Contacts of the helix formed by residues 106 - 116 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65A TRP* 4.1 11.0 - - - -
101A PHE* 3.9 19.1 - - + -
104A GLY 4.0 1.0 + - - -
105A GLY* 1.3 70.5 - - - -
107A PRO* 1.4 66.8 - - - +
108A LEU* 3.4 22.0 - - - -
109A LEU* 3.6 11.4 - - + -
110A ASN* 2.9 35.8 + - - +
168A GLU* 2.9 34.3 - - - +
171A ILE* 4.1 16.0 - - + +
175A ARG* 5.5 0.4 - - - +
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Residues in contact with PRO 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A ASN* 3.3 19.1 - - - +
61A PHE* 3.7 15.3 - - + -
64A ASN* 3.7 19.7 - - + +
65A TRP* 3.6 33.9 - - + +
68A VAL* 4.0 17.0 - - + -
102A PRO* 4.0 4.3 - - + -
105A GLY 3.2 9.8 - - - +
106A CYS* 1.4 83.4 - - - +
108A LEU* 1.3 57.8 + - - +
110A ASN* 3.7 1.6 - - + -
111A THR* 2.7 40.2 + - - +
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Residues in contact with LEU 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A PHE* 4.3 10.5 - - + -
65A TRP* 3.6 36.8 - - + -
106A CYS* 3.2 10.8 - - - -
107A PRO* 1.3 76.5 - - - +
109A LEU* 1.3 66.1 + - - +
111A THR* 4.3 0.4 - - - -
112A THR* 2.7 40.3 + - - +
126A ALA* 4.6 7.3 - - + +
129A ALA* 4.5 3.1 - - + -
130A ILE* 3.5 48.0 - - + +
133A TRP* 3.9 13.2 - - + -
168A GLU* 3.6 11.4 - - - +
172B LEU* 3.8 14.4 - - + -
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Residues in contact with LEU 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A CYS* 3.4 12.8 + - + +
108A LEU* 1.3 86.2 - - - +
110A ASN* 1.3 64.4 + - - +
112A THR* 4.0 0.5 - - - -
113A ILE* 3.2 27.4 + - + +
168A GLU* 3.7 28.0 - - + +
171A ILE* 3.7 31.6 - - + -
172A LEU* 4.3 7.0 - - + +
175A ARG* 6.0 1.1 - - + -
109B LEU* 4.0 23.6 - - + -
113B ILE* 3.3 23.3 - - + -
172B LEU* 3.4 32.3 - - + -
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Residues in contact with ASN 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A ASN* 2.9 39.7 + - - +
104A GLY 2.9 25.7 + - - +
106A CYS 2.9 21.5 + - - +
107A PRO 4.1 0.7 - - - +
109A LEU* 1.3 78.7 - - - +
111A THR* 1.3 62.6 + - - +
113A ILE 3.8 0.3 + - - -
114A GLU* 3.5 21.0 + - - +
175A ARG* 5.7 0.9 - - - -
113B ILE* 3.3 20.8 - - - +
203B SO4 2.9 30.0 + - - +
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Residues in contact with THR 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A ASN* 5.5 0.5 + - - -
61A PHE* 3.3 30.7 - - + +
107A PRO* 2.7 28.6 + - - +
108A LEU 4.3 0.7 - - - -
110A ASN* 1.3 73.6 - - - +
112A THR* 1.3 58.8 + - - +
114A GLU* 3.3 5.4 + - - +
115A ALA* 2.8 35.3 + - + +
122A LEU* 3.9 43.5 - - + +
126A ALA* 4.5 3.1 - - + -
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Residues in contact with THR 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A LEU* 2.7 24.8 + - - +
111A THR* 1.3 79.1 - - - +
113A ILE* 1.3 58.6 + - + +
115A ALA* 4.9 1.3 - - - -
116A ASP* 2.9 36.5 + - + +
123A ARG* 5.8 2.0 - - + +
126A ALA* 3.4 21.0 - - - +
172B LEU* 3.5 25.4 - - + +
175B ARG* 3.7 13.9 - - + +
176B ALA* 3.5 38.2 - - - +
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Residues in contact with ILE 113 (chain A).
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* 3.2 19.4 + - + +
110A ASN 4.2 0.2 - - - +
111A THR 3.3 0.8 - - - -
112A THR* 1.3 77.8 - - + +
114A GLU* 1.3 51.9 + - - +
116A ASP* 4.4 2.2 - - - +
203A SO4 2.2 49.9 + - - +
109B LEU* 3.3 39.0 - - + +
110B ASN* 3.3 47.1 - - + +
113B ILE* 3.5 26.9 - - + -
172B LEU* 4.5 10.1 - - + -
175B ARG* 5.7 2.0 - - - -
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Residues in contact with GLU 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A LYS 5.4 0.2 - - - -
26A GLY* 3.1 13.3 - - - -
27A LEU* 2.8 30.4 + - - +
28A ALA* 2.8 36.4 + - - +
29A GLY 4.7 0.2 + - - -
110A ASN 3.5 11.8 + - - +
111A THR* 3.3 8.1 + - - +
112A THR 3.2 0.2 - - - -
113A ILE* 1.3 81.2 - - - +
115A ALA* 1.3 55.1 - - + +
118A THR* 2.7 32.0 + - + +
203A SO4 3.1 14.1 + - - -
24B VAL 4.4 1.9 - - - +
25B LYS 5.7 4.2 - - - +
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Residues in contact with ALA 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A THR* 2.8 22.4 + - + +
112A THR* 4.5 0.4 - - - +
114A GLU* 1.3 75.9 - - + +
116A ASP* 1.3 67.0 + - - +
117A ASP 3.3 0.2 - - - -
118A THR* 3.6 6.1 - - - -
119A HIS* 2.8 36.6 + - + +
122A LEU* 3.7 17.3 - - + -
123A ARG* 3.6 28.7 - - - +
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Residues in contact with ASP 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A THR* 2.9 17.1 + - + +
113A ILE* 2.9 2.9 - - - +
115A ALA* 1.3 78.1 - - - +
117A ASP* 1.3 70.9 + - - +
118A THR 4.0 0.2 + - - -
123A ARG* 3.7 12.2 - - + +
203A SO4 2.3 50.9 + - - -
175B ARG* 2.7 57.7 + - + +
178B LYS* 3.0 26.0 + - - +
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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