Contacts of the helix formed by residues 216 - 231 (chain N) in PDB entry 6CET
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 216 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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733D VAL* 4.6 1.4 - - - +
734D PRO* 5.1 19.7 - - + +
735D GLY 6.0 1.1 - - - +
556M HIS* 4.6 26.4 - - - +
209N ILE* 3.8 1.6 - - - -
215N VAL* 1.3 78.4 - - - +
217N LEU* 1.3 70.6 + - - +
218N ASN* 3.5 9.1 + - + +
219N LEU* 3.2 30.1 + - + +
220N VAL* 3.0 29.8 + - - +
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Residues in contact with LEU 217 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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518M HIS* 6.1 1.3 - - + -
171N GLU* 3.5 49.1 - - + +
206N ILE* 5.7 2.7 - - + -
209N ILE* 3.8 22.4 - - + +
216N GLU* 1.3 85.1 - - - +
218N ASN* 1.3 58.4 + - - +
220N VAL* 3.3 6.5 - - + +
221N ARG* 2.9 50.6 + - - +
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Residues in contact with ASN 218 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216N GLU* 3.5 6.9 + - + +
217N LEU* 1.3 80.4 - - - +
219N LEU* 1.3 60.6 + - + +
221N ARG* 3.3 38.0 + - - +
222N ILE* 3.0 33.9 + - - +
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Residues in contact with LEU 219 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374D LEU* 3.6 50.7 - - + +
733D VAL* 3.7 33.2 - - + +
735D GLY 4.8 4.5 - - - +
737D CYS* 5.0 11.0 - - - +
192N THR* 6.2 0.7 - - + -
215N VAL* 5.4 2.5 - - + -
216N GLU* 3.2 30.0 + - + +
217N LEU 3.2 0.6 - - - -
218N ASN* 1.3 80.7 - - + +
220N VAL* 1.3 57.5 + - - +
222N ILE* 3.3 7.4 - - + +
223N ALA* 3.0 29.2 + - - +
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Residues in contact with VAL 220 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196N ILE* 4.6 25.6 - - + -
205N HIS* 3.4 30.1 - - + +
208N LYS* 5.6 6.5 - - + -
209N ILE* 3.7 20.9 - - + -
213N ALA* 5.5 1.1 - - + -
215N VAL* 3.7 18.3 - - + +
216N GLU 3.0 11.8 + - - +
217N LEU* 3.3 15.7 - - - +
219N LEU* 1.3 75.7 - - - +
221N ARG* 1.3 58.0 + - - +
223N ALA* 3.8 5.3 - - - +
224N ILE* 2.9 31.5 + - + +
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Residues in contact with ARG 221 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169N ALA* 3.4 34.7 + - + +
170N GLN* 4.4 12.0 - - - +
171N GLU* 5.2 4.2 - - + +
205N HIS* 5.0 5.6 - - + -
217N LEU* 2.9 38.8 + - + +
218N ASN* 3.3 34.2 + - - +
220N VAL* 1.3 78.1 - - + +
222N ILE* 1.3 57.2 + - - +
224N ILE* 3.2 9.9 - - + +
225N GLN* 3.0 29.6 + - - +
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Residues in contact with ILE 222 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374D LEU* 3.8 22.2 - - + -
419D PHE* 5.2 13.9 - - + -
218N ASN* 3.0 26.9 + - - +
219N LEU* 3.3 10.3 - - + +
221N ARG* 1.3 74.3 - - - +
223N ALA* 1.3 62.8 + - - +
225N GLN* 3.2 17.9 + - + +
226N ASN* 3.0 39.3 + - - +
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Residues in contact with ALA 223 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374D LEU* 4.0 15.0 - - + -
419D PHE 5.9 2.5 - - - +
420D THR* 5.6 3.6 - - + +
192N THR* 4.9 11.4 - - - +
193N THR* 5.1 11.1 - - + +
196N ILE* 5.2 9.2 - - + -
219N LEU 3.0 18.6 + - - +
220N VAL* 3.8 7.9 - - - +
222N ILE* 1.3 78.3 - - - +
224N ILE* 1.3 57.5 + - - +
226N ASN* 3.2 10.5 + - - +
227N LEU* 3.0 29.4 + - - +
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Residues in contact with ILE 224 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169N ALA* 4.3 14.8 - - + -
170N GLN 5.8 0.9 - - - +
173N ASP* 5.7 0.9 - - - +
175N PRO* 3.6 39.0 - - + -
196N ILE* 5.7 3.5 - - + +
200N ILE* 6.3 3.4 - - + -
