Contacts of the helix formed by residues 90 - 98 (chain J) in PDB entry 2UX1
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 THR 90 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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89J SER* 1.3 85.3 - - - +
91J LEU* 1.3 65.6 + - - +
92J LYS* 3.9 8.1 + - - +
93J GLU* 2.8 37.2 + - - +
94J PHE* 3.0 28.3 + - - -
41L SER* 3.9 0.2 - - - -
45L GLN* 3.8 2.5 - - - +
102L GLU* 3.5 25.4 - - + -
103L VAL 3.3 32.3 - - - +
104L LEU* 4.4 5.7 - - + +
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Residues in contact with LEU 91 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90J THR* 1.3 70.0 - - - +
92J LYS* 1.3 56.7 + - - +
94J PHE* 3.2 16.6 + - + +
95J SER* 2.8 33.4 + - - -
37L SER* 4.7 6.1 - - - +
38L VAL* 3.9 18.6 - - + -
41L SER* 3.9 20.4 - - - +
91L LEU* 3.9 38.2 - - + +
94L PHE* 3.7 31.0 - - + -
95L SER* 4.2 13.2 - - - +
102L GLU* 2.8 23.4 + - - +
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Residues in contact with LYS 92 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90J THR* 3.2 8.4 - - - +
91J LEU* 1.3 77.7 - - - +
93J GLU* 1.3 57.6 + - + +
95J SER* 3.6 3.9 - - - -
96J GLU* 2.7 72.2 + - - +
95L SER* 4.9 7.1 + - - +
102L GLU* 4.3 1.6 + - - +
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Residues in contact with GLU 93 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34J ALA* 4.3 0.5 - - - +
87J PRO 4.9 1.4 - - - +
88J PHE* 3.3 42.8 - - + -
89J SER* 3.2 16.5 + - - -
90J THR* 2.8 28.9 + - - +
92J LYS* 1.3 75.8 - - + +
94J PHE* 1.3 66.0 + - - +
96J GLU* 4.8 2.0 - - - -
97J ASN* 2.7 37.1 + - - +
104L LEU* 3.4 30.8 - - + +
105L GLY 5.0 0.7 + - - -
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Residues in contact with PHE 94 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33J VAL* 3.7 10.8 - - + -
34J ALA* 3.6 19.6 - - - +
37J SER* 3.6 35.7 - - - -
38J VAL* 4.3 2.2 - - - -
88J PHE* 3.3 37.0 - - + -
89J SER* 3.7 13.0 - - - -
90J THR 3.0 26.6 + - - -
91J LEU* 3.6 19.5 - - + +
93J GLU* 1.3 75.6 - - - +
95J SER* 1.3 64.6 + - - +
98J SER* 3.0 30.1 + - - -
41L SER* 4.1 12.8 - - - -
48L TRP* 4.8 7.9 - + - -
91L LEU* 3.8 12.3 - - + -
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Residues in contact with SER 95 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38J VAL* 4.6 4.9 - - - -
91J LEU 2.8 18.3 + - - -
92J LYS* 3.6 5.6 - - - -
94J PHE* 1.3 78.6 - - - +
96J GLU* 1.3 63.1 + - - +
97J ASN 3.5 0.2 + - - -
98J SER* 3.7 13.0 + - - +
100J LEU 5.3 2.1 - - - +
101J LYS* 5.7 1.0 + - - -
102J GLU* 4.8 3.6 + - - -
91L LEU* 4.2 22.3 - - - +
92L LYS* 4.7 9.5 + - - +
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Residues in contact with GLU 96 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92J LYS* 2.7 61.3 + - + +
93J GLU* 5.4 0.9 - - - -
95J SER* 1.3 78.4 - - - +
97J ASN* 1.3 68.6 + - - +
98J SER 4.6 2.1 - - - +
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Residues in contact with ASN 97 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31J GLN* 3.0 27.4 + - - +
34J ALA* 3.9 5.8 - - + -
88J PHE* 3.3 41.0 - - + -
93J GLU* 2.7 35.9 + - - +
96J GLU* 1.3 84.2 + - - +
98J SER* 1.3 63.8 + - - +
99J GLN* 5.1 1.4 - - - +
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Residues in contact with SER 98 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31J GLN* 4.0 0.9 - - - +
34J ALA* 3.9 8.7 - - - +
35J ASP* 2.6 30.2 + - - -
38J VAL* 3.6 18.8 - - - +
94J PHE 3.0 18.3 + - - -
95J SER 3.7 9.9 + - - +
96J GLU 3.6 2.3 - - - +
97J ASN* 1.3 79.9 + - - +
99J GLN* 1.3 59.5 + - - +
100J LEU* 3.2 20.8 + - - +
101J LYS* 3.6 11.6 + - - -
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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