Contacts of the strand formed by residues 89 - 95 (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 HIS 89 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12B LEU* 5.3 4.5 - - - -
13B PRO* 4.0 28.4 - - + +
51B TYR* 4.5 12.8 - - + +
52B ILE 2.9 25.0 + - - +
53B GLU* 4.1 21.3 + - + +
54B ARG* 3.8 9.2 - - - +
85B LEU* 3.9 0.7 - - - +
86B THR* 2.6 48.4 + - - +
88B THR* 1.3 132.9 + - + +
90B LEU* 1.3 56.2 + - - +
91B ALA 4.0 0.4 - - - -
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Residues in contact with LEU 90 (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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50B LYS 3.7 0.9 - - - +
51B TYR* 3.7 1.3 - - - -
52B ILE* 2.7 38.5 + - + +
54B ARG* 4.3 1.0 - - - +
58B ILE* 4.6 20.2 - - + -
62B VAL* 4.7 7.0 - - + -
66B ILE* 4.1 25.1 - - + -
83B VAL* 4.1 11.9 - - + -
84B ILE 3.8 13.0 - - - +
85B LEU* 4.8 2.7 - - - +
86B THR 4.8 0.2 - - - +
89B HIS* 1.3 72.5 - - - +
91B ALA* 1.3 63.6 + - - +
92B ILE* 3.8 8.5 + - + +
311B ILE* 3.5 37.9 - - + +
312B ILE* 5.0 7.4 - - + -
315B ALA* 4.1 18.6 - - + -
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Residues in contact with ALA 91 (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* 4.8 3.6 - - + +
49B VAL* 3.8 11.4 - - + -
50B LYS 3.4 4.7 - - - -
51B TYR* 3.6 27.8 - - + +
82B GLU 4.0 0.2 - - - +
83B VAL* 3.4 7.8 - - - +
84B ILE* 2.8 50.9 + - + +
86B THR* 4.2 7.2 - - + -
89B HIS 3.9 2.0 + - - -
90B LEU* 1.3 71.3 - - - +
92B ILE* 1.3 61.1 + - - +
93B VAL* 4.0 3.1 + - + +
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Residues in contact with ILE 92 (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 ALA 3.7 1.2 - - - +
49B VAL* 3.4 2.7 - - - -
50B LYS* 2.7 46.5 + - + +
52B ILE* 3.7 28.0 - - + -
66B ILE* 4.1 12.3 - - + -
80B PHE* 3.9 20.2 - - + -
82B GLU 4.0 2.0 - - - -
83B VAL* 4.2 11.9 - - + -
90B LEU* 4.3 7.4 - - + +
91B ALA* 1.3 75.7 - - - +
93B VAL* 1.3 61.2 + - - +
94B MET* 3.9 11.8 - - + +
163B TYR* 3.6 53.8 - - + +
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Residues in contact with VAL 93 (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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21B TYR* 4.0 19.3 - - + +
47B VAL* 3.4 28.5 - - + -
48B ALA 3.6 3.1 - - - -
49B VAL* 4.0 20.6 - - + -
80B PHE* 4.4 3.1 - - - -
81B LYS* 2.7 43.4 + - + +
82B GLU* 2.9 22.7 + - + +
84B ILE* 4.2 26.7 - - + -
91B ALA* 4.5 2.9 - - + +
92B ILE* 1.3 74.5 - - - +
94B MET* 1.3 60.9 + - - +
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Residues in contact with MET 94 (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 PHE* 4.2 10.1 - - + -
47B VAL* 3.6 4.5 - - - +
48B ALA* 2.9 34.4 + - + +
50B LYS* 4.2 13.5 - - + +
69B HIS* 4.0 20.2 - - + -
78B VAL* 4.4 1.3 - - + -
79B ARG 3.6 12.1 - - - +
80B PHE* 4.4 2.0 - - + -
81B LYS* 3.7 11.4 - - - -
92B ILE* 3.9 26.0 - - + +
93B VAL* 1.3 76.4 - - - +
95B GLU* 1.3 75.1 + - - +
96B TYR 3.5 0.2 + - - -
161B PHE* 4.0 30.3 - - + -
163B TYR* 3.6 28.7 - - + -
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Residues in contact with GLU 95 (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 PHE* 3.4 21.1 - - - -
45B GLU* 4.9 6.5 - - - +
46B LEU 4.7 4.3 - - - -
47B VAL* 4.9 1.8 - - - +
77B ILE 3.3 3.8 - - - +
78B VAL* 3.7 10.1 - - + +
79B ARG* 3.1 66.2 + - + +
81B LYS* 4.0 20.0 - - - +
94B MET* 1.3 80.5 - - - +
96B TYR* 1.3 62.9 + - - +
157B LYS* 3.2 26.5 + - + +
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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