Contacts of the helix formed by residues 132 - 152 (chain F) in PDB entry 4JCQ
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 GLU 132 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131F ILE* 1.3 82.8 + - - +
133F ALA* 1.3 66.6 + - - +
134F LYS* 3.3 29.4 - - + +
135F GLU* 3.1 7.8 + - + +
136F ILE* 3.1 19.0 + - - +
165G ASN* 5.1 13.6 - - + +
167G TRP* 6.2 0.2 - - - -
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Residues in contact with ALA 133 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132F GLU* 1.3 74.8 + - - +
134F LYS* 1.3 63.0 + - - +
136F ILE* 3.2 15.9 + - + +
137F ILE* 3.0 31.3 + - + +
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Residues in contact with LYS 134 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132F GLU* 4.3 21.6 - - + +
133F ALA* 1.3 78.4 - - - +
135F GLU* 1.3 67.0 + - + +
137F ILE* 3.6 7.4 + - - +
138F ARG* 3.1 33.0 + - - +
165G ASN 6.1 0.9 - - - -
166G PHE* 6.1 6.1 - - + -
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Residues in contact with GLU 135 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131F ILE* 3.8 11.9 - - + -
132F GLU* 3.1 14.4 + - + +
134F LYS* 1.3 85.3 - - + +
136F ILE* 1.3 58.7 + - - +
137F ILE 3.3 0.2 - - - -
138F ARG* 3.8 22.7 + - - +
139F MET* 2.9 34.2 + - + +
112G ARG* 3.3 43.8 + - - +
167G TRP* 3.5 37.1 + - + +
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Residues in contact with ILE 136 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119F ALA* 3.4 45.1 - - + +
120F GLY* 4.8 4.9 - - - -
131F ILE* 3.7 22.2 - - + +
132F GLU 3.1 14.3 + - - +
133F ALA* 3.2 15.7 + - + +
135F GLU* 1.3 76.1 - - - +
137F ILE* 1.3 65.6 + - + +
139F MET* 3.5 5.3 + - + +
140F ARG* 3.0 32.5 + - + +
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Residues in contact with ILE 137 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133F ALA* 3.0 19.3 + - + +
134F LYS* 3.8 7.4 - - - +
136F ILE* 1.3 82.8 - - + +
138F ARG* 1.3 59.0 + - + +
140F ARG* 3.3 7.3 + - + +
141F GLU* 2.9 52.0 + - + +
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Residues in contact with ARG 138 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134F LYS* 3.1 21.7 + - - +
135F GLU* 3.4 24.5 + - - +
137F ILE* 1.3 75.3 - - + +
139F MET* 1.3 63.8 + - - +
141F GLU* 3.4 12.3 + - - +
142F ARG* 3.0 25.2 + - - +
167G TRP 3.7 16.4 + - - -
169G SER* 4.1 14.5 + - - +
172G GLU* 2.9 43.2 + - - -
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Residues in contact with MET 139 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64F VAL* 3.9 26.0 - - + -
118F PRO 4.8 2.7 - - - +
119F ALA 4.3 13.2 - - - +
120F GLY 4.1 10.8 - - - +
121F GLY* 4.1 14.4 - - - -
131F ILE* 5.3 7.4 - - + -
135F GLU* 2.9 22.1 + - - +
136F ILE* 3.7 4.9 - - - +
138F ARG* 1.3 74.9 - - - +
140F ARG* 1.3 62.9 + - - +
142F ARG* 3.3 20.3 + - - +
143F ILE* 3.0 44.7 + - + +
112G ARG* 3.5 37.9 - - - +
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Residues in contact with ARG 140 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117F GLN* 2.7 40.6 + - - +
118F PRO 3.9 1.4 + - - -
119F ALA* 3.7 24.2 - - - +
136F ILE* 3.0 21.5 + - + +
137F ILE* 3.3 9.4 + - + +
139F MET* 1.3 77.8 - - - +
141F GLU* 1.3 52.9 + - + +
143F ILE* 3.4 5.8 + - - +
144F ASN* 2.8 65.2 + - - +
159F SER* 4.8 1.3 + - - +
162F THR* 3.6 11.4 + - - -
163F ASP* 2.9 48.1 + - - +
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Residues in contact with GLU 141 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137F ILE* 2.9 41.2 + - + +
138F ARG* 3.7 11.2 - - - +
140F ARG* 1.3 75.8 - - + +
142F ARG* 1.3 63.2 + - - +
144F ASN* 3.5 1.4 + - - +
145F ARG* 3.0 56.1 + - - +
155F TYR* 3.3 24.2 - - - +
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Residues in contact with ARG 142 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64F VAL* 3.8 16.0 - - - +
68F ASP* 2.8 41.5 + - - -
138F ARG 3.0 17.2 + - - +
139F MET* 3.6 17.0 + - - +
141F GLU* 1.3 76.8 - - - +
143F ILE* 1.3 71.2 + - - +
145F ARG* 3.5 9.7 + - - +
