Contacts of the helix formed by residues 117 - 132 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81F GLN* 2.7 33.8 + - - +
85F GLU* 3.8 30.1 - - - +
113F PHE 3.4 6.9 - - - +
114F GLY 3.1 8.7 + - - +
115F ILE 3.0 1.6 - - - -
116F GLY* 1.3 80.4 - - - +
118F ILE* 1.3 63.3 + - - +
119F ALA 3.3 3.9 + - - -
120F GLY* 3.7 8.4 + - - -
121F GLU* 4.3 2.8 + - - +
165F LYS* 3.0 22.1 + - - +
168F TYR* 4.3 14.5 + - + -
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Residues in contact with ILE 118 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1E MET* 5.3 0.9 - - + -
85F GLU* 3.9 18.4 - - - +
88F ALA* 3.6 26.0 - - + -
89F LEU* 4.9 4.3 - - - +
98F ILE* 3.7 32.3 - - + -
114F GLY 3.8 14.6 - - - +
115F ILE* 3.2 24.4 + - + +
117F ASP* 1.3 76.8 - - - +
119F ALA* 1.3 66.6 + - - +
120F GLY 3.2 0.2 - - - -
121F GLU* 3.0 9.7 + - + +
122F ILE* 3.0 36.9 + - + +
148F LEU* 3.8 23.6 - - + -
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Residues in contact with ALA 119 (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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115F ILE 4.8 0.4 + - - -
116F GLY 5.0 0.4 + - - +
117F ASP 3.3 1.2 - - - -
118F ILE* 1.3 80.3 - - - +
120F GLY* 1.3 56.5 + - - +
122F ILE* 3.3 3.2 + - - +
123F LEU 2.9 24.6 + - - -
145F LEU* 3.8 27.3 - - + +
148F LEU* 5.1 1.1 - - + +
168F TYR* 4.5 4.7 - - + -
169F VAL* 4.0 27.8 - - + -
172F ILE* 3.5 30.1 - - + +
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Residues in contact with GLY 120 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117F ASP 3.7 2.9 + - - -
118F ILE 3.2 0.8 - - - -
119F ALA* 1.3 80.0 - - - +
121F GLU* 1.3 61.1 + - - +
123F LEU* 3.5 5.6 + - - +
124F ARG* 3.1 25.3 + - - +
168F TYR* 3.2 28.5 + - - -
172F ILE* 4.2 10.5 - - - -
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Residues in contact with GLU 121 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37F ILE* 3.2 32.4 - - + +
41F ILE* 4.3 7.8 - - - +
85F GLU* 2.9 37.3 - - + +
89F LEU* 3.9 27.7 - - + +
117F ASP 4.3 2.8 - - - +
118F ILE* 3.0 9.1 + - - +
120F GLY* 1.3 77.0 - - - +
122F ILE* 1.3 60.0 + - - +
124F ARG* 3.3 8.1 + - - +
125F LYS* 3.0 27.2 + - - +
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Residues in contact with ILE 122 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1E MET* 5.1 3.8 - - + -
89F LEU* 4.2 10.3 - - + -
92F TYR* 3.9 45.3 - - + +
118F ILE* 3.0 35.4 + - + +
119F ALA 3.7 7.0 - - - +
121F GLU* 1.3 75.8 - - - +
123F LEU* 1.3 55.4 + - - +
125F LYS* 3.5 7.1 + - + +
126F SER* 2.7 36.8 + - - +
137F TYR* 5.1 1.1 - - + -
141F ALA* 3.9 24.9 - - + -
144F ASP* 5.9 1.1 - - + -
145F LEU* 3.9 32.1 - - + -
176F LEU* 5.5 0.2 - - + -
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Residues in contact with LEU 123 (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 2.9 13.7 + - - +
120F GLY* 3.5 9.9 - - - +
121F GLU 3.3 0.2 - - - -
122F ILE* 1.3 77.4 - - - +
124F ARG* 1.3 56.6 + - - +
126F SER* 3.2 5.8 + - - -
127F SER* 2.8 36.0 + - - +
145F LEU* 5.1 0.4 - - - +
172F ILE* 3.8 31.6 - - + +
175F LYS* 4.3 21.3 - - + -
176F LEU* 4.0 32.8 - - + +
179F PHE* 3.7 28.5 - - + -
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Residues in contact with ARG 124 (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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38F TYR* 3.9 30.4 - - - +
41F ILE* 3.2 35.0 - - + +
120F GLY 3.1 14.4 + - - +
121F GLU* 3.3 12.1 + - - +
122F ILE 3.3 0.2 - - - -
123F LEU* 1.3 73.2 - - - +
