Contacts of the helix formed by residues 114 - 126 (chain C) in PDB entry 1EGE
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 ASP 114 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69C ASN* 6.3 1.6 - - - -
113C ASN* 1.3 74.9 - - - +
115C GLN* 1.3 76.9 + - - +
117C LYS* 3.3 13.4 + - - +
118C LYS* 3.0 28.5 + - - +
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Residues in contact with GLN 115 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113C ASN* 2.9 15.3 + - - +
114C ASP* 1.3 88.4 - - - +
116C GLN* 1.3 59.5 + - + +
118C LYS* 3.4 14.5 - - + +
119C LYS* 3.0 30.9 + - - +
235C GLU* 6.5 0.2 - - + -
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Residues in contact with GLN 116 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108C ILE* 6.0 4.5 - - + -
112C GLY* 3.2 12.7 - - - -
113C ASN* 2.9 48.6 + - - +
115C GLN* 1.3 75.4 - - + +
117C LYS* 1.3 65.1 + - - +
119C LYS* 3.0 5.5 + - - +
120C TYR* 3.0 34.2 + - + +
198C ILE* 3.3 33.0 - - + +
235C GLU* 3.0 24.2 + - + +
236C ASN* 3.6 1.8 - - - +
237C VAL 2.8 29.5 + - - +
238C LEU* 3.9 4.9 - - - +
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Residues in contact with LYS 117 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67C PRO* 5.0 11.1 - - + +
69C ASN* 5.1 6.7 + - - +
70C CYS* 3.1 12.0 - - - -
108C ILE* 3.7 18.4 - - + +
109C ILE* 3.5 26.2 + - - +
110C ILE 5.5 1.0 - - - -
111C ALA 5.3 0.4 - - - +
112C GLY* 3.0 24.2 + - - +
113C ASN 2.8 17.5 + - - +
114C ASP* 3.7 12.9 + - - +
116C GLN* 1.3 78.6 - - - +
118C LYS* 1.3 56.0 + - - +
121C LEU* 2.8 51.5 + - + +
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Residues in contact with LYS 118 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69C ASN* 5.8 0.9 - - - +
70C CYS* 3.9 13.9 - - + -
114C ASP 3.0 21.1 + - - +
115C GLN* 3.4 20.0 - - + +
117C LYS* 1.3 75.9 - - - +
119C LYS* 1.3 72.2 + - + +
122C GLY* 3.5 19.0 + - - +
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Residues in contact with LYS 119 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115C GLN 3.0 20.3 + - - +
116C GLN* 3.0 4.7 + - - +
118C LYS* 1.3 89.3 - - + +
120C TYR* 1.3 93.0 + - + +
123C ARG* 3.5 39.0 + - - +
200C GLU* 3.7 12.0 + - - -
235C GLU* 4.1 20.6 - - - +
236C ASN* 5.1 0.2 - - - +
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Residues in contact with TYR 120 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108C ILE* 4.4 9.6 - - + -
116C GLN* 3.0 19.0 + - + +
119C LYS* 1.3 105.6 + - + +
121C LEU* 1.3 63.3 + - - +
123C ARG* 3.2 43.7 - - - +
124C MET* 3.4 9.0 - - - +
175C TRP* 3.7 39.7 + + + -
198C ILE* 3.6 33.4 - - + -
200C GLU* 3.3 30.3 + - + -
235C GLU* 5.0 0.2 + - - -
236C ASN* 3.0 32.6 + - - -
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Residues in contact with LEU 121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66C ILE* 3.5 33.0 - - + +
67C PRO* 3.8 16.8 - - + -
70C CYS* 4.2 1.6 - - + -
105C GLN* 4.2 12.8 - - + +
108C ILE* 3.6 27.4 - - + -
109C ILE* 3.2 37.7 - - + -
117C LYS* 2.8 41.9 + - + +
120C TYR* 1.3 73.7 - - - +
122C GLY* 1.3 65.9 + - - +
123C ARG 3.1 0.2 - - - -
124C MET* 2.9 14.9 + - - -
125C THR* 3.3 11.0 + - - -
175C TRP* 5.2 0.2 - - + -
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Residues in contact with GLY 122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70C CYS* 3.9 19.9 - - - +
117C LYS 3.5 2.2 + - - -
118C LYS* 3.5 20.5 + - - -
120C TYR 3.4 0.4 - - - -
121C LEU* 1.3 79.9 - - - +
123C ARG* 1.3 60.4 + - - +
125C THR* 3.0 18.9 + - - -
126C GLU* 3.5 10.7 + - - +
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Residues in contact with ARG 123 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119C LYS* 3.5 32.3 + - - +
120C TYR* 3.2 35.8 + - - +
121C LEU 3.1 1.0 - - - -
122C GLY* 1.3 71.9 - - - +
124C MET* 1.3 70.7 + - - +
125C THR 2.9 6.4 + - - -
126C GLU* 3.1 16.6 + - - +
127C GLU* 3.1 23.5 + - - +
129C LEU* 3.8 13.3 - - + +
174C ASN* 2.8 38.0 + - - +
175C TRP* 3.8 14.8 - - - +
200C GLU* 3.4 26.1 + - - -
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Residues in contact with MET 124 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57C TRP* 2.9 27.2 + - - -
63C ASN* 3.0 14.4 + - - +
66C ILE* 3.8 12.8 - - + -
101C ASN* 3.7 10.5 - - - +
105C GLN* 3.4 22.2 - - - +
120C TYR 3.4 12.1 - - - +
121C LEU* 2.9 8.5 + - - +
123C ARG* 1.3 85.0 - - - +
125C THR* 1.3 55.5 + - - +
127C GLU 3.3 8.8 - - - +
129C LEU* 3.3 41.5 - - - +
130C MET 3.6 17.9 - - - +
131C CYS* 4.0 5.6 - - + +
175C TRP* 3.5 24.9 - - + +
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Residues in contact with THR 125 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57C TRP* 3.4 14.6 + - - +
63C ASN* 4.9 2.0 - - - +
66C ILE* 4.0 10.6 - - - +
70C CYS 3.0 19.1 + - - +
71C GLY* 3.0 36.7 + - - +
72C GLY* 4.4 0.9 - - - -
121C LEU 3.3 9.4 + - - -
122C GLY 3.0 12.3 - - - -
123C ARG 2.9 0.4 - - - -
124C MET* 1.3 79.9 - - - +
126C GLU* 1.3 57.5 + - + +
127C GLU 3.6 0.2 - - - -
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Residues in contact with GLU 126 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57C TRP* 3.6 12.7 - - - -
122C GLY 3.8 12.6 - - - +
123C ARG* 3.1 23.2 + - - +
125C THR* 1.3 78.5 - - + +
127C GLU* 1.3 102.2 + - - +
128C PRO* 4.8 0.2 - - - +
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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