Contacts of the helix formed by residues 141 - 164 (chain J) in PDB entry 1F33
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 141 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21J VAL* 4.8 9.0 - - + +
25J GLU* 3.4 9.6 + - - +
29J THR* 3.8 16.7 + - - +
83J ARG* 2.7 35.7 + - - -
87J LEU* 4.2 6.6 - - - +
139J ALA* 3.5 1.3 - - - +
140J LYS* 1.3 76.7 - - - +
142J ASP* 1.3 67.5 + - - +
143J ASP* 3.8 2.6 + - - +
144J THR* 2.6 32.8 + - - +
145J ALA* 2.9 21.6 + - - +
133L ARG* 4.2 12.3 - - - +
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Residues in contact with ASP 142 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140J LYS 3.3 8.7 + - - +
141J ASP* 1.3 73.3 + - - +
143J ASP* 1.3 65.6 + - - +
145J ALA* 3.0 10.2 + - - +
146J ASP* 2.9 22.0 + - - +
133L ARG* 4.4 7.4 - - + +
136L ILE* 3.7 42.6 - - + +
137L GLY* 4.3 9.6 + - - -
149L THR* 4.2 4.9 - - - +
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Residues in contact with ASP 143 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83J ARG* 3.3 34.3 + - - +
141J ASP* 3.3 2.5 + - - -
142J ASP* 1.3 77.9 - - - +
144J THR* 1.3 62.3 + - - +
146J ASP* 3.2 5.2 + - - +
147J ILE* 3.0 27.5 + - - +
133L ARG* 4.0 4.0 - - - -
136L ILE* 3.5 6.2 - - - +
149L THR* 3.4 26.0 - - - +
152L SER* 2.6 33.0 + - - -
153L ARG* 3.7 19.6 + - - +
156L ASP* 3.4 7.4 - - - +
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Residues in contact with THR 144 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29J THR* 3.1 22.8 - - + +
32J LEU* 5.0 4.5 - - + -
33J LEU* 3.6 28.0 - - + -
83J ARG* 3.6 10.1 + - - +
139J ALA* 4.4 7.6 - - + -
141J ASP* 2.6 33.5 + - - -
143J ASP* 1.3 73.9 - - - +
145J ALA* 1.3 65.9 + - - +
147J ILE* 3.3 9.8 + - - +
148J LEU* 3.0 35.0 + - + +
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Residues in contact with ALA 145 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136J ILE* 4.0 23.8 - - + +
139J ALA* 3.9 16.5 - - + +
141J ASP 2.9 11.5 + - - +
142J ASP* 3.0 13.0 + - - +
144J THR* 1.3 76.3 - - - +
146J ASP* 1.3 54.5 + - - +
148J LEU* 3.4 5.1 + - - +
149J THR* 2.6 38.3 + - - +
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Residues in contact with ASP 146 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142J ASP 2.9 11.9 + - - +
143J ASP 3.3 9.6 - - - +
144J THR 3.1 0.2 - - - -
145J ALA* 1.3 74.0 - - - +
147J ILE* 1.3 66.9 + - - +
149J THR* 3.0 9.1 + - - -
150J ALA* 3.0 23.2 + - - +
612J TRS 2.7 43.4 + - - -
146L ASP* 4.2 8.0 - - - +
149L THR* 3.7 22.5 - - + +
150L ALA 5.2 0.7 + - - -
153L ARG* 2.9 20.6 + - - +
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Residues in contact with ILE 147 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33J LEU* 5.2 2.2 - - + -
76J HIS* 4.8 3.2 + - - +
79J THR* 3.8 24.0 - - + -
80J MET* 3.6 31.0 - - + -
83J ARG* 3.6 40.2 - - + -
143J ASP 3.0 17.9 + - - +
144J THR* 3.5 8.7 - - - +
146J ASP* 1.3 77.1 - - - +
148J LEU* 1.3 59.1 + - + +
150J ALA* 3.3 4.4 + - - +
151J ALA* 3.1 26.0 + - + +
153L ARG* 3.3 37.0 - - + +
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Residues in contact with LEU 148 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32J LEU* 4.2 7.6 - - + -
33J LEU* 4.6 7.6 - - + -
36J GLN* 3.9 11.9 - - + -
80J MET* 3.8 27.6 - - + -
