Contacts of the helix formed by residues 134 - 156 (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 ASN 134 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129C GLU* 2.9 51.8 + - - +
130C LEU* 4.1 3.7 + - - +
132C LYS* 3.4 5.5 - - + +
133C GLY* 1.3 73.6 - - - +
135C ILE* 1.3 60.8 + - - +
136C GLU* 3.6 9.2 + - - +
137C TYR* 3.3 34.5 + - - +
138C ALA 3.9 3.1 + - - -
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Residues in contact with ILE 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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130C LEU* 4.1 23.1 - - + -
133C GLY* 3.3 15.4 + - - +
134C ASN* 1.3 69.9 - - - +
136C GLU* 1.3 63.6 + - - +
138C ALA* 3.1 5.2 + - - +
139C LYS* 3.0 38.7 + - + +
180C ILE* 4.7 9.0 - - + +
183C LYS* 3.1 37.2 - - + +
184C SER* 3.6 23.3 - - - +
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Residues in contact with GLU 136 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134C ASN* 3.3 7.8 - - - +
135C ILE* 1.3 77.7 - - - +
137C TYR* 1.3 61.7 + - - +
139C LYS* 3.4 26.9 + - - +
140C LYS* 3.0 25.5 + - - +
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Residues in contact with TYR 137 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92C TYR* 3.6 25.8 - + - -
93C ILE* 4.0 12.1 - - + +
122C ILE 5.1 0.7 - - - -
125C LYS* 3.3 44.7 - - + +
126C SER* 4.0 18.2 - - - -
129C GLU* 3.6 24.0 - - + -
134C ASN* 3.3 30.0 + - - +
135C ILE 3.3 0.2 - - - -
136C GLU* 1.3 78.2 - - - +
138C ALA* 1.3 58.7 + - - +
140C LYS* 3.3 12.7 + - + +
141C ALA* 2.9 29.0 + - + +
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Residues in contact with ALA 138 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126C SER* 4.4 8.5 - - - +
129C GLU* 5.3 0.2 - - - +
130C LEU* 3.9 37.7 - - + -
134C ASN 3.9 1.0 + - - +
135C ILE 3.1 9.7 + - - +
137C TYR* 1.3 78.6 - - - +
139C LYS* 1.3 60.9 + - - +
141C ALA* 3.3 8.7 + - - +
142C LYS* 2.9 28.2 + - - +
176C LEU* 3.9 13.5 - - + +
180C ILE* 3.7 11.4 - - + +
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Residues in contact with LYS 139 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135C ILE* 3.0 34.2 + - + +
136C GLU* 3.7 30.7 + - - +
138C ALA* 1.3 75.4 - - - +
140C LYS* 1.3 62.5 + - - +
142C LYS* 3.4 6.0 + - - +
143C GLN* 3.3 31.2 + - - +
180C ILE* 4.0 31.4 - - + -
184C SER* 4.2 9.8 + - - -
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Residues in contact with LYS 140 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92C TYR* 4.2 5.1 + - - +
96C ASN* 2.6 40.5 + - - +
136C GLU* 3.0 19.4 + - - +
137C TYR* 3.6 12.8 - - + +
139C LYS* 1.3 74.1 - - - +
141C ALA* 1.3 65.2 + - - +
143C GLN* 3.1 16.6 + - + +
144C ASP* 2.9 54.0 + - - +
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Residues in contact with ALA 141 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92C TYR* 3.6 15.5 + - - +
122C ILE* 3.9 15.0 - - + -
126C SER* 3.2 27.1 - - - +
137C TYR* 2.9 19.8 + - + +
138C ALA 3.3 4.9 + - - +
140C LYS* 1.3 75.9 - - - +
142C LYS* 1.3 57.4 + - - +
144C ASP* 3.3 1.4 + - - +
145C LEU* 2.8 34.5 + - - +
176C LEU* 3.9 5.8 - - + -
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Residues in contact with LYS 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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138C ALA 2.9 13.8 + - - +
