Contacts of the helix formed by residues 90 - 98 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41F SER* 3.9 0.2 - - - -
45F GLN* 4.0 1.1 - - - +
102F GLU* 3.4 29.2 - - + +
103F VAL 3.4 30.1 - - - +
104F LEU* 4.4 4.5 - - + +
89H SER* 1.3 82.0 - - - +
91H LEU* 1.3 59.4 + - - +
92H LYS* 3.8 9.0 + - - +
93H GLU* 2.9 38.5 + - - +
94H PHE* 3.0 33.6 + - - -
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Residues in contact with LEU 91 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37F SER* 4.5 8.7 - - - +
38F VAL* 3.9 17.5 - - + -
41F SER* 3.6 22.2 - - - +
91F LEU* 4.0 23.6 - - + +
94F PHE* 3.7 37.5 - - + -
95F SER* 3.4 16.6 - - - +
102F GLU* 2.8 17.9 + - - +
90H THR* 1.3 68.4 - - - +
92H LYS* 1.3 60.8 + - - +
94H PHE* 3.3 20.0 + - + +
95H SER* 2.8 33.6 + - - -
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Residues in contact with LYS 92 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95F SER* 4.2 8.2 + - - +
102F GLU* 4.4 1.0 + - - -
104F LEU* 6.6 0.4 - - + -
90H THR* 3.2 8.4 - - - +
91H LEU* 1.3 79.3 - - - +
93H GLU* 1.3 59.7 + - + +
95H SER* 3.4 4.6 + - - -
96H GLU* 2.6 76.9 + - - +
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Residues in contact with GLU 93 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104F LEU* 3.5 26.9 - - + +
105F GLY 5.1 0.9 + - - -
34H ALA* 4.5 0.2 - - - +
87H PRO 5.0 0.9 - - - +
88H PHE* 3.6 34.0 - - + -
89H SER* 3.0 23.7 + - - -
90H THR* 2.9 39.8 + - - +
92H LYS* 1.3 77.9 - - + +
94H PHE* 1.3 64.8 - - - +
96H GLU* 4.9 2.9 - - - +
97H ASN* 2.7 36.5 + - - +
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Residues in contact with PHE 94 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41F SER* 4.2 12.6 - - - -
48F TRP* 4.7 9.2 - + - -
91F LEU* 3.7 12.1 - - + -
33H VAL* 3.7 10.8 - - + -
34H ALA* 3.7 15.8 - - - +
37H SER* 3.5 36.6 - - - -
38H VAL* 4.3 2.0 - - - -
73H LEU* 5.9 0.2 - - + -
88H PHE* 3.3 40.4 - - + -
89H SER* 3.8 12.6 - - - -
90H THR 3.0 26.0 + - - -
91H LEU* 3.7 20.2 - - + +
93H GLU* 1.3 74.8 - - - +
95H SER* 1.3 57.6 + - - +
98H SER* 3.0 35.9 + - - -
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Residues in contact with SER 95 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91F LEU* 4.4 16.4 - - - +
92F LYS* 4.6 11.3 + - - +
38H VAL* 4.5 9.8 - - - +
91H LEU 2.8 19.6 + - - -
92H LYS* 3.8 4.9 - - - -
94H PHE* 1.3 77.4 - - - +
96H GLU* 1.3 64.2 + - - +
97H ASN 3.6 0.2 + - - -
98H SER* 4.0 11.1 + - - +
100H LEU 5.4 2.3 - - - +
102H GLU* 5.0 3.5 + - - -
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Residues in contact with GLU 96 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92H LYS* 2.6 62.1 + - + +
93H GLU* 4.3 3.6 - - - +
95H SER* 1.3 80.3 - - - +
97H ASN* 1.3 67.5 + - - +
98H SER 4.5 2.7 - - - +
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Residues in contact with ASN 97 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31H GLN* 2.9 26.4 + - - +
34H ALA* 4.0 5.6 - - + -
88H PHE* 3.5 44.0 - - + -
93H GLU* 2.7 36.0 + - - +
96H GLU* 1.3 85.7 + - - +
98H SER* 1.3 62.1 + - - +
99H GLN* 4.8 1.6 - - - +
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Residues in contact with SER 98 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31H GLN* 3.9 0.7 - - - +
34H ALA* 3.8 8.7 - - - +
35H ASP* 2.7 22.2 + - - -
38H VAL* 3.5 30.0 - - - +
94H PHE 3.0 19.8 + - - -
95H SER 4.1 9.2 - - - +
96H GLU 3.6 3.2 - - - +
97H ASN* 1.3 80.3 - - - +
99H GLN* 1.3 60.7 + - - +
100H LEU* 3.0 20.7 + - - +
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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