125F LYS* 1.3 65.6 + - - +
127F SER* 3.3 7.4 + - - -
128F GLU* 3.1 50.6 + - - +
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Residues in contact with LYS 125 (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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40F MET 4.6 2.0 + - - -
41F ILE* 3.9 27.6 + - + +
43F GLU* 3.5 27.7 + - - +
45F TYR* 4.8 4.0 + - - -
89F LEU* 5.0 1.1 - - + -
92F TYR* 5.9 1.1 - - + -
93F ILE* 4.0 31.9 - - + -
121F GLU 3.0 16.5 + - - +
122F ILE* 3.7 7.2 - - - +
124F ARG* 1.3 77.5 - - - +
126F SER* 1.3 55.5 + - - +
128F GLU* 3.2 9.8 + - + +
129F GLU* 3.0 55.1 + - - +
137F TYR* 3.3 36.6 - - + +
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Residues in contact with SER 126 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122F ILE* 2.7 23.3 + - - +
123F LEU* 3.5 6.0 - - - -
125F LYS* 1.3 74.7 - - - +
127F SER* 1.3 58.5 + - - +
129F GLU* 3.2 4.0 + - - +
130F LEU* 2.8 27.6 + - - +
137F TYR* 4.0 14.4 - - - -
138F ALA* 4.4 13.2 - - - +
141F ALA* 3.2 26.3 - - - +
176F LEU* 3.9 24.0 - - - +
179F PHE* 6.1 0.4 - - - -
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Residues in contact with SER 127 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123F LEU* 2.8 22.7 + - - +
124F ARG* 3.6 9.6 - - - -
125F LYS 3.3 0.2 - - - -
126F SER* 1.3 74.3 - - - +
128F GLU* 1.3 61.5 + - - +
130F LEU* 3.2 8.3 + - - +
131F ILE* 3.0 30.4 + - - +
179F PHE* 3.5 28.1 - - - -
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Residues in contact with GLU 128 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41F ILE* 3.8 27.0 - - + +
42F ARG* 5.6 1.8 - - - -
124F ARG* 3.1 46.1 + - - +
125F LYS* 3.3 13.5 - - + +
127F SER* 1.3 78.8 - - - +
129F GLU* 1.3 59.6 + - + +
131F ILE* 3.1 40.1 - - + +
132F LYS* 3.6 13.9 + - - +
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Residues in contact with GLU 129 (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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43F GLU* 3.6 11.1 - - - +
125F LYS* 3.0 46.4 + - - +
126F SER 3.2 7.8 + - - +
128F GLU* 1.3 74.5 - - - +
130F LEU* 1.3 64.2 + - - +
132F LYS* 3.2 24.3 - - - +
134F ASN* 2.9 54.2 + - - +
137F TYR* 3.6 37.8 - - + -
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Residues in contact with LEU 130 (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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126F SER 2.8 15.6 + - - +
127F SER* 3.2 10.7 + - - +
129F GLU* 1.3 78.3 - - - +
131F ILE* 1.3 55.6 + - - +
133F GLY* 2.8 24.7 + - - +
134F ASN 4.3 4.9 + - - +
135F ILE* 4.7 19.7 - - + +
138F ALA* 5.3 10.5 - - + -
179F PHE* 3.6 45.3 - - + +
180F ILE* 5.6 0.7 - - - -
182F TRP* 4.4 24.1 - - + -
183F LYS* 4.6 12.8 - - + -
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Residues in contact with ILE 131 (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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127F SER 3.0 14.2 + - - +
128F GLU* 3.1 32.3 - - + +
130F LEU* 1.3 77.3 - - - +
132F LYS* 1.3 66.4 + - + +
133F GLY 3.4 2.8 + - - -
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Residues in contact with LYS 132 (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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43F GLU* 3.6 23.0 + - - +
128F GLU* 3.8 16.6 - - - +
129F GLU* 3.2 30.3 - - - +
131F ILE* 1.3 83.3 - - + +
133F GLY* 1.3 58.5 + - - +
134F ASN* 4.5 4.1 - - + +
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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