Contacts of the helix formed by residues 214 - 227 (chain H) in PDB entry 5IC4
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 TRP 214 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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206H TRP* 3.4 54.4 + + + +
208H ASN* 4.4 7.8 - - + +
212H GLY 4.4 7.9 - - - -
213H SER* 1.3 74.7 - - - +
215H PHE* 1.3 57.6 + - - +
217H GLN* 3.6 3.1 - - - +
218H SER* 2.7 33.5 + - - -
243H VAL* 4.2 10.1 - - + -
247H PHE* 3.3 57.4 - + + -
248H GLU* 3.9 6.1 - - - -
249H SER* 3.6 34.3 - - - -
259H LYS 3.9 9.6 - - - -
261H GLN* 3.8 26.7 - - + +
1L ASP* 3.5 26.9 + - - -
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Residues in contact with PHE 215 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159G ILE* 3.6 25.8 - - + -
160G ILE 4.3 3.1 - - - -
161G GLN* 3.3 14.4 + - - +
196H ALA* 3.7 31.6 - - + -
197H TYR 3.8 11.7 - - - -
198H SER* 3.5 28.5 - - - +
213H SER 3.3 0.6 - - - -
214H TRP* 1.3 79.8 - - - +
216H ILE* 1.3 69.9 + - + +
218H SER* 3.3 1.9 + - - -
219H LEU* 2.8 42.3 + - + +
236H LEU* 5.2 3.1 - - + -
239H VAL* 3.7 25.6 - - + -
240H ASN* 5.3 0.7 - - - -
243H VAL* 4.0 6.9 - - - +
261H GLN* 4.2 5.4 - - - +
263H PRO* 3.9 20.4 - - + -
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Residues in contact with ILE 216 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70G ASP* 3.6 22.2 - - + +
73G ASN* 5.3 0.9 - - + -
74G LEU* 3.7 37.7 - - + -
117G VAL* 4.7 0.4 - - + -
119G LEU* 3.7 27.6 - - + -
159G ILE* 4.1 17.7 - - + -
161G GLN* 3.9 10.3 - - + +
213H SER* 3.2 20.9 + - - +
215H PHE* 1.3 89.6 - - + +
217H GLN* 1.3 66.5 + - - +
219H LEU* 3.7 4.0 - - + +
220H CYS* 3.0 27.7 + - - -
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Residues in contact with GLN 217 (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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70G ASP* 4.4 3.3 + - - +
73G ASN* 4.5 12.9 + - - +
208H ASN* 4.5 2.6 - - - +
211H ASP* 3.4 39.7 - - - +
212H GLY 2.8 26.7 + - - -
213H SER 3.0 21.0 + - - +
214H TRP* 3.6 6.1 - - - +
216H ILE* 1.3 77.5 - - - +
218H SER* 1.3 57.0 + - - +
220H CYS* 3.8 2.3 - - - +
221H ALA* 3.0 28.9 + - - +
242H LYS* 5.5 1.6 - - - -
247H PHE* 4.2 23.6 - - + -
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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
----------------------------------------------------------
214H TRP 2.7 21.8 + - - -
215H PHE 3.8 2.7 - - - -
217H GLN* 1.3 74.2 - - - +
219H LEU* 1.3 59.5 + - - +
221H ALA* 3.3 1.4 + - - +
222H MET* 2.8 35.9 + - - +
239H VAL* 4.1 8.1 - - - -
242H LYS* 3.6 29.8 - - - +
243H VAL* 3.5 20.5 - - - +
247H PHE* 3.5 16.8 - - - -
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Residues in contact with LEU 219 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74G LEU* 4.5 15.3 - - + -
159G ILE* 3.6 46.0 - - + -
215H PHE* 2.8 29.6 + - + +
216H ILE* 3.7 7.2 - - + +
218H SER* 1.3 73.0 - - - +
220H CYS* 1.3 58.4 + - - +
222H MET* 4.0 0.7 - - - +
223H LEU* 2.9 53.5 + - + +
232H PHE* 4.8 4.7 - - + -
235H ILE* 5.4 1.1 - - + -
236H LEU* 3.7 29.2 - - + -
239H VAL* 3.8 17.0 - - + +
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Residues in contact with CYS 220 (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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73G ASN* 3.4 45.5 - - - +
