Contacts of the helix formed by residues 121 - 128 (chain B) in PDB entry 3UXP
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 121 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99B PHE* 4.4 6.1 - - - -
100B LEU* 4.9 0.4 - - - -
119B ILE* 4.0 0.5 - - - +
120B LYS* 1.3 78.1 - - + +
122B LEU* 1.3 75.8 + - - +
123B GLU* 2.7 22.7 + - + +
124B ASP* 3.2 32.7 + - - +
125B LEU* 2.8 29.1 + - - +
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Residues in contact with LEU 122 (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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99B PHE* 3.6 29.3 - - + -
103B VAL* 4.6 2.9 - - + -
121B THR* 1.3 77.8 + - - +
123B GLU* 1.3 54.6 + - - +
125B LEU* 2.9 15.6 + - + +
126B ARG* 2.7 72.8 + - - +
140B LEU* 4.2 14.1 - - + -
143B PHE* 3.6 44.6 - - + -
144B GLU* 5.1 4.7 - - + -
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Residues in contact with GLU 123 (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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121B THR* 2.7 24.5 + - + +
122B LEU* 1.3 75.1 - - - +
124B ASP* 1.3 65.2 + - - +
126B ARG* 3.0 21.8 + - - +
127B LYS* 3.1 42.4 + - - +
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Residues in contact with ASP 124 (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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118B GLY 3.2 20.1 - - - +
119B ILE* 3.7 11.2 - - + +
120B LYS* 3.3 21.9 + - - +
121B THR* 3.2 29.7 + - - +
123B GLU* 1.3 81.3 - - - +
125B LEU* 1.3 57.3 + - - +
127B LYS* 3.6 4.4 + - - +
128B ASN* 3.1 35.4 + - - +
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Residues in contact with LEU 125 (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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100B LEU* 4.3 16.2 - - + -
103B VAL* 4.4 5.4 - - + -
106B ILE* 4.0 21.5 - - + -
114B LEU* 3.7 22.2 - - + -
119B ILE* 3.6 24.7 - - + -
121B THR 2.8 14.1 + - - +
122B LEU* 2.9 19.9 + - + +
124B ASP* 1.3 73.1 - - - +
126B ARG* 1.3 59.6 + - - +
128B ASN 3.3 4.7 - - - +
129B GLU* 3.0 27.0 + - - +
132B LEU* 3.9 19.2 - - + +
140B LEU* 3.9 27.2 - - + +
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Residues in contact with ARG 126 (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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122B LEU* 2.7 51.9 + - - +
123B GLU* 3.0 14.0 + - - +
125B LEU* 1.3 74.2 - - - +
127B LYS* 1.3 69.1 - - + +
128B ASN 3.5 0.2 + - - -
129B GLU* 3.6 21.5 - - - +
140B LEU* 3.8 40.7 + - + +
141B LYS* 5.0 4.2 + - - +
144B GLU* 3.8 21.4 + - - -
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Residues in contact with LYS 127 (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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123B GLU* 3.1 40.2 + - - +
124B ASP* 4.0 4.0 - - - +
126B ARG* 1.3 84.6 - - + +
128B ASN* 1.3 71.6 + - - +
129B GLU 3.5 0.9 + - - -
130B ASP* 3.9 7.3 - - - +
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Residues in contact with ASN 128 (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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119B ILE* 3.5 33.6 - - + +
124B ASP* 3.1 17.3 + - - +
125B LEU* 3.3 6.2 - - - +
126B ARG 3.2 0.2 - - - -
127B LYS* 1.3 88.6 + - - +
129B GLU* 1.3 58.5 + - - +
130B ASP* 3.0 14.1 + - - +
131B LYS* 3.1 41.5 + - + +
132B LEU* 4.4 4.0 + - - +
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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