Contacts of the strand formed by residues 91 - 96 (chain B) in PDB entry 2FE3
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 91 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89B SER* 3.2 31.4 + - - -
90B ASP* 1.3 80.9 + - - +
92B TYR* 1.3 68.7 + - - +
93B HIS* 3.6 28.9 - - + +
127B HIS* 5.9 2.0 - + - -
128B HIS 3.0 9.2 + - - +
129B ARG* 3.4 11.6 - - + -
130B LEU 2.9 26.2 + - - -
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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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90B ASP* 3.9 18.4 + - + +
91B HIS* 1.3 77.6 - - - +
93B HIS* 1.3 65.5 + - - +
104B ASP* 3.4 6.8 - - - +
105B PHE* 3.0 63.1 + + + +
106B HIS* 4.6 2.9 - - - -
107B TYR* 3.4 39.5 - + + -
109B GLY* 3.3 24.1 + - - -
110B LEU* 4.3 13.2 - - + -
128B HIS* 2.8 36.9 + + - -
130B LEU* 3.5 24.0 - - + -
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Residues in contact with HIS 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B HIS* 3.6 31.6 - - + +
92B TYR* 1.3 76.8 + - - +
94B ALA* 1.3 54.1 + - - +
95B ILE* 4.4 11.2 - - + +
102B ILE* 3.9 19.2 - - + +
103B VAL 3.5 4.3 - - - -
104B ASP* 2.5 31.7 + - - -
105B PHE* 3.7 7.9 - - - -
129B ARG* 4.1 25.0 + - + +
130B LEU 3.0 9.0 + - - +
131B GLU* 3.5 9.7 - - + -
132B ILE* 2.8 31.7 + - - +
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Residues in contact with ALA 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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117A ALA* 5.7 2.0 - - + -
121A THR* 4.1 19.7 - - + +
123A PHE* 3.8 29.8 - - + -
93B HIS* 1.3 73.9 - - - +
95B ILE* 1.3 60.4 + - - +
101B LYS 3.6 0.9 - - - +
102B ILE* 3.2 4.3 - - - -
103B VAL* 2.8 39.1 + - + +
105B PHE* 3.9 6.4 - - + -
132B ILE* 3.3 11.4 - - + +
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Residues in contact with ILE 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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123A PHE* 3.4 4.0 - - - -
93B HIS* 4.4 8.5 - - + +
94B ALA* 1.3 79.2 - - - +
96B CYS* 1.3 71.8 + - - +
97B GLU* 3.5 1.4 + - - -
100B GLY* 4.7 4.5 - - - +
101B LYS 3.4 2.7 - - - +
102B ILE* 4.0 33.0 - - + -
131B GLU* 3.8 32.8 - - + +
132B ILE 2.7 12.1 + - - +
133B TYR* 3.4 38.7 - - + +
134B GLY 3.0 23.9 + - - -
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Residues in contact with CYS 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A PHE* 3.3 12.2 - - + -
95B ILE* 1.3 75.5 - - - +
97B GLU* 1.3 60.7 + - - +
98B ASN* 3.1 16.4 - - - -
99B CYS* 3.6 1.8 - - - -
100B GLY* 2.9 28.9 + - - -
101B LYS* 2.8 25.4 + - + +
134B GLY 3.3 3.6 - - - -
135B VAL* 3.8 5.4 - - - -
136B CYS* 3.3 20.9 - - + +
139B CYS* 3.9 3.4 - - - -
202B ZN 2.4 36.8 - - - -
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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