Contacts of the helix formed by residues 88 - 95 (chain B) in PDB entry 3EUP
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 VAL 88 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72B LEU* 3.4 33.7 - - + -
75B LYS* 4.0 30.4 - - + +
76B VAL* 4.2 3.1 - - + +
79B CYS* 3.7 19.7 - - - -
84B GLU 3.3 16.8 - - - +
85B MET* 3.6 14.1 - - - +
86B LEU 3.7 0.6 - - - -
87B LEU* 1.3 77.6 - - - +
89B TYR* 1.3 68.4 + - + +
90B SER 3.4 0.7 - - - -
91B SER* 2.9 25.3 + - - +
92B MET* 3.0 10.4 + - + +
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Residues in contact with TYR 89 (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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72B LEU* 3.6 35.3 - - + +
85B MET 4.3 3.5 + - - -
86B LEU* 3.4 30.5 - - - -
87B LEU 3.2 2.4 - - - -
88B VAL* 1.3 81.2 - - + +
90B SER* 1.3 65.0 + - - +
92B MET* 3.1 22.3 + - + +
93B TYR* 2.9 26.0 + - - +
133B TRP* 3.0 41.1 + + - -
137B LEU* 3.5 12.7 - - + +
163B MET* 3.9 13.2 - - + -
167B VAL* 3.7 36.5 - - + +
187B PHE* 3.9 8.1 - - + -
190B LEU* 4.2 7.6 - - + -
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Residues in contact with SER 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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87B LEU 4.3 5.9 + - - -
88B VAL 3.4 0.6 - - - -
89B TYR* 1.3 78.5 - - - +
91B SER* 1.3 58.3 + - - +
93B TYR* 3.9 0.2 - - - -
94B ASN* 2.8 51.6 + - - +
184B ASP* 5.0 2.3 + - - -
187B PHE* 3.7 36.9 - - - +
190B LEU* 5.6 0.4 - - - +
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Residues in contact with SER 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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75B LYS* 3.4 18.8 + - - +
87B LEU 5.2 1.0 + - - -
88B VAL* 2.9 20.9 + - - -
90B SER* 1.3 79.2 + - - +
92B MET* 1.3 58.1 + - - +
94B ASN* 5.0 0.7 - - - -
95B ASP* 2.9 57.4 + - - +
100B LEU* 4.3 0.5 - - - +
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Residues in contact with MET 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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68B VAL* 3.8 17.3 - - + +
71B VAL* 3.6 35.2 - - + -
72B LEU* 3.9 28.9 - - + -
75B LYS* 4.1 13.5 - - + +
88B VAL 3.0 10.3 + - - +
89B TYR* 3.1 33.0 + - + +
91B SER* 1.3 83.1 + - - +
93B TYR* 1.3 60.8 + - - +
95B ASP 4.5 1.7 + - - +
98B GLY* 5.3 0.2 - - - -
100B LEU* 3.6 22.1 + - + +
101B PHE* 3.6 35.4 + - + -
167B VAL* 6.3 0.4 - - + -
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Residues in contact with TYR 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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89B TYR 2.9 14.2 + - - +
92B MET* 1.3 76.6 - - - +
94B ASN* 1.3 68.1 + - - +
95B ASP 3.6 0.2 - - - -
98B GLY* 3.4 28.8 + - - -
101B PHE* 3.8 27.8 - + + -
105B GLY* 5.2 2.2 - - - -
106B CYS 5.3 0.2 - - - -
167B VAL* 6.2 0.9 - - + -
171B ILE* 3.6 45.1 + - + +
174B HIS* 2.8 46.7 - + + -
175B ARG* 3.0 33.6 + - - +
180B ARG* 3.5 15.4 + - - -
183B SER* 5.3 0.2 - - - -
187B PHE* 4.2 18.4 - + + -
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Residues in contact with ASN 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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90B SER* 2.8 37.1 + - - +
93B TYR* 1.3 87.0 - - - +
95B ASP* 1.3 67.8 + - - +
96B ALA 3.5 0.5 + - - -
97B ASP* 3.4 13.0 + - - -
98B GLY 4.3 0.2 - - - -
180B ARG* 2.9 52.6 + - - +
183B SER* 4.7 3.8 + - - -
184B ASP* 4.0 11.7 + - - +
187B PHE* 3.6 18.4 - - - -
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Residues in contact with ASP 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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75B LYS* 4.4 8.1 + - - -
91B SER* 2.9 44.8 + - - +
92B MET 4.8 1.0 - - - +
93B TYR 3.6 0.7 - - - +
94B ASN* 1.3 78.4 - - - +
96B ALA* 1.3 70.3 + - + +
98B GLY* 3.1 11.4 + - - -
99B SER 3.8 3.5 + - - -
100B LEU* 3.9 19.4 - - + +
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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