Contacts of the helix formed by residues 21 - 32 (chain P) 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 VAL 21 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21P LYS* 4.1 16.2 - - + -
72P ASP* 4.4 9.1 - - - +
73P LYS* 4.1 28.9 + - - +
141P TYR* 3.2 46.2 - - + -
146P TYR* 5.1 1.1 - - + +
215P ILE* 3.5 30.5 - - + -
216P ARG 3.5 4.7 - - - +
219P GLU* 1.3 96.2 - - - +
220P TYR* 1.3 65.2 + - - +
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Residues in contact with TYR 220 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21P VAL* 1.3 81.7 - - - +
214P THR 3.5 1.7 - - - +
215P ILE* 3.3 1.7 - - - -
216P ARG* 2.6 44.9 + - + +
219P GLU 3.9 2.9 + - - +
221P GLN* 1.3 82.2 + - - +
222P LYS* 3.8 33.5 - - + +
223V ASP* 5.2 17.5 - - - -
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Residues in contact with GLN 221 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21P VAL* 5.4 0.2 - - + -
69P LYS* 3.0 43.9 + - - +
71P ASN 3.1 3.7 + - - +
72P ASP* 3.3 23.4 + - - +
73P LYS* 3.6 1.7 - - - -
74P ILE 3.1 46.3 + - - +
75P ALA* 3.6 12.2 - - + +
213P ALA* 6.6 0.2 - - + -
214P THR 3.3 6.5 - - - +
215P ILE* 3.8 18.4 - - + +
220P TYR* 1.3 96.9 - - - +
222P LYS* 1.3 62.0 + - - +
223P ILE* 4.2 4.0 + - + -
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Residues in contact with LYS 222 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213P ALA* 3.0 24.5 - - - +
214P THR* 2.8 25.6 + - - +
220P TYR* 3.8 28.7 - - + +
221P GLN* 1.3 74.9 - - - +
223P ILE* 1.3 61.7 + - - +
224P PHE* 3.3 26.8 + - + +
228P GLU* 2.5 44.6 + - - +
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Residues in contact with ILE 223 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64P THR* 6.0 5.4 - - + +
67P LEU* 4.3 32.3 - - + +
68P TYR 5.1 1.1 - - - -
69P LYS* 4.1 39.0 - - + +
75P ALA* 6.0 3.4 - - + -
211P GLU* 5.9 1.8 - - + +
212P PHE 3.5 10.8 - - - +
213P ALA* 4.2 10.1 - - + -
221P GLN* 4.2 3.1 + - + -
222P LYS* 1.3 76.2 - - - +
224P PHE* 1.3 69.5 - - - +
225P LYS* 3.4 7.1 + - - +
228P GLU* 4.2 2.5 - - - +
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Residues in contact with PHE 224 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190P ILE* 4.5 11.2 - - + -
211P GLU* 5.8 0.2 - - - -
212P PHE* 2.8 41.7 + + + +
213P ALA 4.4 0.4 - - - -
214P THR* 3.5 43.3 - - + -
216P ARG* 6.2 1.8 - - - -
222P LYS* 3.3 32.5 - - + +
223P ILE* 1.3 77.0 - - - +
225P LYS* 1.3 61.7 + - - +
226P PRO* 4.6 0.9 - - - +
228P GLU* 3.2 19.7 - - + -
229P ILE* 3.7 24.9 - - + +
232P ILE* 4.4 24.9 - - + -
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Residues in contact with LYS 225 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223P ILE 4.3 5.4 - - - +
224P PHE* 1.3 75.9 - - - +
226P PRO* 1.3 69.3 - - + +
227P GLN* 4.4 4.7 - - + +
228P GLU* 2.6 56.0 + - + +
229P ILE* 2.9 11.4 + - - +
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Residues in contact with PRO 226 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61P GLN* 3.8 43.7 - - + +
62P ASP* 4.0 33.9 - - - +
207P TYR* 3.2 24.1 - - + -
224P PHE 4.6 0.9 - - - +
225P LYS* 1.3 91.2 - - + +
227P GLN* 1.3 57.0 + - - +
229P ILE* 3.3 7.0 + - + +
230P LYS 3.0 22.5 + - - -
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Residues in contact with GLN 227 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207P TYR* 5.6 0.4 - - - -
225P LYS* 3.1 3.5 - - + +
226P PRO* 1.3 75.7 - - - +
228P GLU* 1.3 62.8 + - + +
230P LYS* 3.1 27.8 + - - +
231P ASP* 2.9 61.6 + - - +
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Residues in contact with GLU 228 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222P LYS* 2.5 34.4 + - - +
223P ILE 4.2 0.7 - - - +
224P PHE* 3.2 15.9 - - + -
225P LYS* 2.6 60.0 + - + +
227P GLN* 1.3 75.2 - - + +
229P ILE* 1.3 57.0 + - - +
231P ASP* 3.4 10.6 + - - +
232P ILE* 3.0 29.0 + - - +
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Residues in contact with ILE 229 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61P GLN* 4.7 3.1 - - - +
194P LEU* 5.8 0.7 - - + -
207P TYR* 4.0 18.6 - - + +
210P LEU* 3.3 54.1 - - + +
211P GLU* 4.0 1.3 - - - -
212P PHE* 4.0 20.9 - - + +
224P PHE* 3.7 29.4 - - + +
225P LYS 2.9 12.5 + - - +
226P PRO* 3.6 11.0 - - + +
228P GLU* 1.3 73.2 - - - +
230P LYS* 1.3 67.9 + - - +
232P ILE* 3.0 12.4 - - + +
233P LEU* 2.9 28.0 + - + +
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Residues in contact with LYS 230 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207P TYR* 3.6 45.7 - - + +
226P PRO 3.0 15.2 + - - +
227P GLN* 3.3 31.6 - - - +
229P ILE* 1.3 78.6 - - - +
231P ASP* 1.3 63.6 + - - +
233P LEU* 3.5 5.9 + - - +
234P VAL* 3.2 26.4 + - + +
239P THR 5.6 0.2 - - - -
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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