132J VAL* 3.9 19.4 - - + +
135J ALA* 3.7 34.3 - - + +
136J ILE* 3.9 12.7 - - + +
139J ALA* 4.1 6.7 - - + -
144J THR* 3.0 35.1 + - + +
145J ALA 3.8 3.4 - - - +
147J ILE* 1.3 71.7 - - - +
149J THR* 1.3 56.3 + - - +
151J ALA* 3.7 3.9 - - - +
152J SER* 2.7 36.2 + - - -
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Residues in contact with THR 149 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136J ILE* 3.4 29.6 - - + +
145J ALA 2.6 23.8 + - - -
146J ASP* 3.0 10.3 + - - +
148J LEU* 1.3 75.8 - - - +
150J ALA* 1.3 59.1 + - - +
152J SER* 3.2 1.6 + - - -
153J ARG* 2.8 43.5 + - - +
612J TRS 5.9 4.3 - - - +
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Residues in contact with ALA 150 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76J HIS* 3.4 19.7 + - + +
146J ASP 3.0 12.0 + - - +
147J ILE* 3.5 11.0 - - - +
149J THR* 1.3 78.5 - - - +
151J ALA* 1.3 62.5 + - - +
153J ARG* 3.4 8.7 - - - +
154J ASP* 3.3 16.1 + - - +
612J TRS 4.5 18.6 + - - +
153L ARG* 4.8 10.3 - - - +
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Residues in contact with ALA 151 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40J PHE* 3.9 22.4 - - + -
76J HIS* 3.5 30.7 - - + +
80J MET* 5.0 5.6 - - - -
132J VAL* 4.6 2.2 - - + -
147J ILE* 3.1 16.6 + - + +
148J LEU* 3.7 7.4 - - - +
150J ALA* 1.3 75.6 - - - +
152J SER* 1.3 66.5 + - - +
154J ASP* 3.1 4.3 + - - +
155J LEU* 2.9 27.7 + - - +
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Residues in contact with SER 152 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132J VAL* 4.0 20.3 - - - +
133J ARG* 3.7 29.9 - - - +
136J ILE* 3.7 16.5 - - - +
148J LEU 2.7 21.9 + - - -
149J THR 3.5 4.3 - - - -
151J ALA* 1.3 72.8 - - - +
153J ARG* 1.3 65.8 + - - +
155J LEU* 3.0 2.6 + - - +
156J ASP* 2.8 31.8 + - - +
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Residues in contact with ARG 153 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149J THR* 2.8 28.2 + - - +
150J ALA* 3.4 10.1 - - - +
152J SER* 1.3 77.6 - - - +
154J ASP* 1.3 63.3 + - - +
156J ASP* 3.7 5.8 + - - +
157J LYS* 3.3 18.9 + - - +
612J TRS 4.1 23.6 + - - -
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Residues in contact with ASP 154 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72J ALA* 4.2 9.2 - - - +
76J HIS* 2.7 36.2 + - + +
150J ALA 3.3 3.9 + - - -
151J ALA 3.1 5.7 + - - +
153J ARG* 1.3 79.5 - - - +
155J LEU* 1.3 60.2 + - + +
157J LYS* 3.0 11.6 + - - +
158J PHE* 2.8 59.9 + - + -
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Residues in contact with LEU 155 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40J PHE* 3.2 39.0 - - + -
43J LEU* 3.8 17.5 - - + -
73J LEU* 4.2 14.6 - - + -
76J HIS* 5.4 1.3 - - + -
125J TYR* 4.2 10.0 - - + +
128J VAL* 3.5 33.7 - - + -
129J ALA* 3.8 22.0 - - + +
132J VAL* 4.8 2.0 - - + -
151J ALA* 2.9 25.6 + - - +
152J SER* 3.8 4.9 - - - +
154J ASP* 1.3 77.1 - - + +
156J ASP* 1.3 59.9 + - - +
158J PHE* 3.2 7.3 + - + +
159J LEU* 2.8 30.7 + - - +
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Residues in contact with ASP 156 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129J ALA* 3.7 11.8 - - - +
133J ARG* 2.6 46.2 + - - -
152J SER* 2.8 21.7 + - - +
153J ARG* 4.0 5.4 - - - +
155J LEU* 1.3 75.7 - - - +
157J LYS* 1.3 62.7 + - - +
