Contacts of the helix formed by residues 145 - 157 (chain A) in PDB entry 1JK7
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 145 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32A GLU* 2.8 34.4 + - - +
140A CYS* 2.9 15.0 + - - +
141A LYS* 4.5 3.8 - - - +
144A TYR* 1.3 87.9 + - - +
146A ILE* 1.3 66.0 + - - +
147A LYS* 3.2 14.5 + - + +
148A LEU* 2.9 41.9 + - - +
149A TRP 3.3 7.6 + - - -
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Residues in contact with ILE 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A ARG* 5.8 0.9 - - - +
137A TYR* 3.3 60.3 - - + +
141A LYS* 3.6 29.6 - - + +
145A ASN* 1.3 72.2 - - - +
147A LYS* 1.3 65.6 + - - +
149A TRP* 3.0 15.4 + - + +
150A LYS* 2.9 37.5 + - - +
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Residues in contact with LYS 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A GLU* 5.5 7.6 + - - +
36A ARG* 5.6 13.0 - - - +
145A ASN* 3.2 12.6 + - + +
146A ILE* 1.3 77.4 - - - +
148A LEU* 1.3 58.6 + - - +
150A LYS* 3.3 12.9 + - + +
151A THR* 3.1 31.1 + - - +
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Residues in contact with LEU 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A GLU* 4.4 16.8 - - + +
35A ILE* 4.0 33.7 - - + -
36A ARG* 4.2 22.7 - - + +
39A CYS* 5.6 0.4 - - - -
101A LEU* 5.3 0.4 - - + -
140A CYS* 5.5 2.2 - - - -
144A TYR* 3.5 39.3 - - + -
145A ASN* 2.9 24.0 + - - +
146A ILE 3.1 0.2 - - - -
147A LYS* 1.3 75.2 - - - +
149A TRP* 1.3 63.7 + - - +
151A THR* 3.1 13.2 + - + +
152A PHE* 3.0 38.0 + - + -
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Residues in contact with TRP 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A ALA* 3.6 15.9 - - + -
131A ASN* 2.7 32.1 + - - -
132A ARG* 3.6 55.9 - - + -
136A PHE* 3.6 23.2 - + - -
137A TYR* 3.7 41.2 - + + +
140A CYS* 3.8 22.6 - - + -
145A ASN 3.3 2.4 + - - -
146A ILE* 3.0 18.3 + - + +
148A LEU* 1.3 79.5 - - - +
150A LYS* 1.3 90.9 + - + +
152A PHE* 3.1 7.4 + - - +
153A THR* 3.0 30.9 + - - -
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Residues in contact with LYS 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A ARG* 5.0 8.6 - - - +
146A ILE* 2.9 35.4 + - + +
147A LYS* 3.5 11.9 - - + +
148A LEU 3.2 0.2 - - - -
149A TRP* 1.3 94.3 - - + +
151A THR* 1.3 62.4 + - - +
153A THR* 3.2 11.5 + - - -
154A ASP* 3.1 27.9 + - - +
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Residues in contact with THR 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A ARG* 3.0 43.7 + - + +
39A CYS* 3.7 25.2 - - + +
40A LEU* 4.8 7.2 - - + -
147A LYS* 3.1 17.6 + - - +
148A LEU* 3.3 17.0 - - + +
150A LYS* 1.3 78.5 - - - +
152A PHE* 1.3 62.2 + - - +
154A ASP* 3.3 11.8 + - + +
155A CYS* 3.2 19.1 + - - +
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Residues in contact with PHE 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A ILE* 3.3 33.0 - - + -
39A CYS* 3.4 22.4 - - - -
101A LEU* 3.8 22.4 - - + -
104A ILE* 3.6 32.3 - - + -
105A CYS* 4.4 3.1 - - - -
108A LEU* 4.2 7.0 - - + -
136A PHE* 3.5 28.7 - + + -
140A CYS* 4.3 2.0 - - - -
148A LEU* 3.0 33.1 + - + -
149A TRP* 3.3 9.4 - - - +
151A THR* 1.3 76.8 - - - +
153A THR* 1.3 59.4 + - - +
155A CYS* 2.9 5.0 + - + +
156A PHE* 2.8 50.1 + + + -
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Residues in contact with THR 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A ALA* 3.8 35.6 - - + +
131A ASN* 4.6 2.8 + - - -
149A TRP* 3.0 26.1 + - - -
150A LYS* 3.2 13.7 + - - -
152A PHE* 1.3 76.7 - - - +
154A ASP* 1.3 61.3 + - - +
156A PHE* 3.3 11.4 + - + +
157A ASN* 2.9 45.6 + - - +
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Residues in contact with ASP 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A LEU* 6.4 1.1 - - + -
43A ARG* 3.5 27.1 + - - +
150A LYS* 3.1 17.4 + - - +
151A THR* 3.6 11.5 - - + +
152A PHE 3.2 0.2 - - - -
153A THR* 1.3 79.4 - - - +
155A CYS* 1.3 62.9 + - - +
157A ASN* 3.7 18.9 + - - +
158A CYS* 3.7 8.0 - - - -
192A PRO* 5.1 0.9 - - - +
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Residues in contact with CYS 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A CYS* 3.7 25.6 - - + +
42A SER* 3.2 26.9 - - - -
43A ARG* 4.4 10.3 - - - +
46A PHE* 3.9 16.9 - - - -
108A LEU* 4.3 13.7 - - - -
151A THR 3.2 10.9 + - - +
152A PHE* 2.9 10.9 + - - +
154A ASP* 1.3 75.7 - - - +
156A PHE* 1.3 72.2 + - + +
158A CYS* 2.9 20.8 + - - +
159A LEU* 3.7 4.7 + - - +
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Residues in contact with PHE 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A VAL* 4.3 10.5 - - + -
104A ILE* 3.9 35.7 - - + -
108A LEU* 5.5 0.7 - - + -
122A ARG* 3.4 15.7 + - - -
126A GLU* 3.4 37.0 - - + +
128A ALA 6.0 0.2 - - - -
131A ASN* 3.7 23.8 - - - -
136A PHE* 3.7 31.6 - + - -
152A PHE* 2.8 35.4 + + + +
153A THR* 3.7 8.7 - - + +
155A CYS* 1.3 83.4 - - + +
157A ASN* 1.3 58.6 + - - +
158A CYS 3.0 5.1 + - - -
159A LEU* 3.2 31.2 + - + +
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Residues in contact with ASN 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A ARG* 2.9 30.0 + - - +
126A GLU 4.8 0.5 - - - +
128A ALA 5.4 1.9 + - - -
153A THR* 2.9 37.3 + - - +
154A ASP* 3.8 16.1 + - - +
155A CYS 3.2 0.6 - - - -
156A PHE* 1.3 75.9 - - - +
158A CYS* 1.3 58.3 + - - +
159A LEU 3.6 0.6 - - - +
191A ARG* 4.1 3.8 - - - +
192A PRO* 3.5 10.8 - - + +
193A THR* 3.1 46.5 + - - +
194A ASP* 3.9 13.1 - - - +
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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