 - - - -
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Residues in contact with GLU 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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183B LYS* 3.5 38.1 + - + +
222B ALA 3.0 13.4 + - - +
223B GLU* 3.2 12.5 + - - +
225B LEU* 1.3 76.3 - - - +
227B ILE* 1.3 63.3 + - - +
229B GLY* 3.3 10.2 + - - -
230B SER* 3.4 9.0 + - - -
266B GLN* 4.5 21.4 + - + +
269B TYR* 6.5 0.7 - - - -
668D LYS* 4.1 18.4 - - - +
669D LEU* 3.9 19.2 + - + +
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Residues in contact with ILE 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B PHE* 4.1 7.4 - - + -
183B LYS* 3.6 34.3 - - + +
186B LEU* 3.8 33.2 - - + +
187B HIS* 4.6 14.6 - - + -
190B TYR* 5.5 3.4 - - + -
200B ILE* 6.0 0.9 - - + -
204B ILE* 5.1 9.0 - - + -
223B GLU 3.2 14.0 + - - +
224B LEU* 3.2 10.3 + - + +
226B GLU* 1.3 76.2 - - - +
228B LEU* 1.3 62.4 + - - +
230B SER* 2.7 24.7 + - - +
231B ILE* 3.2 24.1 + - + +
669D LEU* 3.9 16.4 - - + -
672D ILE* 5.9 0.2 - - + -
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Residues in contact with LEU 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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201B ARG* 5.3 12.3 - - + +
204B ILE* 3.9 22.7 - - + -
205B ASN* 6.1 0.9 - - - +
208B PHE* 3.3 37.9 - - + -
224B LEU 3.0 13.3 + - - +
225B LEU* 3.2 14.3 + - + +
227B ILE* 1.3 77.2 - - - +
229B GLY* 1.3 51.8 + - - +
231B ILE* 3.1 22.3 + - + +
232B ILE* 2.7 45.5 + - + +
235B PHE* 6.4 0.9 - - + -
246B PHE* 3.5 29.6 - - + -
251B LEU* 4.9 0.2 - - + -
270B CYS* 4.2 7.0 - - - -
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Residues in contact with GLY 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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225B LEU 2.8 18.6 + - - -
226B GLU* 3.3 3.8 + - - -
227B ILE 3.2 0.8 - - - -
228B LEU* 1.3 73.1 - - - +
230B SER* 1.3 56.0 + - - +
232B ILE* 3.5 5.0 + - - +
233B ASN* 3.1 29.3 + - - +
269B TYR* 3.8 29.5 - - - -
270B CYS* 3.8 12.1 - - - -
273B GLN* 4.7 0.6 - - - +
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Residues in contact with SER 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B HIS* 3.4 22.1 + - - -
226B GLU 3.4 5.5 + - - -
227B ILE 2.7 19.3 + - - -
229B GLY* 1.3 76.0 - - - +
231B ILE* 1.3 64.1 + - - +
233B ASN* 3.8 3.2 - - - +
234B GLY 3.6 6.8 + - - -
269B TYR* 5.6 0.7 - - - -
669D LEU* 4.0 18.2 - - - -
670D ASP 3.3 23.6 - - - -
671D PRO* 3.4 8.4 - - - +
672D ILE* 3.0 23.0 + - - +
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Residues in contact with ILE 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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190B TYR* 3.6 58.3 - - + +
200B ILE* 5.7 1.8 - - + -
201B ARG* 4.6 7.9 - - + -
204B ILE* 5.7 1.6 - - + -
227B ILE* 3.2 30.7 + - + +
228B LEU* 3.1 24.8 + - + +
230B SER* 1.3 82.7 + - - +
232B ILE* 1.3 64.5 + - - +
234B GLY* 3.1 12.3 + - - -
235B PHE* 3.4 34.3 + - + -
672D ILE* 3.9 11.9 - - + +
674D GLU* 5.8 0.2 - - - +
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Residues in contact with ILE 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 LEU* 2.7 31.9 + - + +
229B GLY 4.0 3.1 - - - +
231B ILE* 1.3 71.8 - - + +
233B ASN* 1.3 62.7 + - - +
235B PHE* 3.1 43.8 + - + +
246B PHE* 4.6 5.6 - - + -
251B LEU* 4.3 3.8 - - + -
270B CYS* 3.7 32.8 - - + +
273B GLN* 3.7 24.5 - - + +
274B PHE* 3.6 44.6 - - + +
277B LYS* 3.5 8.3 - - + -
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Residues in contact with ASN 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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229B GLY 3.1 17.7 + - - +
230B SER* 3.8 8.3 - - - +
231B ILE 3.3 0.2 - - - -
232B ILE* 1.3 78.2 - - - +
234B GLY* 1.3 56.5 + - - +
269B TYR* 3.9 11.3 + - - +
273B GLN* 3.0 34.8 + - - +
277B LYS* 2.8 21.0 + - - +
671D PRO* 3.2 25.9 - - + +
673D ILE* 6.0 0.3 - - - +
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Residues in contact with GLY 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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230B SER 3.6 3.8 + - - -
231B ILE 3.1 7.9 + - - -
233B ASN* 1.3 77.8 - - - +
235B PHE* 1.3 65.9 + - - +
236B ALA* 3.5 0.7 + - - +
277B LYS* 4.1 0.4 - - - -
671D PRO* 4.7 0.6 - - - +
672D ILE 3.3 21.3 - - - -
673D ILE* 3.7 16.8 - - - +
674D GLU* 2.9 25.1 + - - +
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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