159J LEU* 3.6 9.0 + - - +
160J TRP* 3.1 23.0 + - - +
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Residues in contact with LYS 157 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153J ARG 3.3 12.2 + - - +
154J ASP* 3.0 16.3 + - - +
156J ASP* 1.3 79.6 - - - +
158J PHE* 1.3 71.7 + - + +
160J TRP* 3.3 25.4 + - + +
161J PHE* 2.9 57.6 + - + +
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Residues in contact with PHE 158 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68J GLY 5.3 0.4 - - - -
69J PHE* 3.4 61.7 - + + -
72J ALA* 3.5 32.5 - - + -
73J LEU* 4.1 13.9 - - + -
125J TYR* 3.7 19.1 - + + -
154J ASP* 2.8 44.6 + - + +
155J LEU* 3.7 6.3 - - - +
157J LYS* 1.3 90.5 - - + +
159J LEU* 1.3 67.2 + - - +
161J PHE* 3.0 1.9 + - - +
162J ILE* 2.8 29.2 + - - +
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Residues in contact with LEU 159 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122J ALA* 3.5 28.9 - - - +
125J TYR* 4.2 12.0 - - + -
126J ALA* 3.9 24.9 - - + +
129J ALA* 4.4 11.4 - - + -
130J ASN* 5.3 6.1 - - - +
133J ARG* 6.2 0.4 - - - +
155J LEU 2.8 17.2 + - - +
156J ASP* 3.7 8.7 - - - +
158J PHE* 1.3 76.2 - - - +
160J TRP* 1.3 57.7 + - - +
162J ILE* 3.1 5.0 + - - +
163J GLU* 2.8 62.4 + - + +
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Residues in contact with TRP 160 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156J ASP 3.1 12.0 + - - +
157J LYS* 3.4 24.5 - - + +
158J PHE 3.1 0.2 - - - -
159J LEU* 1.3 79.6 - - - +
161J PHE* 1.3 88.7 + + - +
163J GLU* 3.8 9.3 - - + +
164J SER* 2.7 64.8 + - - -
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Residues in contact with PHE 161 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65J MET* 4.0 13.9 - - + -
69J PHE* 3.7 29.6 - + + -
157J LYS* 2.9 38.9 + - + +
158J PHE 3.0 6.9 + - - +
160J TRP* 1.3 117.9 - + - +
162J ILE* 1.3 60.0 + - - +
164J SER* 3.5 5.7 + - - -
165J ASN* 2.7 33.6 + - - -
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Residues in contact with ILE 162 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65J MET* 4.4 10.3 - - + -
66J LEU* 4.8 4.7 - - + -
69J PHE* 3.7 15.7 - - + -
118J LEU* 3.3 39.1 - - + +
121J LEU* 4.1 9.9 - - + -
122J ALA* 3.9 12.1 - - + +
125J TYR* 3.5 54.3 - - + -
158J PHE 2.8 18.3 + - - +
159J LEU* 3.5 6.5 - - - +
161J PHE* 1.3 72.9 - - - +
163J GLU* 1.3 64.2 + - - +
165J ASN* 3.0 18.3 + - - +
166J ILE* 3.6 8.1 + - + +
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Residues in contact with GLU 163 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122J ALA* 4.3 13.9 - - + +
126J ALA* 5.7 1.2 - - - +
159J LEU* 2.8 50.4 + - + +
160J TRP* 3.8 7.9 - - + +
162J ILE* 1.3 73.4 - - - +
164J SER* 1.3 58.8 + - - +
166J ILE* 2.9 40.4 + - + +
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Residues in contact with SER 164 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160J TRP* 2.7 54.0 + - - -
161J PHE* 3.9 7.9 - - - -
162J ILE 3.2 0.4 - - - -
163J GLU* 1.3 72.3 - - - +
165J ASN* 1.3 60.4 + - - +
166J ILE 3.4 3.6 + - - +
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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
------------------------------------------------------------
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