Contacts of the strand formed by residues 133 - 138 (chain E) in PDB entry 2WTK
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 TYR 133 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100E ARG* 4.8 9.5 + - - -
118E GLU* 3.2 29.2 + - + -
119E LEU* 4.9 7.4 - - + -
122E SER* 2.6 39.0 + - - +
123E LYS* 3.3 27.2 + - - +
131E VAL* 3.4 26.2 - - + +
132E PRO* 1.3 81.2 - - - +
134E ARG* 1.3 60.9 + - - +
135E ALA 3.6 2.9 - - - +
136E THR* 6.4 0.7 - - - -
145E VAL* 3.1 34.5 - - + -
146E VAL 3.8 3.8 - - - +
147E THR* 4.1 10.1 - - + -
212E SER* 5.5 1.0 - - - -
213E GLY 5.0 2.4 + - - -
214E LEU* 3.7 29.8 + - + +
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Residues in contact with ARG 134 (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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60E SER* 4.5 22.3 + - - +
62E PHE* 3.0 54.6 + - + -
95E GLU* 3.0 32.0 + - - -
97E VAL* 4.3 3.8 - - - +
123E LYS* 4.4 8.1 + - - +
132E PRO* 4.7 10.6 - - + +
133E TYR* 1.3 75.3 - - - +
135E ALA* 1.3 64.5 + - - +
146E VAL* 2.8 16.0 + - + +
147E THR 4.1 3.4 - - - -
148E SER* 2.9 43.0 + - - +
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Residues in contact with ALA 135 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177D THR* 6.1 1.3 - - - -
62E PHE* 3.7 29.4 - - + +
123E LYS* 4.7 5.3 - - - +
133E TYR* 3.6 2.7 - - - +
134E ARG* 1.3 83.1 - - - +
136E THR* 1.3 63.9 + - - +
137E PHE* 4.4 8.3 - - + -
144E TRP 3.9 0.2 - - - +
145E VAL* 3.3 6.1 - - - +
146E VAL* 2.8 43.5 + - + +
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Residues in contact with THR 136 (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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177D THR* 3.7 11.4 - - + +
178D PHE* 3.1 19.0 + - - +
179D ASP* 3.3 47.5 + - + +
119E LEU* 3.6 34.0 - - + +
123E LYS* 5.3 3.1 - - - -
133E TYR* 6.4 0.7 - - - -
135E ALA* 1.3 79.2 - - - +
137E PHE* 1.3 67.6 + - - +
143E LEU* 3.7 6.9 - - - +
144E TRP 3.3 10.7 + - - -
145E VAL* 3.9 3.8 - - - +
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Residues in contact with PHE 137 (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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176D SER 3.3 17.7 - - - +
178D PHE* 3.8 8.9 - - - +
62E PHE* 5.4 1.8 - - + -
63E LEU 4.5 0.7 - - - -
64E PRO* 3.6 42.2 - - + -
69E TYR* 3.3 44.9 - + - -
135E ALA* 4.4 6.3 - - + -
136E THR* 1.3 85.8 + - - +
138E ILE* 1.3 76.2 + - - +
139E ALA* 4.6 6.1 - - + -
143E LEU* 3.8 1.1 - - - +
144E TRP* 3.0 62.7 + + + -
146E VAL* 4.2 11.2 - - + -
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Residues in contact with ILE 138 (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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176D SER 4.9 1.2 + - - -
178D PHE* 3.6 39.2 - - + +
222D ASN* 3.7 31.1 + - - +
223D TYR* 4.8 2.2 - - + +
224D VAL* 3.8 23.8 - - + -
64E PRO* 4.7 5.9 - - - +
104E LEU* 4.1 9.0 - - + -
137E PHE* 1.3 88.8 - - - +
139E ALA* 1.3 65.3 + - - +
140E ASP 3.3 24.0 - - - +
142E GLU 3.5 10.1 - - - +
143E LEU* 3.8 11.9 - - + -
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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