Contacts of the strand formed by residues 219 - 222 (chain A) in PDB entry 3ELY
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 MET 219 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A LYS* 3.9 0.9 - - - +
183A VAL* 2.7 37.3 + - - +
186A PRO* 3.8 18.4 - - + -
206A ILE* 3.8 38.1 - - + -
207A VAL* 3.4 25.6 - - - +
208A ARG* 4.0 11.2 - - - +
217A HIS* 3.5 7.8 + - - +
218A GLU* 1.3 79.5 - - - +
220A TYR* 1.3 67.1 + - - +
232A MET* 3.6 26.0 - - + +
233A VAL* 4.0 16.8 - - - -
236A THR* 3.7 21.8 - - - +
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Residues in contact with TYR 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A LYS* 3.5 39.8 + - + +
65A LEU* 4.4 5.8 - - + -
87A TRP* 3.7 16.3 - + - -
146A ASP* 2.8 30.1 + - - -
180A CYS* 3.9 22.0 - - - -
181A VAL 3.5 3.4 - - - +
182A LYS* 3.6 34.3 - - + +
205A GLY 3.6 0.2 - - - +
206A ILE* 3.3 5.5 - - - -
207A VAL* 2.8 49.5 + - + +
209A VAL* 3.7 23.3 - - + -
212A SER* 4.7 1.1 - - - -
218A GLU* 4.5 14.4 - - + -
219A MET* 1.3 79.4 - - - +
221A TYR* 1.3 61.2 + - - +
222A ILE* 3.4 5.1 + - + -
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Residues in contact with TYR 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A LEU* 5.2 2.2 - - + -
168A PHE* 3.8 25.4 - + - -
179A PHE* 3.6 28.1 - + - -
180A CYS* 3.5 3.6 - - - -
181A VAL* 2.8 46.4 + - + +
183A VAL* 4.0 15.9 - - + +
195A LEU* 4.3 20.9 - - + -
198A LEU* 3.6 24.0 + - + -
199A GLN* 3.6 22.1 + - + -
202A PHE* 3.7 7.6 - - - +
203A GLY 2.7 28.7 + - - -
204A GLY 4.1 1.6 - - - -
205A GLY* 3.5 26.5 - - - -
206A ILE* 4.3 4.3 - - + -
220A TYR* 1.3 69.2 - - - +
222A ILE* 1.3 59.0 + - - +
229A ILE* 5.1 4.7 - - + -
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Residues in contact with ILE 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A LEU* 4.1 16.2 - - + -
70A TYR* 3.4 43.5 - - + +
71A LEU* 4.6 4.9 - - + -
179A PHE* 3.5 14.3 - - - +
180A CYS* 3.8 28.0 - - + -
204A GLY* 3.2 3.3 - - - -
205A GLY 2.8 49.6 + - - +
207A VAL* 3.7 13.9 - - + -
220A TYR* 3.7 12.3 - - + +
221A TYR* 1.3 76.7 - - - +
223A SER* 1.3 61.3 + - - +
225A ALA* 3.8 17.9 - - + +
227A ASN* 5.6 0.4 - - - +
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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