Contacts of the helix formed by residues 217 - 236 (chain H) in PDB entry 4DVQ
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 SER 217 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211H LEU* 3.6 16.6 - - - +
215H SER 3.4 2.9 + - - -
216H PRO* 1.3 75.4 - - - +
218H SER* 1.3 59.6 + - - +
219H ALA* 3.1 12.2 + - - +
220H SER* 3.0 28.4 + - - -
221H LEU* 2.9 29.1 + - - +
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Residues in contact with SER 218 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217H SER* 1.3 74.1 - - - +
219H ALA* 1.3 62.9 + - - +
221H LEU* 4.3 8.5 - - - +
222H ASN* 3.2 37.6 + - - -
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Residues in contact with ALA 219 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217H SER* 3.1 9.3 + - - +
218H SER* 1.3 82.6 + - - +
220H SER* 1.3 57.6 + - - +
222H ASN* 3.8 4.9 - - - +
223H PHE* 3.0 27.1 + - - +
266H TYR* 4.1 20.3 - - + -
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Residues in contact with SER 220 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194H HIS* 2.9 26.7 + - - -
197H ILE* 4.1 10.2 - - - +
211H LEU* 3.5 27.2 - - - +
217H SER* 3.0 28.5 + - - -
219H ALA* 1.3 74.3 - - - +
221H LEU* 1.3 63.4 + - - +
223H PHE* 3.4 8.2 + - - +
224H LEU* 3.1 27.9 + - - +
266H TYR* 4.7 5.3 - - - -
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Residues in contact with LEU 221 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194H HIS* 4.2 10.1 - - - +
216H PRO* 3.6 37.2 - - + +
217H SER 2.9 20.3 + - - +
218H SER* 4.3 7.2 - - - +
220H SER* 1.3 76.4 + - - +
222H ASN* 1.3 60.6 + - - +
224H LEU* 3.3 11.2 + - + +
225H HIS* 3.0 28.3 + - - +
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Residues in contact with ASN 222 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218H SER* 3.2 25.6 + - - +
219H ALA* 3.8 5.7 - - - +
221H LEU* 1.3 76.8 - - - +
223H PHE* 1.3 64.4 + - - +
225H HIS* 4.0 6.7 + - - +
226H ALA* 3.1 24.9 + - - +
262H CYS* 3.6 19.4 - - - -
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Residues in contact with PHE 223 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197H ILE* 4.2 19.3 - - + -
219H ALA 3.0 18.7 + - - +
220H SER* 3.5 8.7 - - - +
221H LEU 3.2 0.2 - - - -
222H ASN* 1.3 76.5 - - - +
224H LEU* 1.3 62.4 + - - +
226H ALA* 3.3 5.9 + - - +
227H LEU* 3.0 43.1 + - + +
262H CYS* 5.0 2.9 - - - -
263H ILE* 4.2 30.5 - - + -
266H TYR* 3.8 53.6 - + + -
312H THR* 3.6 23.6 - - + -
313H ALA* 4.3 5.4 - - - -
316H VAL* 3.6 24.5 - - + -
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Residues in contact with LEU 224 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190H PRO* 6.0 1.3 - - + -
193H PHE* 3.5 40.8 - - + -
194H HIS* 3.9 27.8 - - + +
197H ILE* 3.8 12.8 - - + -
220H SER 3.1 15.8 + - - +
221H LEU* 3.3 12.7 + - + +
223H PHE* 1.3 77.7 - - - +
225H HIS* 1.3 63.8 + - - +
227H LEU* 3.2 11.1 + - + +
228H GLU* 3.1 22.3 + - - +
316H VAL* 3.6 20.9 - - + -
317H ASP* 4.9 2.7 - - - +
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Residues in contact with HIS 225 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221H LEU 3.0 17.2 + - - +
222H ASN* 4.0 8.1 - - - +
224H LEU* 1.3 76.5 - - - +
226H ALA* 1.3 58.5 + - - +
228H GLU* 3.0 20.8 + - - +
229H VAL* 2.9 50.0 + - + +
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Residues in contact with ALA 226 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222H ASN 3.1 17.6 + - - +
223H PHE* 3.6 4.5 - - - +
225H HIS* 1.3 80.3 + - - +
227H LEU* 1.3 56.9 + - - +
229H VAL* 3.3 2.6 + - - +
230H MET* 2.9 32.4 + - - +
259H ALA* 3.5 29.8 - - - +
262H CYS* 3.8 16.8 - - + -
263H ILE* 4.0 10.1 - - + -
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Residues in contact with LEU 227 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223H PHE* 3.0 49.5 + - + +
224H LEU* 3.2 13.2 + - - +
226H ALA* 1.3 75.3 - - - +
228H GLU* 1.3 61.5 + - - +
230H MET* 3.9 10.9 - - + +
231H PHE* 2.8 38.8 + - + -
263H ILE* 4.1 21.1 - - + -
313H ALA* 3.5 32.1 - - + +
316H VAL* 4.2 10.5 - - + -
317H ASP* 3.4 27.8 - - - +