139C LYS* 3.5 11.0 - - + +
141C ALA* 1.3 76.0 - - - +
143C GLN* 1.3 61.4 + - + +
145C LEU* 3.3 3.9 + - - +
146C GLU* 2.9 61.1 + - + +
173C ILE* 4.6 7.7 - - + +
176C LEU* 3.5 16.8 - - + +
177C ILE* 3.5 34.1 - - + -
180C ILE* 4.1 17.0 - - + -
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Residues in contact with GLN 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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139C LYS* 3.4 19.1 - - - +
140C LYS* 3.1 18.2 + - + +
142C LYS* 1.3 79.8 - - + +
144C ASP* 1.3 61.3 + - - +
146C GLU* 3.3 16.3 + - - +
147C SER* 3.0 31.4 + - - -
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Residues in contact with ASP 144 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92C TYR* 2.6 33.1 + - + +
96C ASN* 5.1 0.4 - - - -
122C ILE* 5.9 0.4 - - + -
140C LYS* 2.9 41.9 + - - +
141C ALA 3.6 3.6 - - - +
143C GLN* 1.3 79.9 - - - +
145C LEU* 1.3 56.6 + - + +
147C SER* 3.3 2.7 + - - -
148C LEU* 3.0 24.6 + - - +
1D MET* 3.1 42.4 - - + +
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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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119C ALA* 3.8 28.7 - - + +
122C ILE* 3.9 33.0 - - + -
123C LEU 5.0 1.1 - - - +
141C ALA 2.8 19.3 + - - +
142C LYS 3.9 2.0 - - - +
144C ASP* 1.3 70.7 - - - +
146C GLU* 1.3 61.3 + - - +
148C LEU* 3.3 17.0 + - + +
149C TYR* 2.8 28.9 + - - +
169C VAL* 4.1 4.6 - - + +
172C ILE* 3.7 28.9 - - + -
173C ILE* 3.7 21.8 - - + +
176C LEU* 4.0 21.5 - - + -
1D MET* 6.0 0.4 - - + -
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Residues in contact with GLU 146 (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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142C LYS* 2.9 50.8 + - - +
143C GLN* 3.5 16.2 - - - +
145C LEU* 1.3 74.3 - - - +
147C SER* 1.3 64.6 - - - +
149C TYR* 3.3 4.0 + - + +
150C LEU* 3.0 33.8 + - + +
173C ILE* 4.0 26.0 - - + +
177C ILE* 4.8 1.9 - - - +
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Residues in contact with SER 147 (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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143C GLN 3.0 16.3 + - - -
144C ASP* 3.5 9.6 + - - -
146C GLU* 1.3 77.0 - - - +
148C LEU* 1.3 56.4 + - - +
150C LEU* 3.3 10.1 + - - +
151C ASP* 2.8 36.1 + - - +
0D SER* 3.9 26.3 + - - +
1D MET* 3.7 14.1 - - - -
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Residues in contact with LEU 148 (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* 3.9 16.6 - - + +
118C ILE* 3.8 32.8 - - + -
119C ALA 5.0 1.1 - - - +
122C ILE* 5.7 0.2 - - + -
144C ASP 3.0 14.0 + - - +
145C LEU* 3.5 24.9 - - + +
147C SER* 1.3 75.1 - - - +
149C TYR* 1.3 59.0 + - - +
151C ASP* 3.2 5.3 + - - +
152C LEU* 2.9 39.4 + - + +
169C VAL* 4.7 15.3 - - + -
1D MET* 4.0 13.8 - - + +
2D LEU* 3.6 37.9 - - + -
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Residues in contact with TYR 149 (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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145C LEU 2.8 16.8 + - - +
146C GLU* 3.4 7.4 - - + +
148C LEU* 1.3 76.9 - - - +
150C LEU* 1.3 63.5 + - + +
152C LEU* 3.2 6.2 + - - +
153C LEU* 2.8 60.9 + - + +
166C LEU* 3.6 37.8 - - + +
169C VAL* 4.0 18.4 - - + +
170C SER* 3.5 30.5 + - - -
173C ILE* 4.0 11.0 - - + -
