Contacts of the helix formed by residues 221 - 237 (chain C) in PDB entry 5Z7R
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 ASP 221 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219B GLN* 3.5 34.2 + - + +
220C CYS* 1.3 80.4 - - - +
222C ILE* 1.3 66.1 + - + +
223C ASP* 3.0 17.2 + - - +
224C THR* 2.7 45.9 + - - +
225C ALA* 2.9 18.9 + - - +
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Residues in contact with ILE 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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91B ARG* 3.3 37.2 - - - +
94B GLU* 4.3 12.1 - - - +
147B GLN* 3.8 22.4 - - + +
148B ARG* 4.8 7.6 - - + +
151B ARG* 3.6 34.1 - - - +
219B GLN* 2.9 34.5 + - + +
220C CYS 3.6 0.2 + - - -
221C ASP* 1.3 72.3 - - - +
223C ASP* 1.3 58.7 + - - +
225C ALA* 3.0 3.6 + - + +
226C LEU* 2.8 52.6 + - + +
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Residues in contact with ASP 223 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B ARG* 2.8 49.6 + - - +
95B LEU* 5.4 0.7 - - - +
216B ARG* 4.5 6.8 + - - -
219B GLN* 5.9 0.7 - - - +
221C ASP* 3.0 11.2 + - - +
222C ILE* 1.3 78.1 - - - +
224C THR* 1.3 64.9 + - + +
226C LEU* 3.4 7.1 + - - +
227C ALA* 3.1 20.8 + - - +
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Residues in contact with THR 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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220C CYS* 3.3 21.0 - - + +
221C ASP* 2.7 33.9 + - - +
223C ASP* 1.3 76.4 - - + +
225C ALA* 1.3 61.8 + - - +
227C ALA* 3.2 9.2 + - - +
228C PHE* 3.0 21.8 + - - +
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Residues in contact with ALA 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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147B GLN* 3.2 36.4 + - + +
151B ARG* 3.7 7.2 - - - +
217C GLY* 3.5 18.6 - - - +
220C CYS* 4.0 6.7 - - - -
221C ASP 2.9 14.3 + - - +
222C ILE* 3.3 9.4 - - + +
224C THR* 1.3 78.2 + - - +
226C LEU* 1.3 64.1 + - - +
228C PHE* 2.9 16.4 + - - +
229C GLU 3.0 10.0 + - - -
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Residues in contact with LEU 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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87B ASN* 3.4 33.2 + - + +
91B ARG* 4.1 20.9 - - + +
144B GLY* 3.6 21.3 - - - +
147B GLN* 4.0 17.0 - - + -
148B ARG* 3.6 27.4 - - - +
222C ILE* 2.8 33.9 + - + +
223C ASP* 3.8 5.8 - - - +
225C ALA* 1.3 76.3 - - - +
227C ALA* 1.3 62.2 + - - +
229C GLU* 3.3 15.8 + - - +
230C SER* 3.3 14.7 + - - -
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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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84B ILE* 6.0 3.6 - - + -
223C ASP 3.1 13.7 + - - +
224C THR* 3.6 11.9 - - - +
225C ALA 3.1 0.2 - - - -
226C LEU* 1.3 78.2 - - - +
228C PHE* 1.3 61.9 + - - +
230C SER* 3.2 14.0 + - - -
231C GLU* 3.4 23.6 + - - +
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Residues in contact with PHE 228 (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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147B GLN* 5.4 0.4 - - - +
212C GLN* 3.6 36.3 - - + -
213C ALA* 3.8 25.8 - - + -
216C ARG* 3.8 23.1 - - + -
217C GLY* 5.2 5.8 - - - -
224C THR 3.0 11.4 + - - +
225C ALA* 2.9 13.4 + - - +
227C ALA* 1.3 75.1 - - - +
229C GLU* 1.3 65.0 + - - +
231C GLU* 3.1 19.2 + - + +
232C ALA* 3.2 17.4 + - + -
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Residues in contact with GLU 229 (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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87B ASN* 3.1 9.9 + - - -
140B THR* 4.4 1.2 + - - +
141B PRO 3.5 20.1 - - - +
142B GLY* 3.0 15.6 - - - +
144B GLY* 2.6 48.2 + - - -
145B GLY 2.9 0.9 + - - -
146B THR* 2.6 38.3 + - + +
147B GLN* 4.5 1.9 - - + +
213C ALA* 4.7 3.1 - - + -
225C ALA 3.0 10.1 + - - +
226C LEU* 3.3 11.2 - - - +
228C PHE* 1.3 80.2 - - - +
230C SER* 1.3 51.5 + - - +
