Contacts of the strand formed by residues 131 - 136 (chain E) in PDB entry 3ALQ
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 ARG 131 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45E ASP* 5.8 3.5 + - - -
47E GLN* 3.6 29.6 + - + +
48E LEU 3.5 4.9 - - - +
49E VAL* 4.0 21.3 - - + -
81E SER 4.1 0.2 - - - +
82E ARG* 4.4 0.2 - - - +
83E ILE* 2.9 77.8 + - + +
88E GLN* 4.9 11.5 - - - +
129E GLY 3.2 13.5 + - - +
130E ASP* 1.3 72.6 - - - +
132E LEU* 1.3 65.4 + - - +
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Residues in contact with LEU 132 (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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47E GLN* 3.2 10.1 - - - +
48E LEU* 2.8 41.3 + - + +
50E VAL* 4.5 8.5 - - + -
58E ILE* 3.7 16.6 - - + -
80E ILE* 5.0 3.4 - - + -
81E SER 3.7 11.4 - - - +
82E ARG* 3.8 22.9 - - + -
93E LEU* 4.2 11.9 - - + -
126E LEU* 3.6 30.5 - - + -
130E ASP* 5.6 0.7 - - + -
131E ARG* 1.3 81.7 - - - +
133E SER* 1.3 61.7 + - - +
152E PHE* 4.2 15.5 - - + -
154E ILE* 4.0 23.6 - - + -
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Residues in contact with SER 133 (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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46E ASN 5.2 1.8 - - - -
47E GLN* 3.9 24.9 + - - +
79E THR 3.4 1.0 - - - +
80E ILE* 3.1 5.2 - - - +
81E SER* 2.7 58.9 + - - -
83E ILE* 5.6 5.2 - - - +
131E ARG 4.3 0.2 + - - -
132E LEU* 1.3 75.5 - - - +
134E ALA* 1.3 59.8 + - - +
135E GLU* 3.3 24.2 + - - -
152E PHE* 4.4 4.9 - - - -
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Residues in contact with ALA 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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26E LEU* 4.1 6.6 - - - +
28E TRP* 3.8 38.6 + - + +
46E ASN* 5.4 2.7 + - - -
60E SER* 4.2 6.3 - - - +
78E HIS* 4.4 6.1 - - + -
79E THR 3.4 4.7 - - - +
80E ILE* 4.0 13.0 - - + +
133E SER* 1.3 73.7 - - - +
135E GLU* 1.3 63.0 + - - +
152E PHE* 3.9 27.5 - - + -
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Residues in contact with GLU 135 (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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26E LEU* 5.3 1.3 - - - -
47E GLN* 5.1 3.3 + - - -
77E THR 3.8 0.5 - - - +
78E HIS* 3.5 1.6 + - - -
79E THR* 2.9 39.4 + - - +
81E SER* 4.6 3.7 + - - +
133E SER* 3.3 24.5 + - - +
134E ALA* 1.3 84.6 - - - +
136E ILE* 1.3 72.5 + - - +
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Residues in contact with ILE 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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26E LEU* 4.4 13.9 - - + -
62E VAL* 4.2 11.7 - - + -
64E PHE* 3.9 19.1 - - + -
77E THR* 3.2 15.7 - - - +
78E HIS* 3.6 17.0 - - - +
135E GLU* 1.3 82.9 - - - +
137E ASN* 1.3 61.4 + - - +
138E ARG 3.9 4.3 - - - +
139E PRO* 3.5 33.8 - - + +
142E LEU* 3.4 42.4 - - + -
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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