74G LEU* 3.7 26.7 - - - -
77G THR* 3.4 32.0 + - - +
216H ILE* 3.0 19.9 + - - +
217H GLN 3.8 0.2 - - - +
219H LEU* 1.3 74.2 - - - +
221H ALA* 1.3 60.7 + - - +
223H LEU* 3.7 1.4 - - - +
224H LYS* 2.9 30.8 + - - +
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Residues in contact with ALA 221 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217H GLN 3.0 18.6 + - - +
218H SER* 3.5 8.1 - - - +
220H CYS* 1.3 76.9 - - - +
222H MET* 1.3 76.3 + - + +
224H LYS* 3.3 9.4 + - - +
225H GLN* 3.1 23.6 + - - +
242H LYS* 4.4 9.2 - - - -
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Residues in contact with MET 222 (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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218H SER 2.8 22.6 + - - +
221H ALA* 1.3 77.8 - - + +
223H LEU* 1.3 61.1 - - - +
225H GLN* 3.9 16.8 - - - +
226H TYR* 2.8 57.2 + - + +
235H ILE* 3.9 13.3 - - + +
238H ARG* 3.9 17.9 - - - +
239H VAL* 3.6 35.7 - - + +
242H LYS* 3.7 28.7 - - + +
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Residues in contact with LEU 223 (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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77G THR* 3.7 29.8 - - + -
78G PHE* 3.9 26.9 - - + -
81G LEU* 4.3 12.1 - - + -
219H LEU* 2.9 39.4 + - + +
220H CYS* 3.7 1.3 - - - +
222H MET* 1.3 77.1 - - - +
224H LYS* 1.3 63.0 + - - +
227H ALA* 3.0 34.0 + - + +
232H PHE* 4.3 7.9 - - + -
235H ILE* 4.2 15.9 - - + -
275H PHE* 4.0 29.4 - - + -
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Residues in contact with LYS 224 (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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77G THR* 4.8 6.2 - - + +
220H CYS 2.9 19.0 + - - +
221H ALA* 3.6 7.9 - - - +
222H MET 3.3 0.2 - - - -
223H LEU* 1.3 77.5 - - - +
225H GLN* 1.3 59.6 + - - +
227H ALA* 4.9 0.7 + - - +
228H ASP* 5.2 2.4 - - - +
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Residues in contact with GLN 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 ALA 3.1 15.0 + - - +
222H MET* 3.9 13.7 - - - +
224H LYS* 1.3 79.0 - - - +
226H TYR* 1.3 106.4 + - + +
227H ALA 3.8 0.4 - - - -
228H ASP* 3.8 3.5 - - - +
229H LYS* 3.3 25.1 + - - +
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Residues in contact with TYR 226 (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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222H MET* 2.8 47.1 + - + +
225H GLN* 1.3 121.0 + - + +
227H ALA* 1.3 58.2 + - - +
228H ASP 3.0 6.5 - - - -
229H LYS* 2.8 22.1 + - + -
230H LEU* 2.8 56.8 + - + +
235H ILE* 3.8 11.1 - - + +
238H ARG* 3.7 38.3 + - + -
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Residues in contact with ALA 227 (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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81G LEU* 3.7 29.4 - - + -
222H MET 4.1 0.4 + - - -
223H LEU* 3.0 26.4 + - + +
224H LYS 4.9 0.6 + - - -
225H GLN 3.8 0.6 - - - -
226H TYR* 1.3 76.1 - - - +
228H ASP* 1.3 55.8 + - + +
229H LYS 3.4 0.9 - - - -
230H LEU 4.4 3.2 - - - +
235H ILE* 3.9 11.6 - - - +
275H PHE* 3.7 25.3 + - + +
276H TYR* 3.4 17.0 - - - -
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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