232C ALA* 3.1 6.9 + - - +
233C PHE* 2.7 35.5 + - - +
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Residues in contact with SER 230 (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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80B ARG* 3.7 17.5 - - - -
83B GLY* 3.2 29.0 + - - -
84B ILE* 3.3 26.3 + - - +
87B ASN* 3.7 10.2 + - - -
142B GLY 4.6 0.7 + - - -
226C LEU 3.3 4.7 + - - -
227C ALA* 3.2 10.3 + - - -
228C PHE 3.2 1.0 - - - -
229C GLU* 1.3 77.8 - - - +
231C GLU* 1.3 63.2 + - - +
233C PHE* 3.6 8.3 - - - +
234C GLY* 3.0 18.2 + - - -
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Residues in contact with GLU 231 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B THR* 5.8 0.3 - - - +
80B ARG* 2.8 48.0 + - - +
84B ILE* 5.0 3.3 - - - +
227C ALA* 3.4 21.3 - - - +
228C PHE* 3.1 10.4 + - - +
230C SER* 1.3 78.2 - - - +
232C ALA* 1.3 56.8 + - - +
234C GLY* 3.7 1.4 + - - -
235C GLU* 3.2 33.5 + - - +
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Residues in contact with ALA 232 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B THR* 4.4 6.5 - - + -
209C LEU* 3.7 30.6 - - + +
212C GLN* 6.3 0.2 - - + -
213C ALA* 4.9 2.5 - - + -
228C PHE* 3.2 19.5 + - + +
229C GLU* 3.1 10.0 + - - +
231C GLU* 1.3 77.1 - - - +
233C PHE* 1.3 68.4 + - - +
235C GLU* 3.2 24.0 + - - +
236C CYS* 3.5 15.1 + - - -
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Residues in contact with PHE 233 (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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71B MET* 3.6 24.9 - - + -
79B GLY 3.4 27.4 - - - -
82B PHE* 4.2 9.9 - + - -
83B GLY* 3.8 22.2 - - - -
139B ILE* 3.8 18.6 - - + -
140B THR* 3.4 39.6 + - - +
141B PRO 4.5 1.1 - - - +
142B GLY* 3.6 21.3 - - - -
143B PHE* 5.3 1.8 - + - -
229C GLU 2.7 19.4 + - - +
230C SER* 3.6 7.2 - - - +
232C ALA* 1.3 71.5 - - - +
234C GLY* 1.3 62.3 + - - +
236C CYS* 2.9 23.1 + - - +
237C PHE* 3.2 22.3 - + - -
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Residues in contact with GLY 234 (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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76B THR* 3.2 43.0 + - - -
80B ARG* 3.8 14.1 - - - -
230C SER 3.0 11.7 + - - -
231C GLU 4.0 1.6 - - - -
233C PHE* 1.3 79.8 - - - +
235C GLU* 1.3 63.0 + - - +
236C CYS 3.0 0.9 + - - -
237C PHE* 3.1 14.2 + - - +
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Residues in contact with GLU 235 (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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76B THR* 4.2 11.6 - - + +
205C VAL* 5.2 1.1 - - + +
209C LEU* 4.0 24.7 - - + +
231C GLU* 3.2 21.8 + - - +
232C ALA* 3.2 19.5 + - - +
234C GLY* 1.3 76.2 - - - +
236C CYS* 1.3 58.8 + - - +
238C SER* 2.6 29.4 + - - +
239C THR* 4.2 3.1 - - - +
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Residues in contact with CYS 236 (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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138B GLY 3.5 15.3 - - - +
139B ILE* 3.7 13.9 - - + -
140B THR* 3.8 31.9 - - - -
205C VAL* 4.7 3.4 - - + -
206C ALA* 4.2 8.7 - - - -
209C LEU* 3.9 12.1 - - - -
232C ALA 3.6 14.8 - - - -
233C PHE 2.9 12.0 + - - +
235C GLU* 1.3 74.6 - - - +
237C PHE* 1.3 56.8 + - - +
238C SER 3.0 4.9 - - - -
239C THR* 2.6 37.0 + - - -
242C GLN* 3.4 7.4 - - - +
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Residues in contact with PHE 237 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B MET* 3.5 48.5 - - + -
74B MET* 3.7 27.9 - - + +
75B ASN* 3.4 24.2 - - - +
76B THR* 3.9 7.6 + - - -
79B GLY* 3.9 17.0 - - - -
139B ILE* 3.8 12.1 - - + -
233C PHE* 3.2 42.6 - + - -
234C GLY 3.1 7.5 + - - +
236C CYS* 1.3 78.2 - - - +
238C SER* 1.3 55.9 + - - +
239C THR 3.2 2.9 + - - +
242C GLN* 3.5 33.9 - - - +
246C MET* 4.3 2.2 - - + -
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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