Contacts of the strand formed by residues 158 - 161 (chain E) in PDB entry 5LEZ
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 ALA 158 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37E GLY 3.1 16.2 - - - +
38E LEU* 3.8 12.8 - - + +
144E ILE* 4.9 1.1 - - - -
156E CYS* 3.3 9.4 - - - +
157E ARG* 1.3 81.4 - - + +
159E MET* 1.3 66.2 + - - +
172E LEU* 4.2 14.4 - - + -
176E MET* 5.7 0.4 - - + -
179E PHE* 3.9 18.8 - - + -
57F LEU* 3.2 30.5 + - + +
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Residues in contact with MET 159 (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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36E VAL* 3.4 3.5 - - - -
37E GLY 2.7 36.4 + - - +
133E LEU* 3.8 25.1 - - + -
144E ILE* 4.7 3.1 - - + -
146E GLN* 3.5 24.0 - - - +
156E CYS* 3.9 13.2 - - + -
158E ALA* 1.3 86.3 - - - +
160E SER* 1.3 81.8 + - - +
161E ILE* 4.8 0.2 - - - -
169E ARG* 3.9 13.2 - - - -
172E LEU* 3.7 9.4 - - - +
55F SER* 4.5 3.6 - - - +
57F LEU* 3.9 20.2 - - + -
58F TYR* 3.6 35.4 - - + +
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Residues in contact with SER 160 (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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34E ALA* 4.6 2.3 - - - +
35E THR 2.8 22.4 + - - -
36E VAL* 3.8 4.4 - - - +
133E LEU* 4.5 0.9 - - - -
159E MET* 1.3 83.8 - - - +
161E ILE* 1.3 66.8 + - - +
165E SER* 3.4 21.5 - - - -
168E ALA* 3.4 30.5 - - - +
169E ARG* 2.9 32.3 + - - +
172E LEU* 4.4 2.0 - - - -
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Residues in contact with ILE 161 (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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29E VAL* 4.4 12.3 - - + -
33E SER 4.2 0.7 - - - +
34E ALA* 3.3 3.8 - - - -
35E THR* 3.1 44.5 + - + +
74E ILE 5.1 0.2 - - - -
75E ALA* 4.0 13.5 - - + +
131E GLY* 3.9 32.8 - - - +
132E LEU* 4.2 4.7 - - - +
133E LEU* 4.0 23.1 - - + +
146E GLN* 3.6 31.9 - - + +
148E 6V1 5.1 7.0 - - + +
159E MET* 4.5 0.7 - - + -
160E SER* 1.3 78.7 + - - +
162E GLY* 1.3 61.4 + - - +
165E SER* 3.5 9.4 - - - -
169E ARG* 4.4 1.8 - - - +
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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