Contacts of the strand formed by residues 218 - 224 (chain E) in PDB entry 2ZSU
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 218 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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216E PHE* 3.8 0.7 - - - +
217E ASP* 1.3 87.6 - - + +
219E VAL* 1.3 67.2 - - - +
220E TYR* 3.1 34.0 - - + +
237E VAL 3.9 0.3 - - - +
238E GLY* 3.7 0.2 - - - -
239E VAL* 2.9 34.2 + - + +
241E GLY 5.6 3.8 - - - +
243E ILE 4.6 8.5 - - - +
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Residues in contact with VAL 219 (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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209E TYR* 3.5 40.0 + - + +
212E MET* 3.2 39.5 - - + +
213E ARG* 3.5 26.0 - - + +
216E PHE* 4.2 7.9 - - + +
218E LYS* 1.3 79.7 - - - +
220E TYR* 1.3 72.6 + - - +
236E LEU* 6.3 0.2 - - + -
237E VAL 3.1 9.2 - - - +
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Residues in contact with TYR 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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209E TYR* 4.8 1.8 - - - -
218E LYS* 3.1 44.2 - - + +
219E VAL* 1.3 82.1 - - - +
221E TYR* 1.3 67.5 + - - +
236E LEU* 3.5 7.8 - - - +
237E VAL* 2.8 43.2 + - + +
239E VAL* 3.9 13.0 - - + -
243E ILE 3.8 9.4 + - - -
244E ASP* 4.9 3.6 + - - -
245E PHE* 3.6 47.1 + + + -
246E MET* 3.9 33.0 - - + -
270E PHE* 4.8 1.8 - + + -
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Residues in contact with TYR 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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205E PHE* 3.7 27.6 - + + -
209E TYR* 3.9 15.7 - + + -
220E TYR* 1.3 77.6 - - - +
222E TYR* 1.3 65.7 + - - +
235E PHE 3.3 6.7 - - - +
236E LEU* 3.9 4.9 - - + -
270E PHE* 3.1 28.9 - + + -
272E MET* 3.5 34.8 - - + -
277E VAL* 3.8 19.2 - - + +
280E LEU* 3.4 31.4 - - + -
265F LYS* 3.1 26.1 + - - +
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Residues in contact with TYR 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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65E PRO* 2.7 31.5 + - + -
66E LEU 3.8 2.6 + - - -
69E PRO* 4.2 5.1 - - + +
70E ALA 5.3 0.5 + - - -
192E VAL* 3.6 18.4 - - - +
221E TYR* 1.3 82.4 - - - +
223E SER* 1.3 60.5 + - - +
234E ALA* 3.6 2.6 - - - -
235E PHE* 2.8 62.2 + + + +
237E VAL* 3.4 26.7 - - + -
245E PHE* 3.5 26.9 - + - -
269E LEU* 3.2 46.9 - - + +
270E PHE* 3.8 9.6 - - + +
272E MET* 4.3 5.9 - - - +
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Residues in contact with SER 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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198E VAL* 4.0 20.0 - - - -
222E TYR* 1.3 80.0 - - - +
224E PHE* 1.3 63.6 + - - +
232E PRO* 4.4 10.8 - - - +
233E TRP 3.1 14.1 - - - -
235E PHE* 4.5 0.7 - - - -
269E LEU* 3.2 13.2 + - - +
271E GLN* 2.6 34.0 + - - +
272E MET* 4.3 3.6 - - - -
271F GLN* 3.2 19.1 + - - -
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Residues in contact with PHE 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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61E SER* 3.2 26.2 - - - -
65E PRO* 3.8 28.0 - - + -
223E SER* 1.3 75.7 - - - +
225E PRO* 1.3 100.9 - - + +
226E VAL* 3.0 11.2 + - + +
232E PRO* 4.0 4.7 - - - -
233E TRP 3.0 25.4 + - - +
235E PHE* 4.1 7.6 - - + -
260E TYR* 3.6 41.3 - + + -
261E TYR* 3.9 14.1 - + + -
262E ASP 5.2 0.2 - - - -
269E LEU* 4.1 9.2 - - + -
199F TYR* 3.8 7.4 - - - -
271F GLN* 3.6 24.0 - - + +
272F MET 6.0 0.7 - - - -
273F PRO* 5.0 6.5 - - + -
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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