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Residues in contact with LEU 150 (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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146C GLU* 3.0 25.3 + - + +
147C SER* 3.6 7.4 - - - +
149C TYR* 1.3 81.4 - - + +
151C ASP* 1.3 59.6 + - - +
153C LEU* 3.5 21.0 - - + +
154C TYR* 2.9 30.0 + - - +
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Residues in contact with ASP 151 (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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147C SER 2.8 18.6 + - - +
148C LEU* 3.4 8.0 - - - +
150C LEU* 1.3 77.4 - - - +
152C LEU* 1.3 62.0 + - - +
154C TYR* 3.2 5.0 + - - +
155C ILE* 3.1 24.9 + - - +
0D SER* 3.4 13.7 + - - -
1D MET* 3.0 12.6 + - - +
2D LEU* 3.0 40.1 + - + +
5D LEU* 3.1 40.7 - - + +
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Residues in contact with LEU 152 (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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112C LEU* 4.6 14.6 - - + +
115C ILE* 4.7 7.9 - - + -
116C GLY* 5.0 12.3 - - - +
148C LEU* 2.9 38.2 + - + +
149C TYR* 3.7 5.4 - - - +
151C ASP* 1.3 72.7 - - - +
153C LEU* 1.3 66.4 + - - +
155C ILE* 3.3 34.0 + - + +
156C GLU 3.7 3.6 + - - -
157C LEU* 3.8 23.9 + - + +
165C LYS* 5.6 0.7 - - + -
166C LEU* 3.7 24.2 - - + +
169C VAL* 4.2 20.2 - - + -
2D LEU* 4.3 11.0 - - + -
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Residues in contact with LEU 153 (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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149C TYR* 2.8 52.2 + - + +
150C LEU* 3.5 19.7 - - + +
152C LEU* 1.3 75.0 - - - +
154C TYR* 1.3 62.6 + - - +
156C GLU* 3.1 19.6 + - - +
166C LEU* 3.6 25.3 - - + +
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Residues in contact with TYR 154 (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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150C LEU 2.9 18.6 + - - +
151C ASP* 3.2 6.7 + - - +
153C LEU* 1.3 76.8 - - - +
155C ILE* 1.3 58.6 + - - +
156C GLU* 3.1 4.3 - - - +
5D LEU* 3.9 29.4 - - + -
6D ASP* 2.5 30.0 + - - -
9D LYS* 2.7 68.7 + - + +
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Residues in contact with ILE 155 (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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112C LEU* 4.0 13.9 - - + -
151C ASP 3.1 15.2 + - - +
152C LEU* 3.5 22.9 - - + +
153C LEU 3.3 0.6 - - - -
154C TYR* 1.3 76.0 - - - +
156C GLU* 1.3 52.6 + - - +
157C LEU* 3.8 13.5 - - + -
2D LEU* 4.4 8.7 - - + -
5D LEU* 4.3 9.4 - - + -
8D LEU* 3.3 29.2 - - + -
9D LYS* 3.9 22.0 - - + +
12D TYR* 3.5 35.0 - - + -
13D GLN* 2.7 31.0 + - - -
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Residues in contact with GLU 156 (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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152C LEU 3.7 0.8 + - - -
153C LEU 3.1 15.2 + - - +
154C TYR* 3.1 17.3 - - - +
155C ILE* 1.3 78.4 - - - +
157C LEU* 1.3 67.7 + - - +
158C LYS* 3.3 19.6 + - - +
9D LYS* 3.5 19.2 + - - +
12D TYR* 3.8 0.2 - - - -
13D GLN* 3.0 21.6 + - - +
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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
------------------------------------------------------------
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