Contacts of the helix formed by residues 132 - 145 (chain C) in PDB entry 2JIF
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 132 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76C ILE* 4.0 5.6 - - + -
80C VAL* 3.8 19.2 - - + +
83C MET* 3.4 27.0 - - - +
128C LEU 2.9 18.6 + - - +
129C ALA* 3.6 1.5 + - - -
131C VAL* 1.3 75.3 - - - +
133C ALA* 1.3 63.0 + - - +
134C SER* 3.0 22.5 + - - -
135C VAL* 3.1 19.4 + - + +
136C ALA* 3.1 17.2 + - - +
257C ALA* 5.0 1.4 - - - +
402C LYS* 2.9 27.5 + - - +
403C TYR* 5.7 0.7 - - - -
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Residues in contact with ALA 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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129C ALA* 3.8 14.3 + - - +
132C ASP* 1.3 73.8 + - - +
134C SER* 1.3 56.0 + - - +
136C ALA* 3.3 2.7 + - - +
137C VAL* 3.0 16.8 + - - +
255C LEU* 3.9 7.4 - - + -
300C GLN* 3.0 33.3 + - + +
304C LEU* 3.7 35.2 - - + -
403C TYR* 5.8 2.3 - - + -
406C ASP* 3.9 15.6 + - + +
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Residues in contact with SER 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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89C MET* 3.6 5.7 - - - +
132C ASP* 3.0 15.8 + - - -
133C ALA* 1.3 74.7 - - - +
135C VAL* 1.3 63.8 + - - +
137C VAL* 3.3 7.9 - - - +
138C PHE* 3.2 21.7 + - - +
255C LEU* 3.2 39.2 - - - +
256C ARG 3.6 2.1 + - - -
257C ALA* 3.6 15.4 + - - +
258C SER* 3.8 18.8 - - - -
402C LYS* 4.7 4.7 + - - -
406C ASP* 4.8 0.7 + - - -
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Residues in contact with VAL 135 (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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76C ILE* 3.8 30.5 - - + -
83C MET* 4.2 6.5 - - + -
89C MET* 3.9 18.4 - - + -
93C VAL* 3.8 21.8 - - + -
97C LEU* 3.8 28.3 - - + -
128C LEU* 4.4 5.8 - - + -
132C ASP* 3.1 28.7 + - + +
134C SER* 1.3 75.1 - - - +
136C ALA* 1.3 62.7 + - - +
138C PHE* 3.3 3.5 + - - +
139C CYS* 3.1 21.5 + - - +
257C ALA* 5.9 0.2 - - + -
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Residues in contact with ALA 136 (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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125C ILE* 3.5 32.4 - - + +
128C LEU* 3.9 11.6 - - + +
129C ALA* 3.5 28.3 - - + +
132C ASP 3.1 5.1 + - - -
133C ALA 3.5 7.2 - - - +
134C SER 3.3 0.2 - - - -
135C VAL* 1.3 77.2 - - - +
137C VAL* 1.3 56.6 + - - +
139C CYS* 3.3 4.7 + - - +
140C GLU* 2.9 28.2 + - - +
300C GLN* 4.1 7.0 - - + -
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Residues in contact with VAL 137 (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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133C ALA 3.0 13.8 + - - +
134C SER 3.3 12.1 - - - +
136C ALA* 1.3 72.0 - - - +
138C PHE* 1.3 63.8 + - - +
140C GLU* 3.9 16.6 - - - +
141C ILE* 2.8 46.5 + - + +
209C SER* 5.4 2.0 - - - +
255C LEU* 3.8 16.4 - - + -
258C SER* 3.8 19.7 - - - +
297C ILE* 4.1 6.7 - - + -
300C GLN* 3.5 15.1 - - - +
413C TYR* 3.8 22.9 - - + +
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Residues in contact with PHE 138 (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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89C MET* 3.9 16.6 - - + -
94C ILE* 3.8 33.4 - - + -
97C LEU* 3.4 30.5 - - + -
103C MET* 3.4 26.4 - - + +
134C SER 3.2 14.4 + - - +
135C VAL 3.5 7.0 - - - +
137C VAL* 1.3 79.6 - - + +
139C CYS* 1.3 60.0 + - - +
141C ILE* 4.0 2.9 - - - +
142C GLN* 3.5 20.3 + - - +
171C VAL* 3.7 36.6 - - + -
210C SER* 3.8 22.5 + - - +
258C SER* 5.4 2.9 - - - +
1437C CL 3.9 17.7 - - + -
