Contacts of the helix formed by residues 219 - 232 (chain S) in PDB entry 1I84
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 GLU 219 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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202S LYS* 3.3 38.4 + - - +
218S GLY* 1.3 77.2 - - - -
220S LEU* 1.3 62.1 + - - +
221S GLU* 3.2 0.8 + - - -
222S LYS* 3.1 23.5 - - - +
223S GLN* 3.8 11.4 + - - +
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Residues in contact with LEU 220 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219S GLU* 1.3 77.5 - - - +
221S GLU* 1.3 63.0 + - - +
222S LYS 2.8 5.2 - - - -
223S GLN* 2.9 25.3 + - + +
224S LEU* 2.8 30.0 + - + +
262S ILE* 4.8 9.0 - - + +
263S VAL* 3.2 36.3 - - - +
264S GLY* 4.4 5.8 - - - +
265S ALA* 6.3 0.4 - - + -
449S ALA 3.4 25.8 - - - +
450S LEU* 4.4 8.7 - - - +
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Residues in contact with GLU 221 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195S ALA* 3.7 21.9 - - + +
199S SER* 3.0 36.3 - - - -
200S SER* 3.4 13.7 + - - +
217S TYR* 4.2 6.0 - - + +
218S GLY* 2.8 34.8 - - - +
219S GLU 3.2 1.6 + - - -
220S LEU* 1.3 76.7 + - - +
222S LYS* 1.3 62.6 + - - +
224S LEU* 3.8 11.8 - - - +
225S LEU* 3.2 28.8 + - - +
262S ILE* 4.0 27.3 - - + +
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Residues in contact with LYS 222 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216S SER* 3.9 7.8 - - - +
217S TYR* 2.8 54.1 + - + +
218S GLY 3.3 11.7 + - - +
219S GLU* 3.1 18.4 + - + +
221S GLU* 1.3 78.8 - - - +
223S GLN* 1.3 61.8 + - + +
225S LEU* 3.3 18.9 - - - +
226S GLN* 3.4 11.6 + - - +
341S ILE* 4.2 15.9 - - + +
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Residues in contact with GLN 223 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219S GLU 4.4 9.7 - - - +
220S LEU* 2.9 27.6 + - + +
222S LYS* 1.3 77.4 - - + +
224S LEU* 1.3 54.1 + - - +
225S LEU 2.6 15.1 + - - -
226S GLN* 2.6 19.9 + - - +
227S ALA* 3.0 12.8 + - - +
341S ILE* 3.4 26.9 - - + +
342S MET* 3.6 31.3 - - - +
449S ALA* 3.6 21.0 - - - +
450S LEU* 4.2 6.5 - - + -
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Residues in contact with LEU 224 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191S ILE* 3.7 37.5 - - + +
195S ALA* 5.3 5.2 - - + -
220S LEU* 2.8 23.5 + - + +
221S GLU* 3.8 10.5 - - - +
222S LYS 3.5 0.2 - - - -
223S GLN* 1.3 71.9 - - - +
225S LEU* 1.3 59.1 + - - +
227S ALA* 4.0 9.9 + - + +
228S ASN* 4.8 3.1 + - - +
252S ILE* 5.2 3.6 - - + -
254S ILE* 4.0 15.9 - - + -
262S ILE* 3.4 38.4 - - + -
264S GLY 5.3 0.7 - - - +
265S ALA* 4.2 23.6 - - + -
450S LEU* 4.4 18.0 - - + +
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Residues in contact with LEU 225 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188S LYS 5.8 0.4 - - - +
191S ILE* 4.5 8.3 - - + -
192S GLN* 4.3 18.4 - - + +
195S ALA* 3.9 24.0 - - + -
217S TYR* 4.2 37.9 - - + +
221S GLU 3.2 11.1 + - - +
222S LYS* 3.3 13.7 - - - +
223S GLN 2.6 0.8 + - - -
224S LEU* 1.3 82.0 - - - +
226S GLN* 1.3 63.4 + - - +
227S ALA 3.3 2.2 - - - -
228S ASN* 4.4 2.9 + - - +
229S PRO* 3.3 16.6 - - - +
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Residues in contact with GLN 226 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222S LYS 3.4 7.0 + - - +
