Contacts of the helix formed by residues 117 - 138 (chain C) in PDB entry 2JC6
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 THR 117 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115C PHE* 3.2 36.3 - - + -
116C TYR* 1.3 81.1 - - - +
118C GLU* 1.3 62.7 + - - +
119C LYS* 3.2 18.4 + - - +
120C ASP* 2.9 22.6 + - - +
121C ALA* 3.2 19.2 + - - +
285C LEU 3.8 9.4 - - - -
286C ASN* 3.8 18.3 + - - +
287C LYS 3.5 17.9 - - - +
289C ILE* 4.2 6.9 - - - +
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Residues in contact with GLU 118 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117C THR* 1.3 74.6 - - - +
119C LYS* 1.3 54.3 + - - +
121C ALA* 3.3 1.4 + - - +
122C SER* 2.7 37.1 + - - -
215C LEU* 3.8 25.8 - - + -
247C ASP 4.0 0.7 - - - +
248C ILE* 3.3 21.0 - - + +
249C SER* 2.4 48.0 + - - -
278C TRP* 3.0 20.9 + - - +
284C ALA* 4.0 2.0 - - - -
285C LEU* 3.2 39.3 + - + +
287C LYS 4.5 2.2 + - - +
289C ILE* 4.4 3.6 - - + +
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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
----------------------------------------------------------
117C THR* 3.2 8.9 + - - +
118C GLU* 1.3 79.2 - - - +
120C ASP* 1.3 55.3 + - - +
122C SER* 3.9 2.4 - - - -
123C THR* 2.8 37.3 + - - +
282C ASP* 2.5 31.3 + - - -
284C ALA* 2.6 37.0 + - + +
285C LEU 3.4 8.2 + - - +
286C ASN* 3.4 35.0 - - - +
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Residues in contact with ASP 120 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113C LYS* 4.7 11.3 - - - +
115C PHE* 3.9 6.1 - - - +
116C TYR* 3.3 28.5 - - + -
117C THR* 2.9 34.9 + - - +
118C GLU 3.2 0.2 - - - -
119C LYS* 1.3 77.1 - - - +
121C ALA* 1.3 65.3 + - - +
123C THR* 3.4 6.7 + - - +
124C LEU* 3.1 29.8 + - + +
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Residues in contact with ALA 121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116C TYR* 3.6 21.3 + - - +
117C THR 3.2 7.1 + - - +
118C GLU 3.3 6.5 + - - +
120C ASP* 1.3 78.7 - - - +
122C SER* 1.3 58.1 + - - +
124C LEU* 3.1 6.3 + - - +
125C ILE* 2.9 30.2 + - - +
214C LEU* 4.1 15.7 - - + +
215C LEU* 3.7 26.9 - - + -
278C TRP* 4.1 7.9 - - + -
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Residues in contact with SER 122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118C GLU 2.7 21.5 + - - -
119C LYS* 3.9 3.8 - - - -
121C ALA* 1.3 72.5 - - - +
123C THR* 1.3 58.6 + - - +
125C ILE 3.3 0.6 + - - +
126C ARG* 2.8 31.1 + - - +
278C TRP* 2.7 49.5 + - - -
279C ILE* 3.8 13.7 + - - +
284C ALA* 4.2 7.1 - - - +
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Residues in contact with THR 123 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119C LYS 2.8 22.4 + - - -
120C ASP* 3.6 7.0 - - - +
122C SER* 1.3 75.7 + - - +
124C LEU* 1.3 64.0 + - + +
126C ARG* 3.6 27.9 + - - +
127C GLN* 3.1 37.6 + - - +
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Residues in contact with LEU 124 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106C LEU* 3.8 25.6 - - + -
113C LYS* 4.8 4.5 - - - +
116C TYR* 4.7 13.7 - - + +
120C ASP 3.1 22.5 + - - +
121C ALA* 3.1 8.3 + - - +
123C THR* 1.3 79.7 - - + +
125C ILE* 1.3 60.8 + - - +
127C GLN* 3.3 14.1 + - - +
