Contacts of the helix formed by residues 117 - 132 (chain C) in PDB entry 5JRE
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 117 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81C GLN* 2.7 33.4 + - - +
85C GLU* 3.7 31.1 - - + +
113C PHE 3.4 6.3 - - - +
114C GLY 3.1 8.2 + - - +
115C ILE 3.0 2.0 + - - -
116C GLY* 1.3 79.8 - - - +
118C ILE* 1.3 63.8 + - - +
119C ALA 3.3 3.7 + - - -
120C GLY 3.7 7.8 + - - -
121C GLU* 4.2 3.5 - - - +
165C LYS* 3.0 21.4 + - - +
168C TYR* 4.3 14.5 + - + -
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Residues in contact with ILE 118 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85C GLU* 3.9 18.2 - - - +
88C ALA* 3.6 25.4 - - + -
89C LEU* 4.9 4.5 - - + +
92C TYR* 6.2 0.2 - - + -
98C ILE* 3.7 32.5 - - + -
114C GLY 3.8 15.3 - - - +
115C ILE* 3.2 24.1 + - + +
117C ASP* 1.3 75.7 - - - +
119C ALA* 1.3 68.3 + - - +
120C GLY 3.2 0.2 - - - -
121C GLU* 3.0 9.1 + - + +
122C ILE* 3.0 36.1 + - + +
148C LEU* 3.8 22.9 - - + -
1D MET* 5.2 1.1 - - + -
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Residues in contact with ALA 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 ILE 4.8 0.4 + - - -
116C GLY 5.0 0.8 + - - -
117C ASP 3.3 1.2 - - - -
118C ILE* 1.3 80.5 - - - +
120C GLY* 1.3 58.2 + - - +
122C ILE* 3.3 3.2 + - - +
123C LEU 2.9 23.9 + - - -
145C LEU* 3.8 27.3 - - + +
148C LEU* 5.0 1.3 - - + +
168C TYR* 4.5 4.7 - - + -
169C VAL* 3.9 28.5 - - + -
172C ILE* 3.5 30.6 - - + +
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Residues in contact with GLY 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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174A ASN* 5.2 6.1 + - - -
117C ASP 3.7 2.7 + - - -
118C ILE 3.2 0.8 - - - -
119C ALA* 1.3 79.3 - - - +
121C GLU* 1.3 58.5 + - - +
123C LEU* 3.4 5.1 + - - +
124C ARG* 3.1 26.3 + - - +
168C TYR* 3.1 29.1 + - - -
172C ILE* 4.2 11.0 - - - -
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Residues in contact with GLU 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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37C ILE* 4.4 19.7 - - + -
41C ILE* 4.4 4.1 - - - +
85C GLU* 3.2 34.1 - - + +
89C LEU* 3.9 29.1 - - + +
117C ASP 4.2 4.3 - - - +
118C ILE* 3.0 9.5 + - - +
120C GLY* 1.3 75.0 - - - +
122C ILE* 1.3 61.7 + - - +
124C ARG* 3.4 7.1 + - - +
125C LYS* 3.0 27.0 + - - +
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Residues in contact with ILE 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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89C LEU* 4.2 9.9 - - + -
92C TYR* 4.0 45.8 - - + +
118C ILE* 3.0 35.0 + - + +
119C ALA 3.7 7.4 - - - +
121C GLU* 1.3 75.2 - - - +
123C LEU* 1.3 55.4 + - - +
125C LYS* 3.7 6.4 - - - +
126C SER* 2.7 37.0 + - - +
137C TYR* 5.7 0.9 - - + -
141C ALA* 3.9 24.9 - - + -
144C ASP* 5.9 0.4 - - + -
145C LEU* 3.9 32.5 - - + -
1D MET* 4.8 4.3 - - + -
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Residues in contact with LEU 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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174A ASN* 6.2 5.4 - - + +
119C ALA 2.9 14.1 + - - +
120C GLY 3.6 8.7 - - - +
121C GLU 3.3 0.2 - - - -
122C ILE* 1.3 76.3 - - - +
124C ARG* 1.3 58.6 + - - +
126C SER* 3.2 5.7 + - - -
127C SER* 2.8 37.6 + - - +
145C LEU* 5.0 0.4 - - - +
172C ILE* 3.8 33.6 - - + +
175C LYS* 4.3 20.0 - - + -
176C LEU* 3.9 32.5 - - + +
179C PHE* 3.7 27.4 - - + -
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Residues in contact with ARG 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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146A GLU* 3.1 23.0 + - - +
170A SER* 5.1 7.9 + - - +
173A ILE* 4.0 15.2 - - - +
174A ASN* 3.2 30.0 + - - +
177A ILE* 3.1 26.0 - - - +
38C TYR* 4.9 14.9 - - - -
41C ILE* 3.5 27.8 - - + +
120C GLY 3.1 15.9 + - - +
121C GLU* 3.6 8.3 - - - +
122C ILE 3.3 0.2 - - - -
123C LEU* 1.3 79.0 - - - +