205N HIS* 4.2 22.9 - - + +
208N LYS* 5.7 2.0 - - + -
220N VAL* 2.9 19.1 + - + +
221N ARG* 3.2 20.0 - - + +
223N ALA* 1.3 75.0 - - - +
225N GLN* 1.3 59.3 + - - +
227N LEU* 3.2 19.7 + - + +
228N LEU* 2.9 36.9 + - + +
232N VAL* 5.3 2.2 - - + -
234N THR* 5.7 3.6 - - + -
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Residues in contact with GLN 225 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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416D CYS* 5.6 4.3 - - - -
166N PRO* 4.1 20.5 + - + +
167N PRO 3.0 29.8 + - - +
168N VAL* 4.4 4.8 - - - +
169N ALA* 4.7 14.7 + - + +
221N ARG* 3.0 19.3 + - - +
222N ILE* 3.5 20.6 - - + +
223N ALA 3.2 0.4 - - - -
224N ILE* 1.3 77.9 - - - +
226N ASN* 1.3 59.7 + - - +
228N LEU* 3.3 13.5 + - + +
229N TYR* 2.9 25.5 + - - +
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Residues in contact with ASN 226 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374D LEU* 5.5 0.4 - - - +
416D CYS* 3.9 18.7 - - - -
417D ASN 4.7 1.7 + - - +
418D SER* 3.7 22.3 - - - +
419D PHE* 3.2 32.4 + - - +
420D THR* 4.2 16.2 - - + +
222N ILE* 3.0 32.6 + - - +
223N ALA* 3.2 10.7 + - - +
225N GLN* 1.3 77.0 - - - +
227N LEU* 1.3 63.9 + - - +
229N TYR* 3.1 9.1 + - - +
230N TYR* 3.1 27.9 + - - -
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Residues in contact with LEU 227 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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420D THR* 5.5 6.1 - - + -
177N PHE* 5.6 5.2 - - + -
189N TRP* 4.9 19.5 - - + -
193N THR* 5.3 10.1 - - + -
196N ILE* 4.6 20.0 - - + -
197N LEU* 4.6 16.4 - - + -
200N ILE* 5.3 6.7 - - + -
223N ALA 3.0 16.6 + - - +
224N ILE* 3.2 22.6 + - + +
226N ASN* 1.3 76.8 - - - +
228N LEU* 1.3 53.9 + - - +
230N TYR* 3.0 6.8 + - + +
231N GLY 2.6 34.9 + - - +
232N VAL* 3.2 29.6 + - + +
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Residues in contact with LEU 228 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166N PRO* 5.3 2.2 - - + +
167N PRO* 4.4 30.0 - - + +
168N VAL 5.7 0.2 - - - +
169N ALA* 4.5 15.0 - - + -
224N ILE* 2.9 23.8 + - + +
225N GLN* 3.5 15.5 - - + +
226N ASN 3.3 0.2 - - - -
227N LEU* 1.3 72.4 - - - +
229N TYR* 1.3 64.4 - - - +
230N TYR 3.4 4.5 + - - -
232N VAL* 3.3 43.4 + - + +
233N VAL* 4.2 0.4 - - - -
234N THR* 3.6 38.4 - - + +
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Residues in contact with TYR 229 (chain N).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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416D CYS* 4.4 26.1 + - + +
418D SER* 4.8 9.4 - - - -
162N GLN* 5.0 8.0 + - - +
163N ARG* 2.9 42.0 + - + +
164N PRO 3.2 30.5 - - - +
165N ASP* 4.5 2.4 + - - -
166N PRO* 3.8 30.5 - - + +
225N GLN 2.9 13.2 + - - +
226N ASN* 3.1 15.5 + - - +
228N LEU* 1.3 77.6 - - - +
230N TYR* 1.3 81.4 + + - +
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Residues in contact with TYR 230 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418D SER* 3.3 27.3 + - - -
420D THR* 3.9 27.5 + - - -
422D ARG* 4.4 32.8 - - + +
163N ARG* 3.0 42.0 + - - +
226N ASN 3.1 22.3 + - - +
227N LEU* 3.0 12.1 + - + +
228N LEU 4.2 3.4 - - - +
229N TYR* 1.3 96.3 - + - +
231N GLY* 1.3 58.9 + - - +
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Residues in contact with GLY 231 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177N PHE* 3.6 22.5 - - - -
178N THR* 3.6 21.4 + - - +
179N LYS* 5.3 8.3 - - - +
227N LEU* 2.6 16.6 + - - +
228N LEU 4.3 0.2 + - - -
230N TYR* 1.3 79.1 - - - +
232N VAL* 1.3 60.2 + - - +
233N VAL* 5.6 0.7 - - - -
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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