Contacts of the helix formed by residues 214 - 227 (chain C) in PDB entry 4QUG
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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2B ASP* 3.6 21.0 + - - -
206C TRP* 3.3 44.6 + + + +
207C ARG 4.9 0.2 - - - +
208C ASN* 4.6 6.4 - - + +
212C GLY 4.6 2.2 - - - -
213C SER* 1.3 74.8 - - - +
215C PHE* 1.3 58.5 + - - +
217C GLN* 3.6 6.9 - - - +
218C SER* 2.8 34.4 + - - -
243C VAL* 4.3 10.5 - - + -
247C PHE* 3.4 54.4 - + + -
248C GLU* 3.7 8.5 - - - -
249C SER* 3.4 36.8 - - - -
259C LYS 3.7 7.6 - - - -
261C GLN* 3.7 44.2 - - + +
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Residues in contact with PHE 215 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159C ILE* 3.9 20.2 - - + -
160C ILE 4.3 3.6 - - - -
161C GLN* 3.5 15.2 + - + +
196C ALA* 3.6 37.9 - - + -
197C TYR 3.8 4.5 - - - -
198C SER* 3.4 31.0 - - - -
213C SER* 3.2 1.0 - - - -
214C TRP* 1.3 80.9 - - - +
216C ILE* 1.3 63.7 + - + +
218C SER* 3.2 1.9 + - - -
219C LEU* 2.7 46.0 + - + +
236C LEU* 5.1 4.0 - - + -
239C VAL* 3.8 25.1 - - + -
240C ASN* 5.5 0.2 - - - -
243C VAL* 4.0 7.0 - - + -
261C GLN* 4.3 7.1 - - - +
263C PRO* 3.8 23.1 - - + -
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Residues in contact with ILE 216 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70C ASP* 3.5 30.1 - - + +
73C ASN* 4.9 2.2 - - + +
74C LEU* 3.6 37.2 - - + -
119C LEU* 4.0 10.8 - - + -
159C ILE* 4.2 18.4 - - + -
161C GLN* 3.9 14.1 - - + -
213C SER* 3.2 21.0 + - - +
215C PHE* 1.3 89.4 - - + +
217C GLN* 1.3 65.7 + - - +
219C LEU* 4.2 7.6 - - + -
220C CYS* 3.0 29.9 + - - -
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Residues in contact with GLN 217 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70C ASP* 4.3 1.7 + - - +
73C ASN* 4.4 13.6 + - - +
208C ASN* 4.4 2.0 - - - +
211C ASP* 3.3 41.5 + - - +
212C GLY* 2.8 26.1 + - - -
213C SER 3.0 23.1 + - - +
214C TRP* 3.6 7.4 - - - +
216C ILE* 1.3 78.2 - - - +
218C SER* 1.3 61.2 + - - +
220C CYS* 4.1 1.7 - - - +
221C ALA* 3.2 23.6 + - - +
242C LYS* 5.3 1.3 - - - -
247C PHE* 3.9 28.2 - - + -
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Residues in contact with SER 218 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214C TRP 2.8 20.0 + - - -
215C PHE 3.6 3.1 - - - -
217C GLN* 1.3 75.2 - - - +
219C LEU* 1.3 61.7 + - - +
221C ALA* 3.3 1.4 + - - +
222C MET* 2.9 34.3 + - - +
239C VAL* 4.0 9.4 - - - -
242C LYS* 3.5 26.9 - - - +
243C VAL* 3.6 17.1 - - - +
247C PHE* 3.2 23.2 - - - -
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Residues in contact with LEU 219 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74C LEU* 4.5 9.6 - - + -
159C ILE* 3.6 42.8 - - + -
215C PHE* 2.7 29.1 + - + +
216C ILE* 3.8 13.2 - - + +
218C SER* 1.3 74.0 - - - +
220C CYS* 1.3 57.3 + - - +
222C MET* 3.4 1.0 + - - +
223C LEU* 2.9 55.7 + - + +
232C PHE* 4.8 5.8 - - + -
235C ILE* 5.3 1.1 - - + -
236C LEU* 3.7 29.8 - - + -
239C VAL* 3.7 17.4 - - + +