146F LEU* 3.1 29.3 + - - +
109G PRO 5.5 1.3 - - - -
110G ASN* 2.8 48.8 + - - +
111G THR 5.6 1.3 - - - +
112G ARG* 6.0 4.2 - - - +
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Residues in contact with ILE 143 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64F VAL* 3.9 20.0 - - + -
68F ASP* 5.2 1.6 - - - +
95F THR* 4.2 14.4 - - + +
117F GLN* 3.8 35.0 - - + +
118F PRO 6.2 0.7 - - - +
139F MET* 3.0 36.9 + - + +
140F ARG* 4.0 5.2 - - - +
142F ARG* 1.3 89.4 - - - +
144F ASN* 1.3 66.2 + - - +
146F LEU* 3.2 9.1 + - + +
147F ILE* 3.0 44.3 + - + +
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Residues in contact with ASN 144 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140F ARG* 2.8 45.8 + - - +
143F ILE* 1.3 74.2 - - - +
145F ARG* 1.3 56.3 + - - +
147F ILE 3.5 0.2 + - - -
148F ALA* 2.9 30.3 + - - +
155F TYR* 3.5 29.0 + - + -
158F ILE* 3.5 13.4 - - + +
159F SER* 3.5 34.0 + - - +
162F THR* 2.7 32.2 + - - +
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Residues in contact with ARG 145 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141F GLU* 3.0 54.5 + - - +
142F ARG* 3.8 7.4 - - - +
143F ILE 3.3 0.2 - - - -
144F ASN* 1.3 73.9 - - - +
146F LEU* 1.3 64.5 + - - +
148F ALA* 3.8 6.0 - - - +
149F GLU* 3.0 27.4 + - - +
155F TYR* 3.7 23.1 + - + -
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Residues in contact with LEU 146 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68F ASP* 5.3 0.2 - - - +
71F HIS* 3.7 42.4 - - + +
95F THR* 4.0 27.8 - - + +
98F LEU* 4.7 9.9 - - + +
142F ARG* 3.1 17.3 + - - +
143F ILE* 3.2 11.9 + - + +
145F ARG* 1.3 77.3 - - - +
147F ILE* 1.3 71.1 - - + +
149F GLU* 3.5 4.8 + - - +
150F ALA* 3.2 25.0 + - + +
110G ASN* 4.0 23.3 - - - +
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Residues in contact with ILE 147 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94F ILE* 4.4 8.3 - - + -
95F THR* 4.9 2.9 - - - +
98F LEU* 3.8 27.6 - - + -
115F ILE* 4.4 14.4 - - + +
117F GLN* 3.7 26.2 - - - +
143F ILE* 3.0 30.0 + - + +
146F LEU* 1.3 77.4 - - + +
148F ALA* 1.3 56.4 + - - +
150F ALA* 3.9 0.2 - - - -
151F THR* 2.7 45.0 + - + +
158F ILE* 3.7 28.3 - - + -
162F THR* 4.0 17.3 - - + -
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Residues in contact with ALA 148 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144F ASN 2.9 18.6 + - - +
145F ARG* 3.8 7.4 - - - +
147F ILE* 1.3 77.5 - - - +
149F GLU* 1.3 56.2 + - - +
151F THR* 3.9 0.7 - - - -
152F GLY* 2.9 27.4 + - - -
153F GLN 3.2 24.4 - - - +
155F TYR* 4.2 17.3 - - + +
158F ILE* 3.7 14.5 - - + +
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Residues in contact with GLU 149 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75F LYS* 5.3 7.3 + - - -
145F ARG 3.0 17.3 + - - +
146F LEU* 3.9 5.4 - - - +
148F ALA* 1.3 77.2 - - - +
150F ALA* 1.3 61.8 + - - +
152F GLY* 4.0 5.4 + - - -
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Residues in contact with ALA 150 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98F LEU* 3.8 42.2 - - + +
102F LYS* 4.4 8.0 - - - +
105F ARG* 2.8 27.0 + - - +
146F LEU* 3.2 19.1 + - + +
147F ILE 3.9 2.9 - - - +
148F ALA 3.3 0.2 - - - -
149F GLU* 1.3 79.2 - - - +
151F THR* 1.3 58.3 + - - +
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Residues in contact with THR 151 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98F LEU* 4.0 13.0 - - + -
102F LYS* 4.1 9.7 - - - -
147F ILE* 2.7 34.7 + - + +
148F ALA 3.6 0.7 + - - -
150F ALA* 1.3 78.8 - - - +
152F GLY* 1.3 61.2 + - - +
153F GLN* 3.2 22.4 + - - +
158F ILE* 3.9 2.1 - - - +
176F TYR* 3.9 18.2 - - + +
177F GLY* 3.5 30.8 - - - +
178F ILE* 3.9 23.3 - - + -
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Residues in contact with GLY 152 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148F ALA 2.9 10.5 + - - -
149F GLU 4.0 4.3 + - - -
150F ALA 3.6 1.6 - - - -
151F THR* 1.3 78.6 - - - +
153F GLN* 1.3 64.4 + - - +
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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