Contacts of the strand formed by residues 166 - 170 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B THR* 4.2 5.2 - - + -
137B LEU* 3.4 44.4 - - + -
153B PHE* 4.0 22.0 - + + -
165B VAL* 1.3 84.2 - - - +
167B SER* 1.3 62.6 + - - +
168B MET* 4.7 0.9 - - + -
187B LEU* 4.1 10.5 - - + -
188B VAL 3.2 14.1 - - - +
189B LEU* 4.0 7.6 - - + -
190B GLY 3.8 3.4 - - - +
191B GLY 4.3 0.7 - - - -
212B TYR* 3.2 31.4 - + - -
356B ILE* 4.1 0.2 - - - -
357B PHE* 2.8 60.1 + + + +
359B ARG* 3.7 19.3 - - - -
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Residues in contact with SER 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B PHE* 1.3 78.3 - - - +
168B MET* 1.3 62.4 + - - +
186B SER 3.8 0.2 - - - +
187B LEU* 3.7 4.3 - - - +
188B VAL* 2.9 36.0 + - - +
191B GLY 3.0 16.9 + - - -
192B ILE* 4.8 0.7 - - - -
354B TYR* 2.7 33.9 + - - -
355B VAL 3.2 13.5 - - - -
356B ILE* 3.9 15.7 - - - -
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Residues in contact with MET 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B LEU* 4.2 15.0 - - + -
30B TYR* 5.7 2.2 - - - -
47B VAL* 3.5 25.1 - - + -
49B THR* 3.3 34.8 - - + -
166B PHE* 4.7 1.6 - - + -
167B SER* 1.3 75.3 - - - +
169B GLN* 1.3 67.3 + - - +
170B MET* 4.4 12.1 - - + +
186B SER 3.3 10.1 - - - +
187B LEU* 4.4 10.8 - - + -
242B SER* 3.6 20.2 - - - -
350B MET* 4.1 13.7 - - + +
353B PHE 4.2 0.9 - - - +
354B TYR* 3.3 4.8 - - - -
355B VAL* 2.7 38.7 + - - +
357B PHE* 4.3 9.4 - - + -
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Residues in contact with GLN 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B LEU* 4.8 0.9 - - - +
168B MET* 1.3 78.1 - - - +
170B MET* 1.3 62.7 + - - +
171B CYS* 3.7 12.1 - - - -
185B GLY* 3.0 6.6 - - - -
186B SER* 2.9 45.0 + - - +
196B LEU* 2.7 57.1 + - + +
353B PHE 4.3 4.7 - - - +
354B TYR* 3.7 16.8 - - + +
369B SER* 3.2 27.2 + - - +
370B PRO* 4.0 4.4 - - - +
371B CYS* 3.9 13.7 - - - +
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Residues in contact with MET 170 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B LEU* 5.7 0.2 - - + -
30B TYR* 3.2 54.1 - - + +
168B MET* 4.4 18.2 - - + +
169B GLN* 1.3 77.6 - - - +
171B CYS* 1.3 62.2 + - - +
172B GLY 4.2 0.2 - - - -
185B GLY* 4.4 0.2 - - - -
242B SER* 4.9 8.1 - - - +
347B ALA* 3.7 23.8 - - + +
350B MET* 2.9 56.8 + - + +
351B GLU* 3.3 28.4 - - - +
353B PHE 4.5 4.5 + - - +
369B SER* 4.7 1.0 + - - -
371B CYS* 3.9 4.5 - - - -
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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
------------------------------------------------------------
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