Contacts of the helix formed by residues 216 - 228 (chain B) in PDB entry 1DIZ
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 GLY 216 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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210B GLN* 3.5 14.0 - - - +
215B ILE* 1.3 75.9 - - - +
217B ARG* 1.3 66.4 + - - -
220B ALA 3.1 18.7 + - - -
10C G 2.7 34.9 + - - -
11C C 3.9 9.2 - - - -
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Residues in contact with ARG 217 (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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210B GLN* 3.5 32.5 + - - +
216B GLY* 1.3 71.4 - - - +
218B TRP* 1.3 65.4 + - - +
220B ALA* 3.9 0.5 - - - +
221B ASN* 3.0 44.2 + - - +
236B PRO* 5.6 6.0 - - + +
237B ASP* 3.0 27.7 + - - +
251B ALA* 5.4 11.1 - - - +
254B ARG* 4.4 29.9 - - - +
10C G 3.6 4.6 + - - +
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Residues in contact with TRP 218 (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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120B ALA 3.2 26.0 - - - -
123B GLY* 4.0 15.3 - - - -
124B GLN* 3.8 8.5 - - + -
217B ARG* 1.3 81.5 - - - +
219B THR* 1.3 86.8 + - - +
221B ASN* 3.4 3.4 + - - +
222B TYR* 2.9 66.9 + + + +
235B LEU* 4.0 12.0 - - + +
237B ASP* 3.7 16.5 + - + +
238B ASP* 2.8 47.3 + - + +
272B TRP* 6.1 0.9 - + - -
8C NRI 3.5 20.6 - + - -
9C T 3.5 28.1 + - - -
10C G 3.3 15.7 + - - +
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Residues in contact with THR 219 (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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117B GLY 5.4 0.2 - - - +
120B ALA* 4.0 24.1 - - + +
121B ILE* 4.4 5.4 - - + -
124B GLN* 2.6 32.3 + - - +
215B ILE* 3.7 28.0 - - + -
218B TRP* 1.3 92.2 - - - +
220B ALA* 1.3 58.6 + - - +
222B TYR* 4.0 0.5 - - - +
223B PHE* 2.9 28.8 + - + +
10C G 2.6 18.9 + - - -
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Residues in contact with ALA 220 (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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206B MET* 3.9 31.3 - - + +
209B LEU* 4.0 17.8 - - + +
210B GLN* 4.0 12.3 - - + +
215B ILE* 3.8 6.2 - - + +
216B GLY 3.1 18.1 + - - +
217B ARG 4.1 1.8 - - - +
219B THR* 1.3 74.3 - - - +
221B ASN* 1.3 67.3 + - - +
223B PHE* 3.7 5.5 - - - +
224B ALA* 3.1 23.7 + - - +
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Residues in contact with ASN 221 (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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206B MET* 3.3 28.9 - - - +
210B GLN* 4.8 2.0 - - - +
217B ARG* 3.0 39.0 + - - +
218B TRP* 3.8 2.7 - - - +
220B ALA* 1.3 80.7 - - - +
222B TYR* 1.3 62.5 + - - +
224B ALA* 3.3 4.5 + - - +
225B LEU 3.2 17.7 + - - -
233B VAL* 3.6 14.5 - - + +
234B PHE 2.8 19.2 - - - +
235B LEU* 3.4 21.1 - - + -
236B PRO* 4.3 7.4 - - - +
237B ASP* 4.7 1.0 - - - +
254B ARG* 4.6 10.8 + - - +
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Residues in contact with TYR 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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18B PHE* 4.4 3.8 - + - -
22B ARG* 4.1 15.1 + - - -
116B GLN* 4.3 12.8 - - - -
119B ARG* 5.3 2.5 - - + -
120B ALA* 4.1 20.4 - - + -
123B GLY* 6.1 1.3 - - - -
218B TRP* 2.9 48.5 + + + +
219B THR 4.0 2.5 - - - +
221B ASN* 1.3 74.8 - - - +
223B PHE* 1.3 66.0 + - - +
