Contacts of the strand formed by residues 80 - 85 (chain B) in PDB entry 3UDB
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 80 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66B ILE* 3.9 26.7 - - + -
69B HIS* 3.4 38.7 + + + +
70B ARG* 3.6 32.1 - - + -
72B LEU 4.6 1.2 + - - -
79B ARG* 1.3 81.2 - - - +
81B LYS* 1.3 65.5 + - - +
82B GLU* 3.2 39.7 - - - -
83B VAL* 3.8 10.1 - - + -
92B ILE* 3.9 23.6 - - + -
93B VAL 4.4 1.6 - - - -
94B MET* 4.4 1.3 - - - -
163B TYR* 3.9 16.4 - - - -
303B GLN* 4.1 9.6 - - + -
308B ILE* 4.5 2.2 - - + -
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Residues in contact with LYS 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B TYR* 5.5 5.3 + - - +
40B ASP* 4.9 8.5 + - - -
43B ALA* 5.2 2.8 - - - +
45B GLU* 3.5 34.3 + - - +
47B VAL* 4.2 12.9 - - + +
79B ARG* 3.8 1.3 + - + +
80B PHE* 1.3 84.6 - - - +
82B GLU* 1.3 64.9 + - + +
93B VAL* 2.7 41.4 + - + +
94B MET* 3.8 19.3 - - - +
95B GLU* 4.0 14.6 - - + +
302B GLY* 5.4 2.6 - - - -
303B GLN* 4.7 9.5 + - - +
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Residues in contact with GLU 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B ARG* 3.3 29.8 + - - -
21B TYR* 3.3 18.4 + - - +
80B PHE* 3.2 14.2 - - - -
81B LYS* 1.3 84.9 - - + +
83B VAL* 1.3 67.9 + - - +
84B ILE* 4.3 12.8 - - + +
92B ILE 3.9 0.2 - - - -
93B VAL* 2.9 35.0 + - + +
303B GLN* 3.2 27.4 - - + +
307B GLU* 5.4 1.0 - - - +
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Residues in contact with VAL 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B ILE* 3.9 29.2 - - + -
80B PHE* 4.2 9.0 - - + -
82B GLU* 1.3 81.6 - - - +
84B ILE* 1.3 63.0 + - - +
90B LEU* 4.1 16.2 - - + -
91B ALA 3.4 10.8 - - - +
92B ILE* 4.2 8.5 - - + -
303B GLN* 2.8 36.6 - - - +
308B ILE* 4.1 20.2 - - + +
311B ILE* 3.6 25.5 - - + +
312B ILE* 5.3 0.7 - - + -
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Residues in contact with ILE 84 (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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16B HIS* 5.6 8.5 - - + -
17B ASP* 3.7 27.1 - - - +
20B ARG* 4.1 9.6 - - - +
21B TYR* 4.1 26.9 - - + -
82B GLU* 4.3 11.7 - - - +
83B VAL* 1.3 80.2 - - - +
85B LEU* 1.3 71.1 + - - +
86B THR* 5.1 4.5 - - + -
90B LEU* 3.8 6.5 - - - +
91B ALA* 2.8 42.2 + - + +
93B VAL* 4.2 18.2 - - + -
311B ILE* 4.6 1.3 - - - -
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Residues in contact with LEU 85 (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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54B ARG* 3.1 39.7 - - + +
84B ILE* 1.3 79.9 - - - +
86B THR* 1.3 87.7 + - - +
87B PRO* 3.9 3.5 - - - +
89B HIS 3.9 3.4 - - - +
90B LEU* 4.8 3.1 - - + -
311B ILE* 4.1 27.5 - - + +
314B GLU* 3.7 39.9 - - + +
315B ALA* 4.2 3.4 - - + +
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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