125C LYS* 1.3 61.2 + - - +
127C SER* 3.4 4.1 + - - -
128C GLU* 2.9 53.2 + - - +
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Residues in contact with LYS 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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40C MET 4.6 2.4 + - - -
41C ILE* 3.9 27.4 + - + +
43C GLU* 3.5 28.1 + - - +
45C TYR* 4.8 4.0 + - - -
89C LEU* 5.0 1.6 - - + -
92C TYR* 5.9 0.2 - - + -
93C ILE* 4.1 32.1 - - + -
121C GLU 3.0 16.9 + - - +
122C ILE* 3.7 7.4 - - + +
124C ARG* 1.3 75.1 - - - +
126C SER* 1.3 57.1 + - - +
128C GLU* 3.2 7.2 + - + +
129C GLU* 3.0 53.7 + - - +
137C TYR* 3.3 37.7 - - + +
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Residues in contact with SER 126 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122C ILE* 2.7 22.8 + - - +
123C LEU* 3.5 5.1 - - - -
125C LYS* 1.3 75.5 - - - +
127C SER* 1.3 57.6 + - - +
129C GLU* 3.1 3.8 + - - +
130C LEU* 2.8 34.6 + - - +
137C TYR* 4.0 14.7 - - - -
138C ALA* 4.4 8.3 - - - +
141C ALA* 3.2 25.5 - - - +
176C LEU* 3.9 24.6 - - - +
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Residues in contact with SER 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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177A ILE* 3.5 26.9 - - - +
181A ILE* 3.8 10.4 - - - +
123C LEU* 2.8 25.7 + - - +
124C ARG* 3.7 8.0 - - - -
126C SER* 1.3 70.2 - - - +
128C GLU* 1.3 62.4 + - - +
130C LEU* 3.2 5.5 + - - +
131C ILE* 3.0 34.7 + - - +
179C PHE* 3.6 23.7 - - - -
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Residues in contact with GLU 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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142A LYS* 3.5 25.7 + - - -
146A GLU* 3.6 1.4 - - - +
177A ILE* 4.6 3.4 - - + -
41C ILE* 3.7 28.0 - - + +
42C ARG* 5.5 6.5 - - - +
124C ARG* 2.9 52.0 + - - +
125C LYS* 3.6 6.7 - - + +
127C SER* 1.3 80.3 - - - +
129C GLU* 1.3 62.3 + - - +
131C ILE* 3.6 18.2 + - - +
132C LYS* 3.6 22.4 + - - +
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Residues in contact with GLU 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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43C GLU* 3.6 1.6 - - - +
125C LYS* 3.0 46.9 + - - +
126C SER 3.1 7.6 + - - +
128C GLU* 1.3 74.7 - - - +
130C LEU* 1.3 61.2 + - - +
132C LYS* 3.2 38.1 + - - +
133C GLY 3.3 0.2 + - - -
134C ASN* 2.9 54.1 + - - +
137C TYR* 3.6 38.2 - - + -
138C ALA 5.3 0.2 - - - +
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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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181A ILE* 4.3 10.3 - - + -
126C SER 2.8 26.4 + - - +
127C SER* 3.2 6.7 + - - +
129C GLU* 1.3 69.7 - - - +
131C ILE* 1.3 57.1 + - - +
133C GLY* 2.7 25.2 + - - +
134C ASN 4.4 2.0 - - - +
135C ILE* 4.1 29.8 - - + -
138C ALA* 3.9 28.5 - - + -
176C LEU* 4.6 2.9 - - + -
179C PHE* 3.6 41.3 - - + +
180C ILE* 5.1 1.8 - - - +
183C LYS* 3.9 34.8 + - + +
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Residues in contact with ILE 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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139A LYS* 6.2 3.6 - - - -
142A LYS* 4.5 13.2 - - + +
177A ILE* 4.1 21.1 - - + -
180A ILE* 4.9 16.4 - - + -
181A ILE* 4.2 16.2 - - + -
127C SER 3.0 20.5 + - - +
128C GLU* 3.7 25.4 - - - +
129C GLU 3.3 0.4 - - - -
130C LEU* 1.3 75.8 - - - +
132C LYS* 1.3 65.1 + - + +
133C GLY 3.3 0.9 + - - -
183C LYS* 4.8 8.5 + - - +
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Residues in contact with LYS 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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43C GLU* 2.7 31.1 + - - -
128C GLU 3.6 15.5 - - - +
129C GLU* 3.2 34.7 + - - +
130C LEU 3.2 0.6 - - - -
131C ILE* 1.3 79.9 - - + +
133C GLY* 1.3 60.4 + - - +
134C ASN* 3.4 3.6 + - + +
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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