Contacts of the strand formed by residues 133 - 136 (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 GLY 133 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44B GLN 3.5 2.7 + - - +
45B ILE* 3.8 16.6 - - - -
46B LEU* 2.7 35.2 + - - +
55B ALA 2.9 15.3 - - - -
56B VAL* 3.8 1.8 - - - -
118B ILE* 5.9 0.4 - - - -
124B PHE* 5.3 2.2 - - - -
125B PHE* 5.2 1.6 - - - -
131B TRP* 3.7 9.3 - - - -
132B ASN* 1.3 78.3 - - - +
134B ILE* 1.3 54.9 + - - -
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Residues in contact with ILE 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B ILE* 3.5 4.5 - - - +
46B LEU* 3.4 12.1 - - + +
48B ASP* 3.5 37.9 - - + +
51B SER* 4.2 2.2 - - - +
53B ASN 3.1 8.1 - - - +
54B PHE* 3.5 2.6 - - - -
55B ALA* 2.8 44.2 + - + +
87B TYR* 3.6 33.7 - - + +
92B TRP* 4.3 0.2 - - - +
124B PHE* 3.7 21.5 - - + -
133B GLY* 1.3 74.8 - - - +
135B LEU* 1.3 62.9 + - - +
136B GLY 4.7 0.7 - - - +
1002B DBO 3.9 21.8 - - + -
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Residues in contact with LEU 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B LEU* 4.4 11.9 - - + -
34B MET* 4.0 19.5 - - + -
45B ILE* 3.2 17.0 - - + +
46B LEU 2.7 13.2 + - - +
47B VAL* 4.6 5.6 - - + -
48B ASP 2.9 25.3 + - - +
53B ASN 4.0 0.2 - - - -
54B PHE* 4.4 7.2 - - + -
103B ILE* 6.0 0.2 - - + -
134B ILE* 1.3 72.9 - - - +
136B GLY* 1.3 61.3 + - - +
137B LEU* 3.4 26.8 + - + +
152B PHE* 3.4 49.8 - - + -
187B LEU* 4.5 11.2 - - + -
189B LEU* 5.7 1.6 - - + -
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Residues in contact with GLY 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B ASP 3.3 4.7 - - - -
51B SER* 2.9 33.0 - - - -
52B SER* 3.9 8.5 - - - -
53B ASN 3.0 21.6 + - - -
134B ILE* 4.7 0.2 - - - +
135B LEU* 1.3 76.7 - - - +
137B LEU* 1.3 63.6 + - - +
138B ALA 3.4 0.8 + - - -
151B THR* 4.2 11.8 - - - +
152B PHE* 4.7 2.8 + - - +
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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