Contacts of the helix formed by residues 106 - 116 (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 CYS 106 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65B TRP* 4.0 12.6 - - - -
93B TYR* 5.3 0.4 - - - -
101B PHE* 3.9 19.9 - - + -
105B GLY* 1.3 68.5 - - - -
107B PRO* 1.3 64.6 - - - +
108B LEU* 3.4 22.0 - - - -
109B LEU* 3.5 9.4 - - + +
110B ASN* 2.9 35.5 + - - +
168B GLU* 3.1 34.3 - - - +
171B ILE* 4.1 20.0 - - + +
175B ARG* 5.3 1.2 - - - +
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Residues in contact with PRO 107 (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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23B ASN* 3.3 19.3 - - - +
61B PHE* 3.5 12.7 - - + -
64B ASN* 3.7 21.1 - - + +
65B TRP* 3.6 33.0 - - + +
68B VAL* 4.0 17.5 - - + -
102B PRO* 4.3 2.9 - - + -
105B GLY 3.2 10.3 - - - +
106B CYS* 1.3 83.3 - - - +
108B LEU* 1.3 62.2 + - - +
110B ASN* 3.8 1.1 - - + -
111B THR* 2.9 35.8 + - - +
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Residues in contact with LEU 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A LEU* 5.3 2.7 - - + -
61B PHE* 4.0 7.5 - - + -
65B TRP* 3.7 32.1 - - + -
106B CYS* 3.3 11.4 - - - -
107B PRO* 1.3 78.6 - - - +
109B LEU* 1.3 67.4 + - - +
112B THR* 2.8 37.4 + - - +
126B ALA* 3.4 38.4 - - + +
129B ALA* 4.0 8.3 - - + -
130B ILE* 3.6 31.4 - - + -
133B TRP* 4.0 18.6 - - + -
168B GLU* 4.6 5.8 - - + +
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Residues in contact with LEU 109 (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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109A LEU* 4.0 17.7 - - + -
113A ILE* 3.3 34.3 - - + -
172A LEU* 3.7 34.1 - - + -
106B CYS* 3.5 12.6 - - + +
108B LEU* 1.3 83.2 - - - +
110B ASN* 1.3 63.8 + - - +
112B THR* 3.9 0.9 - - - -
113B ILE* 3.2 28.7 + - + +
168B GLU* 3.7 28.0 + - - +
171B ILE* 3.6 32.1 - - + -
172B LEU* 4.2 7.2 - - + +
175B ARG* 5.3 2.7 - - - -
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Residues in contact with ASN 110 (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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113A ILE* 3.3 24.9 - - + +
203A SO4 3.1 26.7 + - - +
23B ASN* 3.0 38.4 + - - +
104B GLY 2.9 26.7 + - - +
106B CYS 2.9 21.4 + - - +
107B PRO* 4.1 1.1 - - + +
109B LEU* 1.3 78.4 - - - +
111B THR* 1.3 65.1 + - - +
113B ILE 3.6 0.3 + - - -
114B GLU* 3.3 21.1 + - - +
175B ARG* 5.5 1.9 - - - -
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Residues in contact with THR 111 (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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23B ASN* 5.4 0.7 + - - -
61B PHE* 3.3 25.7 - - + +
107B PRO* 2.9 20.8 + - - +
108B LEU 4.2 0.4 - - - -
110B ASN* 1.3 77.0 - - - +
112B THR* 1.3 60.5 + - - +
114B GLU* 3.1 4.6 + - - +
115B ALA* 2.8 30.4 + - + +
122B LEU* 3.3 49.9 - - + +
126B ALA* 4.6 3.8 - - + -
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Residues in contact with THR 112 (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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172A LEU* 3.6 28.5 - - + +
175A ARG* 3.8 13.0 - - + +
176A ALA* 3.6 36.4 - - - +
108B LEU* 2.8 25.8 + - - +
111B THR* 1.3 75.6 - - - +
113B ILE* 1.3 59.5 + - + +
115B ALA* 5.1 1.6 - - - -
116B ASP* 2.8 38.4 + - + +
123B ARG* 5.9 0.9 - - + +
126B ALA* 3.4 21.3 - - - +
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Residues in contact with ILE 113 (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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109A LEU* 3.3 38.6 - - + +
110A ASN* 3.3 46.4 - - + +
113A ILE* 3.5 22.7 - - + -
172A LEU* 4.2 12.8 - - + -
175A ARG* 5.8 2.5 - - + -
109B LEU 3.2 16.5 + - - +
110B ASN 4.0 3.6 - - - +
111B THR 3.3 0.6 - - - -
112B THR* 1.3 77.6 - - + +
114B GLU* 1.3 54.8 + - - +
116B ASP* 4.4 1.3 - - - +
203B SO4 1.8 47.7 + - - +
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Residues in contact with GLU 114 (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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24A VAL 4.5 2.5 - - - +
25A LYS 5.5 3.8 - - - +
25B LYS 5.0 0.3 - - - +
26B GLY* 3.2 12.6 - - - -
27B LEU* 2.8 30.1 + - - +
28B ALA* 2.9 36.6 + - - +
29B GLY 4.8 0.2 + - - -
110B ASN 3.3 12.9 + - - +
111B THR* 3.1 6.1 + - - +
113B ILE* 1.3 81.4 - - - +
115B ALA* 1.3 57.7 + - - +
116B ASP 3.5 0.3 + - - -
118B THR* 2.6 38.9 + - + +
203B SO4 3.7 2.9 + - - -
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Residues in contact with ALA 115 (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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111B THR* 2.8 22.3 + - + +
112B THR 4.5 0.2 - - - +
114B GLU* 1.3 72.4 - - + +
116B ASP* 1.3 66.8 + - - +
117B ASP 3.1 3.3 + - - -
118B THR* 3.5 7.9 - - - -
119B HIS* 3.0 45.1 + - + +
122B LEU* 3.8 19.7 - - + -
123B ARG* 3.6 18.3 - - - +
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Residues in contact with ASP 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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175A ARG* 2.9 54.9 - - + +
178A LYS* 6.1 1.4 - - - -
112B THR 2.8 18.8 + - - +
113B ILE* 4.6 0.9 - - - +
115B ALA* 1.3 78.0 - - - +
117B ASP* 1.3 71.9 + - - +
118B THR 4.0 0.2 + - - -
120B ASP* 5.6 2.3 - - - +
123B ARG* 3.6 18.3 - - + +
203B SO4 2.0 49.4 + - - -
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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