Contacts of the helix formed by residues 221 - 237 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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219A GLN* 3.6 33.8 + - + +
220B CYS* 1.3 80.7 - - - +
222B ILE* 1.3 58.8 + - + +
223B ASP* 3.1 14.9 + - - +
224B THR* 2.6 46.7 + - - +
225B ALA* 2.9 24.4 + - - +
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Residues in contact with ILE 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A ARG* 3.1 38.8 - - - +
94A GLU* 4.3 12.1 - - - +
147A GLN* 3.9 15.5 - - + -
148A ARG* 4.6 9.4 - - + +
151A ARG* 3.6 39.2 - - - +
219A GLN* 3.0 31.4 + - + +
220B CYS 3.6 0.4 + - - -
221B ASP* 1.3 74.0 - - - +
223B ASP* 1.3 57.2 + - - +
225B ALA* 4.0 2.5 - - - -
226B LEU* 2.8 53.0 + - + +
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Residues in contact with ASP 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A ARG* 2.9 46.7 + - - +
95A LEU* 5.3 1.0 - - - +
216A ARG* 4.2 8.0 + - - -
221B ASP* 3.1 10.6 + - - +
222B ILE* 1.3 76.4 - - - +
224B THR* 1.3 63.5 + - - +
226B LEU* 3.3 6.5 + - - +
227B ALA* 3.0 22.9 + - - +
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Residues in contact with THR 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220B CYS* 3.5 16.9 - - + +
221B ASP* 2.6 39.1 + - - +
223B ASP* 1.3 73.0 - - - +
225B ALA* 1.3 56.0 + - - +
227B ALA* 3.5 7.1 + - - +
228B PHE* 2.9 28.4 + - - +
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Residues in contact with ALA 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A GLN* 3.4 28.0 - - + +
151A ARG* 3.9 7.0 - - - +
217B GLY* 3.3 28.7 - - - +
220B CYS* 3.8 6.9 - - - -
221B ASP 2.9 19.5 + - - +
222B ILE* 3.5 6.1 - - - +
223B ASP 3.2 0.2 - - - -
224B THR* 1.3 76.8 + - - +
226B LEU* 1.3 61.9 - - - +
228B PHE* 3.2 6.8 + - - +
229B GLU 3.1 17.5 + - - -
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Residues in contact with LEU 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A ASN* 3.3 34.7 + - + +
91A ARG* 4.2 17.7 - - + -
144A GLY* 3.6 20.2 - - - -
147A GLN* 4.1 17.5 - - + -
148A ARG* 3.9 21.1 - - - +
222B ILE* 2.8 46.7 + - + +
223B ASP* 3.8 7.4 - - - +
225B ALA* 1.3 73.5 - - - +
227B ALA* 1.3 64.9 + - - +
229B GLU* 3.2 14.0 + - - +
230B SER* 3.3 15.5 + - - -
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Residues in contact with ALA 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A ILE* 5.9 4.3 - - + -
223B ASP 3.0 17.1 + - - +
224B THR* 3.7 8.3 - - - +
226B LEU* 1.3 72.1 - - - +
228B PHE* 1.3 70.8 + - - +
230B SER* 3.1 15.7 + - - +
231B GLU* 3.2 22.9 + - + +
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Residues in contact with PHE 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A GLN* 5.5 0.2 - - - +
212B GLN* 3.8 32.8 - - + -
213B ALA* 4.1 23.1 - - + -
216B ARG* 3.8 26.7 - - + -
217B GLY* 5.2 5.2 - - - -
220B CYS* 6.0 0.9 - - - -
224B THR* 2.9 15.7 + - - +
225B ALA* 3.2 13.4 + - - +
227B ALA* 1.3 78.2 - - - +
229B GLU* 1.3 64.5 + - - +
231B GLU* 3.2 10.9 + - + +
232B ALA* 3.2 22.5 + - + -
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Residues in contact with GLU 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A ASN* 3.1 10.3 + - - -
140A THR* 4.5 1.5 + - - +
141A PRO 3.3 21.3 - - - +
142A GLY* 3.1 16.9 - - - +
144A GLY* 2.9 46.8 + - - -
145A GLY 3.2 0.7 + - - -
146A THR* 2.8 37.7 + - + +
147A GLN* 4.2 1.4 + - + +
213B ALA* 4.6 8.2 - - + +
225B ALA 3.1 11.5 + - - +
226B LEU* 3.2 11.2 + - - +
228B PHE* 1.3 78.6 - - - +
230B SER* 1.3 57.5 + - - +
232B ALA* 2.9 3.9 + - - +
233B PHE* 2.7 28.8 + - + +
