Contacts of the helix formed by residues 21 - 34 (chain O) in PDB entry 3TDD
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 LYS 21 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21O ASP* 1.3 197.1 + + + +
218O GLY* 1.3 58.4 - - - +
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Residues in contact with GLY 218 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21O LYS* 1.3 128.6 - - - +
73O ASP* 4.7 2.8 - - - +
219O PRO* 1.3 74.2 - - - +
220O ARG 3.9 0.3 + - - -
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Residues in contact with PRO 219 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21O ASN* 2.9 79.4 + - + +
69O LEU* 5.5 4.3 - - + -
72O PRO* 3.3 37.0 - - + +
73O ASP* 4.1 0.9 - - - +
218O GLY* 1.3 83.8 - - - +
220O ARG* 1.3 59.5 + - - +
221O PHE* 4.2 13.2 - - + +
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Residues in contact with ARG 220 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21O ASN* 3.7 39.7 + - + +
72O PRO 3.0 4.8 + - - -
73O ASP* 3.0 22.3 + - - +
141O HIS* 3.0 53.1 + - - -
147O PHE* 4.4 6.5 - - - -
214O ILE* 5.5 0.2 - - - +
215O ILE* 3.4 11.2 - - + -
216O GLY* 2.7 61.0 + - - +
217O ASP* 3.3 24.7 + - - +
219O PRO* 1.3 74.2 - - - +
221O PHE* 1.3 61.4 + - - +
222O ARG* 3.6 2.9 + - - +
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Residues in contact with PHE 221 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21O ASN* 4.3 4.0 - - - +
48O ILE* 4.9 1.3 - - + -
67O VAL* 4.2 10.1 - - + -
68O SER 4.0 6.1 - - - -
69O LEU* 3.8 42.1 - - + +
71O THR 4.5 3.1 - - - +
72O PRO 3.1 20.1 + - - +
73O ASP* 4.5 0.2 - - - +
74O ILE 3.9 2.0 - - - -
75O GLY* 3.6 26.9 - - - -
213O ALA* 4.0 25.8 - - + -
214O ILE 3.4 8.5 - - - -
215O ILE* 3.6 26.4 - - + +
219O PRO* 4.2 16.0 - - + +
220O ARG* 1.3 78.6 - - - +
222O ARG* 1.3 61.5 + - - +
223O LYS* 4.0 19.3 - - + -
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Residues in contact with ARG 222 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21O LEU* 3.6 53.3 - - + +
213O ALA* 3.4 2.4 - - - -
214O ILE* 2.8 57.5 + - + +
220O ARG 3.6 1.3 + - - +
221O PHE* 1.3 77.1 - - - +
223O LYS* 1.3 72.8 + - - +
224O LEU* 3.8 19.5 + - - +
228O GLU* 3.2 28.6 + - - -
232O ARG* 5.5 6.7 - - - +
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Residues in contact with LYS 223 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52O LYS* 6.2 0.9 - - - +
65O SER* 3.4 12.6 + - - +
67O VAL* 3.2 23.2 + - + +
211O GLU* 2.6 44.2 + - - +
212O LEU 3.7 12.1 - - - +
213O ALA* 3.8 11.9 - - + -
221O PHE* 4.0 13.7 - - + -
222O ARG* 1.3 83.3 - - - +
224O LEU* 1.3 75.6 + - - +
225O THR* 3.8 4.7 + - - +
228O GLU* 4.1 2.8 - - - +
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Residues in contact with LEU 224 (chain O).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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190O ILE* 4.6 20.9 - - + -
212O LEU* 2.8 46.9 + - + +
214O ILE* 4.5 12.8 - - + -
222O ARG* 3.8 29.1 + - - +
223O LYS* 1.3 89.5 - - - +
225O THR* 1.3 63.6 + - - +
228O GLU* 3.2 16.4 - - + +
229O ILE* 4.1 24.0 - - + +
232O ARG* 4.6 21.3 - - - +
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Residues in contact with THR 225 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223O LYS 4.8 3.4 - - - +
224O LEU* 1.3 74.7 - - - +
226O SER* 1.3 65.5 + - - +
227O GLN* 3.2 9.2 + - - +
228O GLU* 2.7 47.1 + - - +
229O ILE* 3.2 26.0 + - - +
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Residues in contact with SER 226 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208O GLY* 3.2 27.0 + - - -
209O ASP* 2.7 32.9 + - - -
225O THR* 1.3 74.7 - - - +
227O GLN* 1.3 62.5 + - - +
229O ILE* 3.3 4.9 + - - +
230O ASN* 3.0 29.6 + - - -
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Residues in contact with GLN 227 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225O THR* 3.1 8.0 + - - +
226O SER* 1.3 75.4 - - - +
228O GLU* 1.3 66.4 + - + +
229O ILE 2.8 6.0 + - - -
230O ASN* 2.9 25.7 + - - +
231O ASP* 2.7 51.9 + - - +
234O GLU* 5.4 1.2 + - - -
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Residues in contact with GLU 228 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222O ARG* 3.2 33.2 + - - -
223O LYS 4.1 2.3 - - - +
224O LEU* 3.2 19.4 - - + +
225O THR* 2.7 53.2 + - - +
227O GLN* 1.3 76.5 - - + +
229O ILE* 1.3 61.7 - - - +
231O ASP* 3.7 10.5 - - - +
232O ARG* 2.7 44.5 + - - +
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Residues in contact with ILE 229 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194O LEU* 4.5 18.5 - - + +
207O ASN 4.4 2.0 - - - +
208O GLY* 3.6 23.3 - - - +
210O ILE* 3.8 35.4 - - + +
212O LEU* 4.3 18.6 - - + +
224O LEU* 4.1 20.9 - - + +
225O THR 3.2 16.4 + - - +
226O SER 3.4 7.9 - - - +
227O GLN 2.8 1.4 + - - -
228O GLU* 1.3 76.5 - - - +
230O ASN* 1.3 66.2 + - - +
232O ARG* 3.0 9.7 + - - +
233O LEU* 3.0 30.7 + - + +
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Residues in contact with ASN 230 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207O ASN* 3.5 13.5 - - - +
208O GLY 2.9 21.9 + - - +
209O ASP* 4.9 4.6 + - - -
226O SER* 3.0 31.6 + - - -
227O GLN* 2.9 19.7 + - - +
229O ILE* 1.3 76.5 - - - +
231O ASP* 1.3 65.2 + - - +
233O LEU* 2.8 24.6 + - - +
234O GLU* 3.2 17.7 + - - +
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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