128C VAL* 3.3 27.0 + - + +
150C LEU* 6.3 1.3 - - + -
152C TYR* 3.5 25.6 - - + +
159C SER 5.9 0.2 - - - +
161C ILE* 3.9 30.8 - - + +
214C LEU* 4.1 17.3 - - + -
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Residues in contact with ILE 125 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121C ALA 2.9 20.3 + - - +
122C SER 3.9 3.1 - - - +
124C LEU* 1.3 74.4 - - - +
126C ARG* 1.3 59.3 + - - +
128C VAL* 3.3 8.4 + - + +
129C LEU* 2.9 36.2 + - + +
207C ILE* 3.9 18.2 - - + +
210C ILE* 3.8 18.2 - - + -
211C ALA* 3.8 34.8 - - + +
214C LEU* 3.9 11.2 - - + -
255C PHE* 3.6 31.2 - - + -
278C TRP* 4.4 5.8 - - + -
279C ILE* 3.9 4.7 - - + -
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Residues in contact with ARG 126 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122C SER* 2.8 21.2 + - - +
123C THR* 3.6 36.1 + - - +
125C ILE* 1.3 73.4 - - - +
127C GLN* 1.3 76.1 + - - +
129C LEU* 3.4 6.1 + - + +
130C ASP* 3.0 30.3 + - + +
274C ALA* 6.4 0.7 - - + -
279C ILE* 3.9 38.0 - - + +
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Residues in contact with GLN 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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80C ASN* 3.1 32.6 + - - +
123C THR* 3.1 34.4 + - - +
124C LEU* 3.3 17.1 + - - +
125C ILE 3.3 0.6 - - - -
126C ARG* 1.3 91.9 - - - +
128C VAL* 1.3 60.7 + - - +
130C ASP* 3.2 6.9 + - - +
131C ALA* 2.9 29.2 + - - +
159C SER 5.2 1.8 + - - -
160C LYS* 3.2 12.3 - - - +
161C ILE* 3.0 37.5 + - + +
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Residues in contact with VAL 128 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124C LEU* 3.3 16.8 - - + +
125C ILE* 3.3 14.9 + - + +
127C GLN* 1.3 73.2 - - - +
129C LEU* 1.3 61.1 + - - +
131C ALA* 3.7 5.1 - - - +
132C VAL* 2.8 45.5 + - + +
145C LEU* 4.9 3.6 - - + -
150C LEU* 4.1 31.6 - - + -
161C ILE* 4.3 9.6 - - + -
163C ILE* 4.5 10.5 - - + -
207C ILE* 4.0 24.9 - - + -
210C ILE* 4.8 12.8 - - + -
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Residues in contact with LEU 129 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125C ILE* 2.9 37.3 + - + +
126C ARG* 3.6 5.2 - - - +
128C VAL* 1.3 76.3 - - - +
130C ASP* 1.3 56.8 + - - +
132C VAL 3.9 0.2 - - - -
133C TYR* 2.9 32.7 + - - +
207C ILE* 3.6 32.8 - - + -
255C PHE* 4.1 1.3 - - + -
259C LEU* 5.1 2.0 - - + -
270C CYS* 3.9 20.5 - - - +
273C ALA* 3.7 24.0 - - + -
274C ALA* 4.1 23.1 - - + +
279C ILE* 4.0 26.2 - - + -
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Residues in contact with ASP 130 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78C HIS* 2.8 33.4 + - + +
80C ASN* 4.6 2.2 - - - +
126C ARG* 3.0 19.1 + - + +
127C GLN* 3.6 7.0 - - - +
128C VAL 3.2 0.2 - - - -
129C LEU* 1.3 74.2 - - - +
131C ALA* 1.3 64.5 + - - +
133C TYR* 3.8 12.9 - - - +
134C TYR* 3.1 18.2 + - - +
137C ARG* 5.3 3.5 + - - -
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Residues in contact with ALA 131 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78C HIS* 3.6 17.7 - - - +
80C ASN* 4.0 8.3 - - + -
81C ILE* 3.8 26.8 - - + +
127C GLN 2.9 15.9 + - - +
128C VAL* 3.7 4.3 - - - +
130C ASP* 1.3 75.5 - - - +
132C VAL* 1.3 61.7 + - - +
