Contacts of the helix formed by residues 124 - 134 (chain C) in PDB entry 1EZF
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 124 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42C THR* 4.0 2.9 - - - +
46C TYR* 2.6 34.4 + - + +
110C ARG* 4.3 11.8 + - - +
120C GLN* 2.9 19.6 + - - +
121C VAL 3.9 4.0 - - - -
123C GLU* 1.3 78.6 - - - +
125C PHE* 1.3 64.1 + - - +
126C PRO* 3.2 4.5 - - - +
127C THR* 2.7 43.0 + - - +
128C ILE* 3.7 7.1 + - - +
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Residues in contact with PHE 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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75C VAL* 4.4 7.2 - - + -
78C ALA* 3.6 27.1 - - + -
100C PHE* 3.5 15.3 - + - -
103C PHE* 4.0 20.4 - - + -
104C LEU* 3.5 33.4 - - + -
106C GLN 5.7 0.2 - - - -
109C TRP* 3.5 34.8 - + + +
121C VAL 3.4 18.0 + - - -
122C LEU* 3.8 12.1 - - + +
123C GLU 3.5 1.2 - - - -
124C ASP* 1.3 76.3 - - - +
126C PRO* 1.4 58.6 - - + +
128C ILE* 2.7 43.9 + - + +
129C SER* 2.7 29.1 + - - -
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Residues in contact with PRO 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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107C PRO 3.3 22.5 - - - +
108C ASP* 4.1 8.3 - - - -
109C TRP 3.1 21.5 - - - +
110C ARG* 3.6 31.2 - - + +
124C ASP* 3.3 5.8 - - - +
125C PHE* 1.4 87.7 - - - +
127C THR* 1.3 57.8 + - - +
129C SER* 3.3 10.1 + - - +
130C LEU* 3.1 30.2 + - - +
133C ARG* 4.6 1.6 + - - -
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Residues in contact with THR 127 (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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39C SER* 3.7 32.6 - - - +
42C THR* 3.8 23.6 - - + +
43C CYS* 3.8 3.9 - - - -
46C TYR* 4.8 2.2 - - + -
124C ASP* 2.7 38.1 + - - -
125C PHE 3.0 0.8 - - - -
126C PRO* 1.3 79.2 - - - +
128C ILE* 1.3 60.8 + - - +
130C LEU* 3.7 6.7 - - - +
131C GLU* 3.5 23.2 + - - +
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Residues in contact with ILE 128 (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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43C CYS* 4.0 9.4 - - - -
46C TYR* 4.2 17.3 - - + -
71C ILE* 4.3 7.3 - - + +
74C LEU* 4.1 30.1 - - + +
75C VAL* 4.0 26.0 - - + -
121C VAL* 3.3 47.8 - - + +
124C ASP 4.2 6.3 - - - +
125C PHE* 2.7 23.5 + - + +
127C THR* 1.3 70.7 - - - +
129C SER* 1.3 59.9 + - - +
130C LEU 3.1 0.9 - - - -
131C GLU* 3.0 5.0 + - - +
132C PHE* 2.8 25.3 + - - +
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Residues in contact with SER 129 (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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103C PHE 4.0 4.5 - - - -
104C LEU* 3.6 9.9 - - - +
106C GLN 4.3 5.5 + - - -
107C PRO* 4.4 0.3 - - - +
125C PHE* 2.7 38.7 + - - -
126C PRO* 3.3 16.8 + - - +
128C ILE* 1.3 74.2 - - - +
130C LEU* 1.3 65.0 + - - +
132C PHE* 3.1 9.9 + - - +
133C ARG* 2.9 49.2 + - - +
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Residues in contact with LEU 130 (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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39C SER* 3.6 28.9 - - - +
126C PRO 3.1 16.2 + - - +
127C THR* 3.7 6.1 - - - +
129C SER* 1.3 82.7 + - - +
131C GLU* 1.3 64.2 + - - +
133C ARG* 3.4 24.5 + - + +
134C ASN* 3.1 37.0 + - - +
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Residues in contact with GLU 131 (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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39C SER* 2.9 23.1 + - - -
40C LEU* 3.4 41.9 + - + +
43C CYS* 3.5 21.8 - - - -
67C ASN* 5.5 0.5 + - - -
71C ILE* 3.6 24.2 - - + -
127C THR 3.5 6.2 + - - +
128C ILE 3.0 5.7 + - - +
130C LEU* 1.3 77.4 - - - +
132C PHE* 1.3 67.0 + - - +
134C ASN* 2.9 39.7 + - - +
135C LEU* 3.3 15.5 + - - +
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Residues in contact with PHE 132 (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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71C ILE* 3.7 22.6 - - + +
75C VAL* 5.1 1.1 - - + -
104C LEU* 3.6 46.0 - - + -
105C TYR* 3.6 32.8 - + - -
128C ILE 2.8 12.7 + - - +
129C SER* 3.3 11.0 - - - +
131C GLU* 1.3 77.0 - - - +
133C ARG* 1.3 60.5 - - + +
135C LEU* 3.0 28.8 + - + +
140C GLN* 3.5 41.1 - - - +
143C ILE* 3.6 43.1 - - + -
144C ALA* 4.1 2.5 - - + -
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Residues in contact with ARG 133 (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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104C LEU 3.1 28.9 + - - +
105C TYR* 3.8 25.1 - - + +
107C PRO* 3.5 45.4 - - - +
126C PRO 4.6 1.2 + - - -
129C SER* 2.9 33.2 + - - +
130C LEU* 3.4 36.7 - - + +
131C GLU 3.2 0.2 - - - -
132C PHE* 1.3 82.6 - - + +
134C ASN* 1.3 59.2 + - - +
135C LEU 3.2 1.9 - - - +
140C GLN* 2.9 25.2 + - - +
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Residues in contact with ASN 134 (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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130C LEU* 3.1 24.6 + - - +
131C GLU* 2.9 40.4 + - - +
133C ARG* 1.3 77.6 - - - +
135C LEU* 1.3 64.2 + - - +
136C ALA 4.0 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