Contacts of the helix formed by residues 126 - 137 (chain F) in PDB entry 5JKL
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 126 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115D LEU* 6.1 0.2 - - - +
11F ASN* 3.2 26.5 + - - +
12F TYR* 3.7 11.6 - - - -
13F HIS 4.8 0.2 + - - -
16F SER* 4.7 4.1 + - - +
76F ARG* 3.0 22.8 + - - -
121F ALA* 2.9 17.2 + - + +
122F THR* 5.1 0.2 - - - +
124F LYS* 4.3 7.6 - - + +
125F ASN* 1.3 73.5 - - - +
127F PRO* 1.3 59.4 - - - +
128F HIS* 3.5 4.2 + - - +
129F LEU* 3.0 35.7 + - + +
130F CYS* 3.0 31.1 + - - -
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Residues in contact with PRO 127 (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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115D LEU* 3.7 21.3 - - + +
118D HIS* 3.4 46.4 - - + +
134D GLU* 4.2 5.3 - - + +
138D LEU* 3.8 10.5 - - + -
11F ASN* 3.9 8.5 - - - +
125F ASN* 3.2 13.9 - - + +
126F ASP* 1.3 82.6 - - - +
128F HIS* 1.3 60.0 + - - +
130F CYS* 3.5 9.0 + - + +
131F ASP* 3.0 30.7 + - - +
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Residues in contact with HIS 128 (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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115D LEU* 5.2 5.1 - - + +
138D LEU* 3.8 18.9 - - + +
139D ASN* 2.9 45.0 + - + -
142D VAL* 3.5 25.9 - - + +
72F LEU* 3.7 27.1 - - + +
75F GLN* 5.3 0.7 - - - -
76F ARG* 3.1 37.1 + - - +
126F ASP* 3.3 2.8 + - - +
127F PRO* 1.3 81.7 - - - +
129F LEU* 1.3 57.6 + - - +
131F ASP* 3.4 9.7 + - - +
132F PHE* 2.9 31.4 + + + +
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Residues in contact with LEU 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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12F TYR* 4.5 6.3 - - + -
16F SER* 3.9 28.7 - - - +
20F ILE* 4.0 27.8 - - + -
72F LEU* 4.2 18.4 - - + -
76F ARG* 4.2 2.9 - - - +
117F LEU* 4.9 5.8 - - + -
120F LEU* 6.5 0.2 - - + -
121F ALA* 3.7 20.6 - - + -
126F ASP* 3.0 29.3 + - - +
128F HIS* 1.3 75.9 + - - +
130F CYS* 1.3 65.6 + - - +
132F PHE* 3.1 12.4 + - + +
133F ILE* 2.9 40.7 + - + +
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Residues in contact with CYS 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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134D GLU* 5.4 3.1 - - - +
118F HIS* 3.6 22.8 - - + +
121F ALA* 3.8 8.0 - - - +
122F THR* 3.6 40.2 - - - -
126F ASP 3.0 19.9 + - - +
127F PRO* 3.7 11.0 - - + +
128F HIS 3.4 0.2 - - - -
129F LEU* 1.3 75.4 - - - +
131F ASP* 1.3 56.7 + - - +
133F ILE* 3.3 3.2 + - - +
134F GLU* 2.9 39.8 + - - +
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Residues in contact with ASP 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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134D GLU* 3.5 46.0 + - + +
135D THR* 4.5 3.5 + - - -
138D LEU* 6.3 0.7 - - + -
139D ASN* 5.0 10.6 - - - +
202E MG 3.5 13.9 - - - -
127F PRO 3.0 19.1 + - - +
128F HIS* 3.7 8.9 + - - +
130F CYS* 1.3 72.7 - - - +
132F PHE* 1.3 64.2 + - - +
134F GLU* 4.3 6.1 - - - -
135F THR* 2.8 51.9 + - - +
136F HIS* 5.9 0.3 + - - -
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Residues in contact with PHE 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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68F LYS* 3.9 25.1 - - + -
69F LEU* 3.6 20.4 - - + -
72F LEU* 3.8 45.3 - - + -
75F GLN* 5.3 3.4 - - - -
128F HIS* 2.9 22.6 + + + +
129F LEU* 3.1 11.9 + - + +
131F ASP* 1.3 80.9 + - - +
133F ILE* 1.3 74.8 + - + +
136F HIS* 3.0 47.2 + + - +
137F TYR* 3.4 32.2 - + - -
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Residues in contact with ILE 133 (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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114F LEU* 4.1 16.8 - - + +
117F LEU* 3.6 38.6 - - + +
118F HIS* 3.9 26.2 - - + +
121F ALA* 4.7 0.9 - - + -
129F LEU* 2.9 35.0 + - + +
130F CYS 3.6 3.6 - - - +
132F PHE* 1.3 88.7 - - + +
134F GLU* 1.3 57.1 + - - +
137F TYR* 2.9 36.1 + - + +
138F LEU* 3.0 34.1 + - + -
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Residues in contact with GLU 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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134D GLU* 4.4 3.4 - - - +
203D MG 3.8 16.8 - - - -
127E PRO* 4.2 13.4 - - - +
130E CYS* 5.4 1.7 - - - +
131E ASP* 3.7 40.8 + - + +
134E GLU* 4.3 5.5 - - - +
202E MG 4.3 7.3 - - - -
118F HIS* 2.8 33.1 + - + +
130F CYS* 2.9 26.6 + - - +
131F ASP* 3.7 6.2 + - - +
133F ILE* 1.3 79.3 - - - +
135F THR* 1.3 62.8 + - - +
136F HIS 3.6 0.2 + - - -
138F LEU* 3.8 27.2 + - + +
139F ASN* 4.1 8.8 + - - +
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Residues in contact with THR 135 (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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131E ASP* 4.7 3.9 + - - -
202E MG 4.1 8.3 - - - -
131F ASP* 2.8 41.5 + - - +
134F GLU* 1.3 78.2 - - - +
136F HIS* 1.3 88.6 + - + +
139F ASN* 5.7 3.3 + - - +
140F GLU* 5.4 2.1 - - - +
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Residues in contact with HIS 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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139D ASN* 6.0 1.8 + - - -
65F HIS* 5.5 3.8 + - - -
68F LYS* 3.3 33.5 + - + +
131F ASP* 5.9 0.2 - - - -
132F PHE* 3.0 40.1 + + - +
135F THR* 1.3 101.6 + - + +
137F TYR* 1.3 80.1 + - + +
140F GLU* 3.4 22.4 - - - +
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Residues in contact with TYR 137 (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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27F GLU* 4.2 8.5 - - - -
65F HIS* 2.7 53.6 + + + -
68F LYS* 3.3 20.5 - - + +
69F LEU* 3.4 22.2 + - + +
114F LEU* 3.9 37.0 - - + -
132F PHE* 3.4 36.8 - + - -
133F ILE* 2.9 16.2 + - + +
135F THR 3.7 0.4 - - - -
136F HIS* 1.3 99.0 - - + +
138F LEU* 1.3 66.2 + - - +
139F ASN 3.3 2.2 - - - +
140F GLU* 3.2 5.6 + - + +
141F GLN* 3.0 28.1 + - - +
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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