Contacts of the strand formed by residues 219 - 225 (chain E) 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 THR 219 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45E HIS* 3.5 20.5 + - - -
214E ILE* 4.1 32.1 - - + +
215E VAL* 3.4 4.8 - - - +
216E GLY* 2.5 38.1 + - - +
218E ASP* 1.3 78.8 + - - +
220E PRO* 1.3 77.3 - - + +
221E PHE 3.4 1.7 + - - -
222E THR* 4.5 4.3 - - + +
224E TYR* 5.4 2.7 - - - +
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Residues in contact with PRO 220 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72E GLU* 3.4 31.2 - - + +
214E ILE 3.9 1.1 - - - +
215E VAL* 5.0 0.2 - - + -
218E ASP 4.4 3.8 - - - +
219E THR* 1.3 86.4 - - + +
221E PHE* 1.3 69.2 + - - +
222E THR* 2.8 32.3 + - + +
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Residues in contact with PHE 221 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48E LEU* 4.4 0.7 - - + -
67E ILE* 3.7 22.0 - - + -
68E ILE 4.0 1.6 - - - -
69E LYS* 3.7 46.0 + - + +
71E ASP 4.1 9.2 - - - +
72E GLU 3.0 17.3 + - - +
74E MET 3.7 6.5 - - - +
75E GLY* 3.1 38.4 - - - -
139E ILE* 3.7 21.8 - - + -
213E ALA* 3.8 9.0 - - + -
214E ILE 3.1 11.0 - - - -
215E VAL* 3.7 23.1 - - + +
219E THR 3.4 4.0 + - - -
220E PRO* 1.3 68.6 - - - +
222E THR* 1.3 64.0 + - - +
223E ILE* 3.6 24.5 - - + -
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Residues in contact with THR 222 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69E LYS* 6.2 0.2 - - - +
213E ALA* 3.3 3.8 - - - +
214E ILE* 2.9 37.2 + - - +
219E THR* 4.5 3.3 - - - +
220E PRO* 2.8 30.7 + - + +
221E PHE* 1.3 75.9 - - - +
223E ILE* 1.3 64.6 + - - +
224E TYR* 3.4 30.7 + - - +
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Residues in contact with ILE 223 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67E ILE* 3.5 44.2 - - + +
69E LYS* 4.3 11.7 - - + +
211E SER* 4.4 6.3 - - - +
212E ILE 3.5 7.9 - - - +
213E ALA* 4.2 0.7 - - + +
221E PHE* 3.6 24.9 - - + -
222E THR* 1.3 72.8 - - - +
224E TYR* 1.3 69.9 + - - +
225E ASP* 3.4 25.1 + - - +
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Residues in contact with TYR 224 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190E ILE* 5.0 10.3 - - + -
212E ILE* 2.6 52.3 + - + +
214E ILE* 3.7 27.9 - - + +
219E THR* 5.4 2.9 - - - +
222E THR* 3.4 24.6 + - - +
223E ILE* 1.3 79.9 - - - +
225E ASP* 1.3 65.3 + - - +
228E ALA* 4.1 23.1 - - + +
229E VAL* 3.2 18.8 - - + +
232E TYR* 5.9 5.2 - + + -
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Residues in contact with ASP 225 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52E LYS* 3.5 18.5 + - - +
210E LEU 3.4 3.7 - - - +
211E SER* 2.7 35.1 + - - -
223E ILE* 3.4 22.5 + - - +
224E TYR* 1.3 74.5 - - - +
226E GLY* 1.3 64.5 + - - +
227E GLU* 2.9 19.4 - - - +
228E ALA* 3.8 7.4 + - - +
229E VAL* 4.0 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