Contacts of the strand formed by residues 90 - 97 (chain B) in PDB entry 3O4O
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 90 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52B TRP* 4.5 0.7 - - - -
54B ARG* 3.6 13.5 - - - -
88B ASP 3.3 1.7 + - - -
89B THR* 1.3 77.9 - - - +
91B ASN* 1.3 65.1 + - - -
92B TYR* 3.0 15.3 - - - -
109B LEU 3.0 27.9 + - - -
1D NAG 3.5 18.4 - - - -
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Residues in contact with ASN 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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9B LEU* 3.7 12.9 - - + +
52B TRP* 3.4 4.3 - - - +
53B THR* 3.1 42.0 + - + +
54B ARG* 3.9 7.9 + - - +
90B GLY* 1.3 74.5 - - - -
92B TYR* 1.4 61.6 + - - +
106B ALA* 5.0 5.6 - - + -
107B PHE 5.0 0.4 - - - -
108B PRO* 3.0 30.6 - - + +
1D NAG 1.5 60.7 + - - +
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Residues in contact with TYR 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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50B TRP* 4.5 7.4 - + + -
51B TYR 4.1 3.4 - - - -
52B TRP* 3.7 35.0 - + + -
72B ILE* 5.8 3.1 - - + +
79B LEU* 4.2 18.2 - - + -
81B PHE* 3.9 28.2 - + - -
88B ASP* 3.0 38.5 + - - +
90B GLY 3.0 28.3 - - - -
91B ASN* 1.4 77.1 - - - +
93B THR* 1.3 63.4 + - - +
105B VAL 3.6 0.2 - - - +
106B ALA* 2.8 27.9 - - - +
107B PHE* 3.0 37.7 + + + +
109B LEU* 4.1 16.6 - - + -
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Residues in contact with THR 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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49B ILE 3.9 0.2 - - - +
50B TRP* 3.4 9.7 - - - -
51B TYR* 2.9 78.7 + - + +
53B THR* 5.3 2.9 - - - +
59B LEU* 4.5 8.8 - - - +
92B TYR* 1.3 80.9 + - - +
94B CYS* 1.3 65.4 + - - +
104B LYS* 4.0 20.9 - - + -
105B VAL 3.2 11.9 - - - +
106B ALA* 3.7 10.9 - - - +
107B PHE* 5.4 0.2 - - - -
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Residues in contact with CYS 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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27B CYS* 2.1 48.0 - - - -
28B PRO* 4.2 3.4 - - - -
48B LEU* 4.0 4.7 - - + -
49B ILE 3.1 10.1 - - - +
50B TRP* 3.9 22.4 - - + -
93B THR* 1.3 77.9 - - - +
95B MET* 1.3 61.0 + - - +
103B SER 3.6 0.5 - - - +
104B LYS* 3.2 2.3 - - - -
105B VAL* 3.2 44.0 + - - +
107B PHE* 4.7 2.7 - - - -
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Residues in contact with MET 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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4B CYS* 5.3 1.6 - - - -
47B THR 3.5 0.5 - - - +
48B LEU* 3.4 5.9 - - - +
49B ILE* 2.9 67.2 + - + +
51B TYR* 4.1 24.5 - - + +
94B CYS* 1.3 73.5 - - - +
96B LEU* 1.3 62.0 + - - +
97B ARG* 4.9 13.2 - - + -
102B CYS* 4.3 19.5 - - - -
103B SER 2.7 20.9 - - - +
104B LYS* 3.6 14.4 - - + -
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Residues in contact with LEU 96 (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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29B LEU* 5.4 15.0 - - + -
32B HIS* 6.1 1.6 - - + +
34B LEU* 5.8 10.1 - - + -
46B LEU* 3.4 33.7 - - + +
47B THR 3.4 14.8 - - - +
48B LEU* 3.5 29.2 - - + -
95B MET* 1.3 76.9 - - - +
97B ARG* 1.3 60.4 + - - +
101B TYR* 3.2 12.8 - - + +
102B CYS* 3.0 29.3 + - - +
103B SER* 3.0 21.8 + - - +
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Residues in contact with ARG 97 (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 GLY 3.4 3.5 - - - +
46B LEU* 2.7 31.6 - - - -
47B THR* 3.1 21.6 + - - +
49B ILE* 4.3 14.1 - - + -
95B MET* 4.9 10.3 - - + -
96B LEU* 1.3 75.7 - - - +
98B ASN* 1.3 78.9 + - - +
99B THR* 3.7 17.7 + - - +
101B TYR* 3.2 4.7 - - - +
102B CYS* 5.7 2.7 - - + -
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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