Contacts of the helix formed by residues 115 - 126 (chain B) in PDB entry 3UXA
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 LYS 115 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16B SER 3.2 22.2 - - - +
17B LEU* 3.2 29.9 + - + +
18B ARG 4.4 0.8 - - - -
19B ARG 2.8 26.7 + - - +
21B SER 5.3 0.4 - - - +
113B ILE* 3.8 3.7 - - - +
114B VAL* 1.3 83.3 - - + +
116B GLU* 1.3 67.0 + - - +
117B SER* 3.2 27.2 + - - +
118B GLN* 3.0 34.4 + - - +
119B ILE* 3.7 2.4 + - - +
145B LEU* 3.5 12.5 - - - +
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Residues in contact with GLU 116 (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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115B LYS* 1.3 71.5 - - - +
117B SER* 1.3 54.6 + - - +
119B ILE* 2.7 27.5 + - - +
120B ASP* 2.9 15.3 + - - +
144B SER* 4.5 11.4 + - - +
145B LEU* 3.3 17.1 - - + +
148B TYR* 3.6 51.8 - - + +
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Residues in contact with SER 117 (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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19B ARG 4.4 2.9 + - - -
21B SER* 3.4 22.1 + - - -
115B LYS* 3.2 35.6 + - - +
116B GLU* 1.3 77.1 - - - +
118B GLN* 1.3 61.4 + - - +
120B ASP* 3.3 15.9 + - - +
121B ASP* 2.9 35.9 + - - +
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Residues in contact with GLN 118 (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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16B SER* 3.7 17.9 + - - +
19B ARG* 5.2 8.5 - - - +
93B TYR* 4.1 14.8 - - - +
109B MET* 3.6 16.6 - - + +
111B ASP* 4.4 9.8 - - - +
112B PHE 3.0 19.6 - - - +
113B ILE* 3.5 16.3 - - + +
114B VAL* 2.7 38.1 - - - +
115B LYS* 3.0 28.3 + - + +
117B SER* 1.3 87.9 + - - +
119B ILE* 1.3 58.6 + - - +
121B ASP* 3.8 9.4 - - - +
122B ALA* 3.2 18.9 + - - +
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Residues in contact with ILE 119 (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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113B ILE* 4.0 20.9 - - + -
115B LYS 4.2 2.0 - - - +
116B GLU 2.7 11.6 + - - +
118B GLN* 1.3 75.6 - - - +
120B ASP* 1.3 65.4 + - - +
122B ALA* 3.1 7.5 + - - +
123B TYR* 3.0 20.3 + - - +
130B VAL* 4.9 9.6 - - + -
132B LEU* 4.8 4.7 - - + -
145B LEU* 3.3 51.1 - - + +
148B TYR* 3.7 22.0 - - + -
149B ALA* 3.9 13.5 - - + -
152B TYR* 4.0 5.4 - - + -
154B MET* 3.6 23.9 - - + +
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Residues in contact with ASP 120 (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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21B SER* 4.9 3.8 + - - +
22B LEU 5.9 1.1 - - - +
116B GLU* 2.9 12.6 + - - +
117B SER* 3.3 19.4 + - - +
119B ILE* 1.3 72.2 - - - +
121B ASP* 1.3 55.2 + - - +
123B TYR* 2.9 5.2 + - - +
124B ASN* 2.8 45.8 + - - +
148B TYR* 2.6 32.0 + - - -
152B TYR* 2.9 23.1 + - - +
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Residues in contact with ASP 121 (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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20B PRO 4.1 1.2 - - - +
21B SER* 3.6 14.0 + - - -
22B LEU* 3.0 36.1 + - + +
93B TYR* 2.9 41.5 + - + +
117B SER* 2.9 26.7 + - - +
118B GLN* 3.8 8.6 - - - +
120B ASP* 1.3 70.9 - - - +
122B ALA* 1.3 65.7 + - - +
124B ASN* 3.1 5.1 + - - +
125B LEU* 2.8 37.6 + - + +
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Residues in contact with ALA 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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96B LEU* 4.7 2.2 - - - -
109B MET* 3.7 24.1 - - - -
118B GLN 3.2 8.4 + - - +
119B ILE 3.1 9.4 + - - +
121B ASP* 1.3 78.8 - - - +
123B TYR* 1.3 60.3 + - - +
125B LEU* 4.0 0.7 - - - +
126B GLY 3.3 3.5 + - - -
127B ALA* 2.8 38.3 + - + +
130B VAL* 3.5 31.6 - - + -
154B MET* 4.9 2.7 - - - -
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Residues in contact with TYR 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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26B ARG* 2.6 67.6 + - + +
30B ILE* 3.7 24.3 - - + +
119B ILE 3.0 10.3 + - - +
120B ASP 2.9 7.9 + - - +
122B ALA* 1.3 76.1 - - - +
124B ASN* 1.3 91.3 + - - +
126B GLY 3.4 0.3 + - - -
127B ALA 4.6 1.8 - - - -
152B TYR* 3.4 51.6 + + + -
154B MET* 4.1 15.0 - - + +
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Residues in contact with ASN 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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22B LEU* 4.7 9.9 - - + +
23B ARG* 5.8 0.2 - - - -
24B ALA* 3.4 39.7 + - + +
25B SER* 3.6 8.0 - - - +
26B ARG* 3.5 23.9 + - - +
120B ASP* 2.8 28.2 + - - +
121B ASP* 4.0 4.9 - - - +
123B TYR* 1.3 101.9 - - - +
125B LEU* 1.3 59.0 + - + +
152B TYR* 4.9 3.3 + - - -
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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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22B LEU* 3.6 26.5 - - + -
24B ALA* 5.2 6.7 - - + -
26B ARG* 5.6 0.4 - - - -
27B GLN 6.2 0.2 - - - -
93B TYR* 3.6 44.2 - - + +
94B GLU* 5.6 0.2 - - - -
96B LEU* 3.7 24.9 - - + +
97B ARG* 3.7 45.1 - - + +
100B ALA* 3.4 17.7 - - - +
121B ASP* 2.8 26.9 + - + +
122B ALA 4.1 0.7 - - - +
124B ASN* 1.3 80.1 - - + +
126B GLY* 1.3 55.7 + - - +
127B ALA 3.7 0.2 - - - -
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Residues in contact with GLY 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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26B ARG* 3.2 22.7 + - - -
27B GLN 5.8 0.7 - - - -
28B ARG* 3.0 34.7 + - - -
100B ALA* 4.0 11.7 - - - +
107B ILE* 4.7 0.3 - - - +
122B ALA 3.3 2.0 + - - -
123B TYR 3.4 4.2 + - - -
124B ASN 3.5 1.0 + - - -
125B LEU* 1.3 78.8 - - - +
127B ALA* 1.3 68.2 + - - +
128B ASP 3.4 0.9 + - - -
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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