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Residues in contact with GLU 228 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224H LEU 3.1 11.2 + - - +
225H HIS* 3.0 24.9 + - - +
227H LEU* 1.3 76.3 - - - +
229H VAL* 1.3 59.6 + - + +
231H PHE* 3.4 8.4 + - - +
232H LYS* 3.0 30.7 + - + +
317H ASP* 5.1 4.0 + - - +
486H SER* 5.1 0.5 + - - -
490H ARG* 4.6 20.5 + - - +
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Residues in contact with VAL 229 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225H HIS* 2.9 45.9 + - + +
226H ALA* 3.9 4.0 - - - +
228H GLU* 1.3 74.6 - - + +
230H MET* 1.3 60.9 + - - +
232H LYS* 3.6 6.1 - - + +
233H SER* 2.8 34.2 + - - +
255H GLU* 4.1 36.6 - - + +
259H ALA* 3.7 17.5 - - + -
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Residues in contact with MET 230 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116H TRP* 3.5 15.5 - - + -
226H ALA 2.9 18.0 + - - +
227H LEU* 3.9 9.9 - - + +
229H VAL* 1.3 76.5 - - - +
231H PHE* 1.3 85.1 + - + +
233H SER* 3.2 7.5 + - - -
234H THR* 2.5 54.0 + - - -
256H HIS* 3.6 3.2 + - + -
259H ALA* 3.7 10.5 - - + +
260H TRP* 3.4 56.3 - - + +
263H ILE* 4.0 14.8 - - + -
313H ALA* 5.9 1.6 - - + +
602H 1CA 5.9 1.1 - - + -
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Residues in contact with PHE 231 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116H TRP* 4.3 2.2 - + - -
227H LEU* 2.8 36.0 + - + +
228H GLU* 3.7 6.5 - - - +
230H MET* 1.3 98.5 - - + +
232H LYS* 1.3 67.5 + - - +
234H THR* 2.9 20.4 + - - -
235H VAL* 3.1 5.0 + - - +
313H ALA 5.1 2.2 - - - -
317H ASP* 3.7 35.9 - - + -
486H SER* 3.4 23.3 - - - +
487H PHE* 3.8 29.6 - + + +
488H ILE* 4.1 27.8 - - + -
602H 1CA 4.2 20.9 - - + -
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Residues in contact with LYS 232 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58H GLU 5.1 2.2 + - - -
59H GLN* 3.8 34.2 + - - +
60H GLY* 5.4 1.6 - - - -
62H GLU* 5.1 8.7 + - - -
228H GLU* 3.0 20.0 + - + +
229H VAL* 3.6 7.2 - - + +
231H PHE* 1.3 73.1 - - - +
233H SER* 1.3 64.8 + - - +
235H VAL* 3.0 18.8 + - - +
236H GLN* 3.4 23.0 + - - +
255H GLU* 5.8 4.7 - - - +
486H SER* 3.5 18.9 + - - +
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Residues in contact with SER 233 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229H VAL* 2.8 22.8 + - - -
230H MET* 3.2 1.2 + - - -
232H LYS* 1.3 71.6 - - - +
234H THR* 1.3 66.1 + - - +
236H GLN* 3.2 20.0 + - - +
237H LEU* 3.4 18.9 - - - +
252H VAL* 3.9 19.5 - - - -
255H GLU* 4.4 12.3 - - - -
256H HIS* 2.7 44.1 + - - +
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Residues in contact with THR 234 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113H LEU* 4.4 3.1 - - + -
115H PRO* 4.6 3.7 - - + +
116H TRP* 3.0 34.5 + - + +
230H MET* 2.5 32.3 + - - -
231H PHE* 2.9 14.5 + - - -
233H SER* 1.3 72.2 + - - +
235H VAL* 1.3 61.2 + - - +
237H LEU* 3.0 13.9 + - - +
238H MET* 3.2 24.1 + - + +
256H HIS* 3.4 9.6 - - - -
487H PHE* 3.5 33.0 - - + -
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Residues in contact with VAL 235 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55H ILE* 4.0 5.7 - - + +
60H GLY* 4.1 8.7 - - - -
61H TYR* 3.8 37.2 - - + +
231H PHE 3.1 2.7 + - - +
232H LYS* 3.0 10.7 + - - +
234H THR* 1.3 79.8 - - - +
236H GLN* 1.3 56.8 + - - +
237H LEU 3.1 5.0 + - - -
238H MET* 3.7 9.8 + - - -
239H PHE* 3.6 23.4 + - + +
485H TYR* 3.6 18.2 - - + +
486H SER* 3.7 10.8 - - - +
487H PHE* 3.3 36.6 - - + +
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Residues in contact with GLN 236 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55H ILE* 3.9 14.6 - - + +
59H GLN* 3.1 58.2 - - - +
60H GLY* 4.2 1.6 - - - +
232H LYS* 3.4 28.9 + - - +
233H SER* 3.2 14.2 + - - +
234H THR 3.1 1.6 + - - -
235H VAL* 1.3 73.0 - - - +
237H LEU* 1.3 67.5 + - - +
239H PHE* 5.4 0.7 - - - -
240H MET* 5.0 9.2 - - - +
249H SER* 4.7 7.7 + - - +
252H VAL* 3.4 34.5 - - + +
255H GLU* 4.6 6.4 + - - +
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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
------------------------------------------------------------
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