225B LEU* 3.5 7.2 + - + +
226B ARG* 3.0 63.6 + - + +
235B LEU* 3.8 25.8 - - + +
272B TRP* 4.3 20.2 - + - -
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Residues in contact with PHE 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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113B ALA* 3.1 39.9 - - + -
116B GLN* 4.2 10.5 - - + -
117B GLY* 3.5 26.2 - - - -
120B ALA* 4.6 8.1 - - + -
185B LEU* 5.9 0.4 - - + -
194B LEU* 4.0 26.7 - - + -
195B PRO 4.2 0.2 - - - -
209B LEU* 3.4 22.2 - - + -
219B THR* 2.9 22.5 + - + +
220B ALA* 3.7 5.4 - - - +
222B TYR* 1.3 79.2 - - - +
224B ALA* 1.3 55.2 + - - +
226B ARG* 5.0 1.3 - - - -
227B GLY* 2.5 39.1 + - - +
228B TRP* 3.4 38.0 + + - -
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Residues in contact with ALA 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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202B VAL* 4.5 0.9 - - + -
206B MET* 3.9 14.6 - - - -
220B ALA 3.1 18.3 + - - +
221B ASN 3.3 4.9 + - - +
223B PHE* 1.3 76.7 - - - +
225B LEU* 1.3 63.2 + - - +
228B TRP* 2.9 54.8 + - + +
230B ALA* 3.0 23.1 + - + -
233B VAL* 4.3 3.6 - - + -
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Residues in contact with LEU 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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107B LEU* 3.4 33.8 - - + +
108B PRO* 5.3 0.7 - - + -
221B ASN 3.2 7.7 + - - +
222B TYR* 3.8 12.8 - - + +
224B ALA* 1.3 78.5 - - - +
226B ARG* 1.3 78.8 + - + +
229B GLN* 3.0 22.2 - - - +
230B ALA 3.8 10.5 - - - +
233B VAL* 3.5 18.3 - - + +
235B LEU* 5.1 1.8 - - + -
265B SER* 3.4 33.0 - - - +
268B LEU* 3.6 29.8 - - + -
269B LEU* 4.8 8.3 - - + -
272B TRP* 5.7 0.2 - - + -
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Residues in contact with ARG 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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18B PHE* 3.7 14.5 - - - -
19B LEU* 4.5 9.9 - - - +
22B ARG* 3.9 22.0 - - - +
81B LEU* 5.1 0.4 - - - +
108B PRO* 2.9 35.8 + - - +
109B GLY* 2.8 43.9 + - - -
110B CYS* 3.4 1.4 + - - -
116B GLN* 3.7 36.2 + - + +
119B ARG* 5.0 10.1 - - - +
222B TYR* 3.0 49.2 + - + +
225B LEU* 1.3 95.7 - - + +
227B GLY* 1.3 60.4 + - - +
228B TRP 3.5 0.2 - - - -
229B GLN* 2.9 18.2 + - - -
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Residues in contact with GLY 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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110B CYS* 3.6 19.1 - - - -
113B ALA* 4.1 9.8 - - - +
116B GLN* 3.6 12.1 - - - +
196B MET 4.3 4.5 - - - +
197B THR* 5.3 0.5 - - - -
223B PHE* 2.5 29.4 + - - -
226B ARG* 1.3 74.6 - - - +
228B TRP* 1.3 66.0 + - - +
229B GLN* 3.3 10.6 + - - +
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Residues in contact with TRP 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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195B PRO* 2.7 49.5 + - + +
196B MET 4.5 0.4 - - - -
197B THR* 3.8 15.0 - - - +
198B ILE* 3.6 35.2 - - + +
199B PRO* 3.7 21.8 - - + -
202B VAL* 4.2 11.0 - - + -
205B ALA* 3.6 24.7 - - + -
206B MET* 4.0 13.7 - - + -
209B LEU* 3.9 20.2 - - + -
223B PHE* 3.4 21.8 + + - -
224B ALA* 2.9 41.2 + - + +
227B GLY* 1.3 83.9 - - - +
229B GLN* 1.3 77.0 + - - +
230B ALA* 3.0 2.0 + - + +
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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