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Residues in contact with CYS 139 (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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97C LEU* 4.7 4.0 - - + -
102C LEU* 3.3 29.8 - - - -
103C MET* 4.1 13.2 - - - -
105C ILE* 4.3 1.8 - - - -
124C VAL* 3.9 14.8 - - - -
125C ILE* 4.8 7.0 - - + -
128C LEU* 3.6 29.6 - - + -
135C VAL 3.1 7.6 + - - +
136C ALA 3.5 8.5 - - - +
138C PHE* 1.3 75.6 - - - +
140C GLU* 1.3 63.6 + - - +
142C GLN* 3.5 1.4 + - - +
143C ASN* 3.0 36.8 + - - -
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Residues in contact with GLU 140 (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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125C ILE* 3.6 33.4 - - + -
136C ALA 2.9 17.2 + - - +
137C VAL* 3.1 9.3 + - - +
139C CYS* 1.3 73.6 - - - +
141C ILE* 1.3 79.1 + - - +
143C ASN* 5.0 0.2 - - - -
144C THR* 2.7 56.5 + - - +
145C LEU* 4.6 1.0 - - - +
293C GLY* 3.2 13.2 - - - +
296C GLY* 4.0 13.9 - - - -
297C ILE* 3.7 18.2 - - + +
414C GLU* 2.9 26.1 - - - +
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Residues in contact with ILE 141 (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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137C VAL* 2.8 40.7 + - + +
138C PHE* 4.0 3.6 - - - +
140C GLU* 1.3 84.4 - - - +
142C GLN* 1.3 63.7 + - - +
145C LEU* 3.0 40.4 + - + +
146C ILE* 3.0 17.0 + - + -
172C GLY 4.1 18.4 - - - +
173C SER* 5.0 0.9 - - - -
174C PHE* 4.6 11.4 - - + +
209C SER* 3.3 35.0 - - - +
210C SER* 3.6 14.4 - - - +
258C SER* 5.1 0.4 - - - +
1433C FAD 4.8 3.1 - - - +
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Residues in contact with GLN 142 (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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98C PHE* 3.9 5.7 - - - -
103C MET* 3.4 48.4 - - + +
138C PHE 3.5 5.2 + - - +
139C CYS 3.8 6.1 - - - +
140C GLU 3.4 0.6 - - - -
141C ILE* 1.3 78.9 - - - +
143C ASN* 1.3 56.1 + - - +
146C ILE* 3.5 6.6 - - - +
147C ASN* 2.8 40.7 + - - +
166C LEU* 2.9 30.4 + - - +
170C LYS 2.8 27.3 + - - -
171C VAL* 3.7 4.4 - - - +
172C GLY* 3.0 27.8 + - - +
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Residues in contact with ASN 143 (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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102C LEU 2.8 26.4 + - - -
103C MET* 3.6 12.9 - - - +
104C GLY* 3.8 1.0 - - - -
105C ILE* 2.9 40.0 + - - +
106C GLU* 4.4 8.0 + - - +
121C THR* 4.0 20.2 - - + +
139C CYS* 3.0 31.4 + - - +
140C GLU 4.2 0.7 - - - +
142C GLN* 1.3 82.2 - - - +
144C THR* 1.3 60.0 + - - +
147C ASN* 3.5 8.7 + - - +
148C THR* 3.0 26.5 + - - -
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Residues in contact with THR 144 (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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106C GLU* 5.2 1.1 - - - +
118C PHE* 4.6 8.1 - - + -
121C THR* 3.8 27.1 - - + -
125C ILE* 4.2 4.0 - - + -
140C GLU* 2.7 56.6 + - + +
143C ASN* 1.3 72.3 - - - +
145C LEU* 1.3 70.0 + - - +
148C THR* 3.5 20.7 + - - +
289C SER* 4.1 10.4 - - - +
292C GLU* 4.1 16.5 - - - +
293C GLY* 3.9 11.8 - - - -
296C GLY* 5.0 4.7 - - - -
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Residues in contact with LEU 145 (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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141C ILE* 3.0 28.6 + - + +
144C THR* 1.3 91.0 + - - +
146C ILE* 1.3 66.4 + - - +
149C LEU* 3.2 32.4 + - - +
174C PHE* 3.9 43.1 - - + -
289C SER* 3.5 39.5 - - - +
290C LEU* 4.2 10.3 - - + +
293C GLY* 4.3 0.4 - - - -
414C GLU* 4.0 22.4 - - - +
1433C FAD 5.8 1.8 - - + +
1434C COS 5.2 4.0 - - - -
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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