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Residues in contact with SER 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A ARG* 3.9 17.3 - - - -
83A GLY* 3.2 26.3 + - - -
84A ILE* 3.3 26.6 + - - +
87A ASN* 3.8 10.4 + - - +
142A GLY 4.6 0.2 + - - -
226B LEU 3.3 5.2 + - - -
227B ALA* 3.1 9.1 + - - -
229B GLU* 1.3 77.5 - - - +
231B GLU* 1.3 60.1 + - - +
233B PHE* 3.4 8.8 - - - +
234B GLY* 2.7 29.1 + - - -
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Residues in contact with GLU 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A ARG* 3.0 47.0 + - - +
84A ILE* 5.1 2.6 - - - +
227B ALA* 3.2 20.3 + - + +
228B PHE* 3.5 11.0 - - + +
230B SER* 1.3 78.3 - - - +
232B ALA* 1.3 62.3 + - - +
234B GLY* 3.5 1.4 + - - -
235B GLU* 3.3 26.6 + - - +
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Residues in contact with ALA 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A THR* 4.7 4.9 - - + -
209B LEU* 3.7 29.9 - - + +
212B GLN* 6.3 0.2 - - + -
213B ALA* 4.9 3.1 - - + -
228B PHE* 3.2 19.3 + - + +
229B GLU* 2.9 11.3 + - + +
231B GLU* 1.3 77.7 - - - +
233B PHE* 1.3 66.4 + - - +
235B GLU* 3.3 25.5 + - - +
236B CYS* 3.4 16.5 + - - -
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Residues in contact with PHE 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A MET* 4.7 4.5 - - - -
79A GLY 3.6 23.8 - - - -
82A PHE* 4.2 15.9 - + - -
83A GLY* 3.9 22.0 - - - -
139A ILE* 3.9 26.7 - - + -
140A THR* 3.2 39.4 + - - +
141A PRO 4.5 1.6 - - - +
142A GLY* 3.7 20.0 - - - -
143A PHE* 5.8 0.9 - + - -
229B GLU 2.7 17.4 + - - +
230B SER* 3.4 7.2 - - - +
232B ALA* 1.3 75.2 - - - +
234B GLY* 1.3 68.4 + - - +
236B CYS* 3.1 20.2 + - - +
237B PHE* 3.4 34.0 - + - -
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Residues in contact with GLY 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A THR* 3.4 41.2 - - - -
79A GLY 4.3 0.7 - - - -
80A ARG* 3.6 15.5 - - - +
230B SER 2.7 17.9 + - - -
231B GLU 3.9 2.0 - - - -
233B PHE* 1.3 72.8 - - - +
235B GLU* 1.3 65.2 + - - +
236B CYS 2.8 1.6 + - - -
237B PHE* 2.9 14.1 + - - +
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Residues in contact with GLU 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A THR* 4.0 12.8 - - + +
205B VAL* 5.6 0.4 - - - +
209B LEU* 3.9 27.5 - - + +
231B GLU* 3.3 20.6 + - - +
232B ALA* 3.3 19.4 + - - +
234B GLY* 1.3 72.8 - - - +
236B CYS* 1.3 60.1 + - - +
238B SER* 2.7 28.4 + - - +
239B THR* 3.9 3.9 - - - +
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Residues in contact with CYS 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138A GLY 3.5 16.2 - - - +
139A ILE* 4.0 13.2 - - + -
140A THR* 3.8 29.8 - - - -
205B VAL* 5.0 2.0 - - - -
206B ALA* 4.4 8.5 - - - -
209B LEU* 3.8 17.3 - - - -
232B ALA 3.6 14.6 - - - -
233B PHE* 3.1 11.1 + - - +
234B GLY 2.8 3.6 + - - -
235B GLU* 1.3 73.8 - - - +
237B PHE* 1.3 58.2 + - - +
238B SER 3.0 5.8 + - - -
239B THR* 3.0 27.8 + - - -
242B GLN* 3.2 9.7 - - - +
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Residues in contact with PHE 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A MET* 3.4 30.7 - - + -
74A MET* 3.5 31.6 - - + +
75A ASN* 3.6 21.6 - - - +
76A THR* 4.0 3.8 + - - -
79A GLY* 3.6 19.5 - - - -
139A ILE* 3.7 20.0 - - + -
233B PHE* 3.4 49.8 - + - -
234B GLY 2.9 6.7 + - - +
236B CYS* 1.3 75.5 - - - +
238B SER* 1.3 57.8 + - - +
239B THR 3.3 1.2 - - - +
242B GLN* 3.3 30.6 - - + +
243B LYS* 6.1 0.5 - - - +
246B MET* 3.9 18.6 - - + -
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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