134C TYR* 3.3 6.6 + - - +
135C LEU* 3.1 23.5 + - - +
163C ILE* 3.8 15.5 - - + -
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Residues in contact with VAL 132 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128C VAL* 2.8 31.0 + - + +
131C ALA* 1.3 69.2 - - - +
133C TYR* 1.3 59.5 + - - +
135C LEU* 3.3 12.3 + - + +
136C HIS* 2.9 56.5 + - + +
142C HIS* 5.8 0.2 - - + -
145C LEU* 3.6 23.8 - - + -
163C ILE* 4.1 11.7 - - + -
203C ASP* 3.8 17.3 - - + +
207C ILE* 4.0 8.3 - - + -
270C CYS* 3.7 13.7 - - - -
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Residues in contact with TYR 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 LEU 2.9 20.7 + - - +
130C ASP* 3.8 13.5 - - - +
132C VAL* 1.3 76.0 - - - +
134C TYR* 1.3 59.4 + - - +
136C HIS* 3.3 8.5 + - + +
137C ARG* 2.9 65.4 + - + +
270C CYS* 3.8 16.9 - - + -
271C GLU* 3.5 47.4 + - + +
274C ALA* 6.1 2.9 - - + -
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Residues in contact with TYR 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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75C LYS 3.4 10.9 + - - -
76C ILE* 3.6 15.8 - - + -
77C LYS* 2.7 49.1 + - - +
78C HIS* 3.5 33.0 - + + -
81C ILE* 4.1 7.2 - - + -
130C ASP 3.1 8.2 + - - +
131C ALA 3.4 6.3 - - - +
133C TYR* 1.3 74.5 - - - +
135C LEU* 1.3 71.6 + - + +
137C ARG* 3.2 25.1 + - - +
138C MET* 3.1 60.5 + - + +
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Residues in contact with LEU 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 46.0 - - + -
81C ILE* 3.9 15.0 - - + -
131C ALA 3.1 17.2 + - - +
132C VAL* 3.3 19.5 + - + +
134C TYR* 1.3 76.6 - - + +
136C HIS* 1.3 65.2 + - + +
138C MET* 3.2 7.3 + - - +
139C GLY 3.1 5.7 + - - -
140C ILE* 3.0 45.2 + - + +
142C HIS* 4.4 33.2 - - + +
163C ILE* 5.3 4.3 - - + -
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Residues in contact with HIS 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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132C VAL* 2.9 36.2 + - + +
133C TYR* 3.6 11.1 - - + +
134C TYR 3.2 0.2 - - - -
135C LEU* 1.3 77.5 - - + +
137C ARG* 1.3 61.2 + - - +
139C GLY 3.1 6.1 + - - -
140C ILE 3.4 18.4 - - - -
200C LYS* 2.6 76.3 + - + +
203C ASP* 2.9 27.4 + - + +
204C CYS* 4.1 7.1 - - - -
270C CYS* 4.0 18.1 + - - +
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Residues in contact with ARG 137 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78C HIS* 5.7 1.6 - - - -
130C ASP* 5.3 3.2 + - - -
133C TYR* 2.9 78.0 + - + +
134C TYR* 3.2 31.0 + - - +
136C HIS* 1.3 75.1 - - - +
138C MET* 1.3 70.2 + - + +
139C GLY 3.5 0.9 + - - -
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Residues in contact with MET 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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75C LYS* 5.3 9.0 - - + +
76C ILE* 5.8 1.3 - - + -
134C TYR* 3.1 64.7 + - + +
135C LEU* 3.4 7.6 - - - +
137C ARG* 1.3 88.6 - - + +
139C GLY* 1.3 57.1 + - - +
140C ILE* 3.6 21.8 - - + +
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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
------------------------------------------------------------
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