223S GLN* 2.6 12.9 + - - +
225S LEU* 1.3 81.9 + - - +
227S ALA* 1.3 53.9 + - - +
229S PRO* 2.8 30.3 - - - +
230S ILE* 3.1 19.0 - - - +
334S GLU 4.9 2.4 - - - +
337S GLU* 5.9 0.7 - - - +
338S ALA* 3.4 34.2 - - + +
341S ILE* 3.5 36.9 - - + +
342S MET* 4.4 4.5 - - + +
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Residues in contact with ALA 227 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223S GLN 3.0 9.5 + - - +
224S LEU* 4.0 7.0 - - + +
225S LEU 3.3 1.6 - - - -
226S GLN* 1.3 71.7 - - - +
228S ASN* 1.3 56.2 + - - +
229S PRO* 3.0 4.0 - - - -
230S ILE* 2.7 35.0 + - - +
231S LEU* 3.3 8.8 + - + +
267S ILE* 5.1 3.1 - - + -
342S MET* 4.4 12.1 - - - -
446S VAL* 4.1 13.0 - - + -
450S LEU* 3.8 29.4 - - + -
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Residues in contact with ASN 228 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184S THR* 5.0 0.9 - - - +
187S THR* 5.1 2.2 - - - +
188S LYS* 4.5 25.6 - - + +
191S ILE* 4.2 22.2 - - - +
224S LEU 4.8 2.8 + - - +
225S LEU 4.4 3.1 + - - +
227S ALA* 1.3 78.1 - - - +
229S PRO* 1.4 65.5 - - + +
231S LEU* 3.7 9.4 + - - +
232S GLU* 3.1 39.9 + - - +
250S LYS* 3.3 39.8 + - - +
252S ILE* 4.6 6.9 - - - +
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Residues in contact with PRO 229 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188S LYS* 6.1 0.2 - - - -
225S LEU 3.3 11.9 - - - +
226S GLN* 2.8 45.3 - - + +
227S ALA 3.0 4.9 - - - -
228S ASN* 1.4 93.4 - - + +
230S ILE* 1.3 59.1 + - - +
232S GLU* 4.0 15.8 - - + +
233S ALA* 4.1 3.1 + - - +
334S GLU 6.5 0.2 - - - -
335S THR* 4.6 17.1 - - - +
338S ALA* 4.4 7.9 - - + -
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Residues in contact with ILE 230 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226S GLN 3.1 22.0 - - - +
227S ALA 2.7 13.5 + - - +
229S PRO* 1.3 71.5 - - - +
231S LEU* 1.3 72.6 + - + +
232S GLU 2.7 3.5 + - - -
233S ALA* 2.6 37.5 + - - +
234S PHE* 3.8 11.0 + - + -
335S THR* 4.7 2.7 - - - +
338S ALA* 3.7 10.5 - - + -
339S MET* 3.6 36.3 - - + +
342S MET* 3.3 28.9 - - + -
344S PHE* 5.1 2.9 - - + -
442S ILE* 4.0 20.0 - - + -
446S VAL* 4.1 6.1 - - + -
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Residues in contact with LEU 231 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227S ALA* 3.3 11.6 + - + +
228S ASN* 3.7 9.6 + - - +
230S ILE* 1.3 95.1 - - + +
232S GLU* 1.3 61.5 + - + +
233S ALA* 3.1 0.8 + - - -
234S PHE* 3.5 19.4 - - - +
235S GLY* 3.5 9.4 - - - -
236S ASN* 3.6 1.7 - - - +
248S PHE* 3.7 22.8 - - + -
250S LYS* 5.5 7.2 - - + +
267S ILE* 4.0 24.7 - - + -
269S THR* 5.8 0.2 - - - -
439S PHE* 4.5 11.7 - - + -
442S ILE* 4.7 7.6 - - + -
443S LEU* 3.9 32.8 - - + +
446S VAL* 4.1 20.2 - - + -
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Residues in contact with GLU 232 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184S THR* 5.2 4.7 - - + -
188S LYS* 2.7 42.3 + - - +
228S ASN* 3.1 31.2 + - - +
229S PRO* 4.0 13.1 - - + +
230S ILE 2.7 0.6 + - - -
231S LEU* 1.3 75.9 - - - +
233S ALA* 1.3 66.6 + - - +
236S ASN* 2.7 39.6 - - - +
244S ASN* 3.2 33.0 + - - +
246S SER* 5.9 0.2 - - - +
248S PHE* 6.3 0.2 - - + -
250S LYS* 5.4 4.9 - - - +
288S HIS* 4.3 7.0 + - - +
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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