Contacts of the strand formed by residues 166 - 170 (chain D) in PDB entry 2EWY
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 PHE 166 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49D THR* 4.2 5.8 - - + -
137D LEU* 3.4 44.2 - - + -
153D PHE* 4.0 20.2 - + + -
165D VAL* 1.3 83.1 - - - +
167D SER* 1.3 61.9 + - - +
168D MET* 4.7 0.9 - - + -
187D LEU* 4.1 11.2 - - + -
188D VAL 3.2 13.2 - - - +
189D LEU* 4.0 8.3 - - + -
190D GLY 3.8 3.8 - - - +
191D GLY 4.3 0.7 - - - -
212D TYR* 3.2 30.7 - + - -
357D PHE* 2.8 60.8 + + + +
359D ARG* 3.7 20.2 - - - -
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Residues in contact with SER 167 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166D PHE* 1.3 77.9 - - - +
168D MET* 1.3 61.9 + - - +
186D SER 3.8 0.2 - - - +
187D LEU* 3.7 4.3 - - - +
188D VAL* 2.9 35.5 + - - +
191D GLY 3.0 16.6 + - - -
192D ILE* 4.8 0.9 - - - -
354D TYR* 2.7 35.5 + - - -
355D VAL 3.2 12.8 - - - -
356D ILE* 3.9 14.8 - - - -
357D PHE* 4.6 0.2 - - - -
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Residues in contact with MET 168 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22D LEU* 4.2 15.0 - - + -
30D TYR* 5.7 2.7 - - - -
47D VAL* 3.5 26.0 - - + -
49D THR* 3.3 33.9 - - + -
166D PHE* 4.7 2.0 - - + -
167D SER* 1.3 76.1 - - - +
169D GLN* 1.3 67.3 + - - +
170D MET* 4.3 12.6 - - + +
186D SER 3.4 10.3 - - - +
187D LEU* 4.4 10.8 - - + -
242D SER* 3.6 19.7 - - - -
350D MET* 4.1 14.6 - - + +
353D PHE 4.2 1.0 - - - +
354D TYR* 3.3 5.3 - - - -
355D VAL* 2.7 38.4 + - - +
357D PHE* 4.3 9.4 - - + -
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Residues in contact with GLN 169 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22D LEU* 4.8 0.9 - - - +
168D MET* 1.3 77.7 - - - +
170D MET* 1.3 62.9 + - - +
171D CYS* 3.7 11.6 - - - -
185D GLY* 3.0 6.2 - - - -
186D SER* 2.9 46.2 + - - +
196D LEU* 2.7 55.9 + - + +
353D PHE 4.3 5.2 - - - +
354D TYR* 3.7 16.7 - - + +
369D SER* 3.2 26.9 + - - +
370D PRO* 4.0 4.6 - - - +
371D CYS* 3.9 13.7 - - - +
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Residues in contact with MET 170 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22D LEU* 5.7 0.4 - - + -
30D TYR* 3.2 52.7 - - + +
168D MET* 4.4 19.1 - - + +
169D GLN* 1.3 77.3 - - - +
171D CYS* 1.3 62.3 + - - +
184D GLY 4.1 0.4 - - - -
242D SER* 4.9 8.5 - - - +
347D ALA* 3.7 23.8 - - - +
350D MET* 2.9 55.5 + - + +
351D GLU* 3.3 28.7 - - - +
353D PHE 4.5 4.7 + - - +
369D SER* 4.7 1.0 + - - -
371D CYS* 3.9 4.9 - - - -
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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