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Residues in contact with CYS 220 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73C ASN* 3.4 44.9 - - - +
74C LEU* 3.8 27.1 - - - -
77C THR* 3.3 32.9 + - - +
216C ILE* 3.0 17.9 + - - +
217C GLN 4.1 0.2 - - - +
219C LEU* 1.3 76.9 - - - +
221C ALA* 1.3 58.4 + - - +
223C LEU* 3.4 1.4 + - - +
224C LYS* 2.9 31.4 + - - +
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Residues in contact with ALA 221 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217C GLN 3.2 18.1 + - - +
218C SER 3.3 4.2 + - - +
220C CYS* 1.3 77.7 - - - +
222C MET* 1.3 59.0 + - - +
224C LYS* 3.4 7.5 + - - +
225C GLN* 3.0 30.6 + - - +
242C LYS* 4.1 19.3 - - + -
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Residues in contact with MET 222 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218C SER 2.9 19.4 + - - +
219C LEU 3.9 0.2 - - - +
221C ALA* 1.3 72.7 - - + +
223C LEU* 1.3 61.4 + - - +
225C GLN* 4.4 7.0 - - - +
226C TYR* 2.8 65.7 + - + +
235C ILE* 3.9 12.9 - - + +
238C ARG* 3.7 28.7 - - + +
239C VAL* 3.6 27.8 - - + +
242C LYS* 3.7 28.5 - - + +
246C GLU* 5.9 0.4 - - - +
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Residues in contact with LEU 223 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77C THR* 3.7 28.7 - - + -
78C PHE* 4.0 23.6 - - + -
81C LEU* 4.3 14.0 - - + +
219C LEU* 2.9 43.2 + - + +
220C CYS* 4.8 0.4 - - - -
222C MET* 1.3 77.2 - - - +
224C LYS* 1.3 63.4 + - - +
227C ALA* 2.9 31.3 + - + +
232C PHE* 4.1 8.3 - - + -
235C ILE* 4.0 20.4 - - + -
275C PHE* 3.9 28.5 - - + -
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Residues in contact with LYS 224 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77C THR* 4.8 6.7 - - + +
80C ASN* 5.9 5.8 - - - +
220C CYS 2.9 18.4 + - - +
221C ALA* 3.7 7.9 - - - +
223C LEU* 1.3 79.0 - - - +
225C GLN* 1.3 60.9 + - - +
227C ALA* 4.7 1.0 + - - +
228C ASP* 5.2 1.9 - - - +
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Residues in contact with GLN 225 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221C ALA 3.0 16.7 + - - +
222C MET* 4.4 8.1 - - - +
224C LYS* 1.3 80.0 - - - +
226C TYR* 1.3 99.3 + - + +
227C ALA 3.8 0.4 - - - -
228C ASP* 3.7 4.0 - - - +
229C LYS* 3.5 29.3 + - - +
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Residues in contact with TYR 226 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222C MET* 2.8 54.3 + - + +
225C GLN* 1.3 107.9 + - + +
227C ALA* 1.3 58.1 + - - +
228C ASP 3.1 3.4 - - - -
229C LYS* 2.9 26.7 + - + -
230C LEU* 2.8 53.1 + - + -
235C ILE* 3.7 11.8 - - + +
238C ARG* 2.8 40.4 + - + -
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Residues in contact with ALA 227 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81C LEU* 3.5 30.7 - - + -
223C LEU* 2.9 27.1 + - + +
224C LYS 4.7 0.4 + - - -
225C GLN 3.8 0.6 - - - -
226C TYR* 1.3 75.8 - - - +
228C ASP* 1.3 56.1 + - - +
229C LYS 3.3 1.1 - - - -
230C LEU 4.4 2.8 - - - +
235C ILE* 3.8 11.2 - - - +
275C PHE* 3.9 25.3 + - + +
276C TYR* 3.3 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