Contacts of the helix formed by residues 144 - 163 (chain B) in PDB entry 1JT6
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 144 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177A LYS* 3.4 25.8 - - - +
142B ILE* 3.7 11.8 - - - +
143B ASN* 1.3 91.9 + - + +
145B VAL* 1.3 64.6 + - - +
146B ASN 3.3 2.9 - - - -
147B ALA* 3.2 22.2 + - + +
148B VAL* 3.2 21.3 + - - +
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Residues in contact with VAL 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B HIS* 3.7 37.0 - - + +
131B PHE* 3.9 19.9 - - + -
132B LYS* 4.2 10.5 - - + +
135B ASN* 3.5 28.0 - - - +
142B ILE* 3.7 19.3 - - + +
143B ASN 3.7 2.9 + - - +
144B ASP* 1.3 72.0 - - - +
146B ASN* 1.3 54.5 + - - +
148B VAL* 3.4 2.1 + - - +
149B SER* 2.7 42.3 + - - +
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Residues in contact with ASN 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B ILE* 4.0 17.4 - - - +
128B HIS* 3.1 35.4 + - - -
144B ASP 3.3 1.0 - - - -
145B VAL* 1.3 75.0 - - - +
147B ALA* 1.3 68.1 + - - +
149B SER* 3.8 5.5 - - - -
150B LYS* 3.0 42.4 + - + +
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Residues in contact with ALA 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A GLU* 5.7 1.1 - - - +
173A LYS* 6.5 0.4 - - + -
174A LEU* 3.9 22.1 - - + +
177A LYS* 5.2 4.7 - - + -
144B ASP* 3.2 32.6 + - + +
146B ASN* 1.3 79.2 - - - +
148B VAL* 1.3 59.1 + - + +
150B LYS* 3.2 5.9 + - - +
151B ILE* 2.9 34.3 + - - +
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Residues in contact with VAL 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A LYS* 4.9 3.8 - - - -
181A ILE* 4.3 15.5 - - + -
131B PHE* 3.7 21.8 - - + -
142B ILE* 3.5 28.5 - - + -
144B ASP* 3.2 14.8 + - - +
145B VAL 3.9 5.8 - - - +
147B ALA* 1.3 75.8 - - + +
149B SER* 1.3 59.8 + - - +
151B ILE* 3.7 6.5 - - + +
152B ALA* 2.8 27.9 + - - +
182B PHE* 3.7 26.9 - - + -
186B LEU* 4.2 13.2 - - + -
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Residues in contact with SER 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B ILE* 3.8 22.2 - - - +
127B TYR* 3.6 26.0 - - - -
128B HIS* 3.4 21.7 + - - +
131B PHE* 3.7 6.4 - - - -
145B VAL 2.7 24.6 + - - -
146B ASN* 3.8 5.7 - - - -
147B ALA 3.3 0.4 - - - -
148B VAL* 1.3 76.1 - - - +
150B LYS* 1.3 58.7 + - - +
152B ALA* 3.7 0.7 - - - +
153B ALA* 2.9 33.8 + - - +
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Residues in contact with LYS 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A GLN* 4.4 11.3 - - - +
170A GLU* 4.4 14.5 + - - +
174A LEU* 4.1 24.2 - - + -
120B GLU* 4.1 27.8 - - - +
124B ILE* 4.0 22.4 - - + -
146B ASN* 3.0 37.3 + - - +
147B ALA* 3.5 6.1 - - - +
149B SER* 1.3 78.9 - - - +
151B ILE* 1.3 62.3 + - - +
153B ALA* 3.8 0.7 - - - +
154B ASN* 3.1 33.8 + - - +
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Residues in contact with ILE 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A ILE* 4.1 10.7 - - + +
174A LEU* 3.4 39.0 - - + +
177A LYS* 3.6 21.3 - - + -
178A PHE* 3.5 46.7 - - + +
181A ILE* 4.2 7.6 - - + -
147B ALA 2.9 22.7 + - - +
148B VAL* 3.7 4.0 - - - +
150B LYS* 1.3 76.6 - - - +
152B ALA* 1.3 58.0 + - - +
154B ASN* 3.2 3.0 + - - +
155B ALA* 2.9 28.9 + - - +
182B PHE* 3.9 13.7 - - + -
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Residues in contact with ALA 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B PHE* 4.0 15.0 - - + -
127B TYR* 3.7 28.0 - - + -
131B PHE* 4.0 5.6 - - + -
148B VAL 2.8 21.7 + - - +
149B SER 3.7 1.6 - - - +
151B ILE* 1.3 71.7 - - - +
153B ALA* 1.3 63.9 + - - +
155B ALA* 3.9 2.5 - - - +
156B VAL* 2.9 30.7 + - - +
178B PHE* 5.2 1.8 - - - -
182B PHE* 4.1 16.1 - - + -
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Residues in contact with ALA 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B TYR* 5.6 1.2 + - - -
123B TYR* 3.4 30.6 + - + +
124B ILE* 4.1 10.5 - - + -
127B TYR* 3.4 29.0 + - + -
149B SER 2.9 21.9 + - - +
150B LYS 3.8 3.6 - - - +
152B ALA* 1.3 73.0 - - - +
154B ASN* 1.3 59.2 + - - +
156B VAL* 3.8 1.6 - - - +
157B ASN* 2.9 28.6 + - - +
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Residues in contact with ASN 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158A GLY* 3.4 22.3 - - - +
159A ILE* 3.9 11.9 - - + -
162A PHE* 3.1 28.8 + - - +
163A THR* 3.4 19.2 + - - +
166A GLN* 4.8 1.4 - - - +
120B GLU* 4.5 9.0 - - - +
123B TYR* 2.8 35.6 + - - -
124B ILE* 5.9 0.2 - - - +
150B LYS* 3.1 23.6 + - - +
151B ILE* 4.1 1.6 - - - +
153B ALA* 1.3 76.2 - - - +
155B ALA* 1.3 60.4 + - - +
157B ASN* 3.2 1.7 + - - +
158B GLY 2.8 24.3 + - - -
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Residues in contact with ALA 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155A ALA* 3.6 31.5 - - + +
159A ILE* 4.0 4.1 - - + +
178A PHE* 4.3 10.3 - - + -
151B ILE 2.9 18.7 + - - +
152B ALA 3.9 0.4 - - - +
154B ASN* 1.3 75.7 - - - +
156B VAL* 1.3 58.2 + - - +
158B GLY* 2.9 16.3 + - - -
159B ILE* 2.9 20.3 + - - +
178B PHE* 3.8 24.5 - - + -
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Residues in contact with VAL 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B PHE* 5.2 0.2 - - + -
83B ASN* 3.4 24.9 - - + +
86B SER* 4.2 15.9 - - - +
93B TYR* 4.7 3.1 - - - +
127B TYR* 3.4 25.1 - - + +
152B ALA* 2.9 21.8 + - - +
153B ALA 3.8 1.8 - - - +
155B ALA* 1.3 75.0 - - - +
157B ASN* 1.3 67.0 + - - +
159B ILE* 3.0 9.2 + - - +
160B VAL* 2.9 24.5 + - + +
175B MET* 3.9 17.5 - - + -
178B PHE* 3.6 22.2 - - + -
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Residues in contact with ASN 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162A PHE* 3.5 16.8 - - + -
93B TYR* 3.8 20.7 - - + -
96B GLN* 2.7 38.6 + - - +
123B TYR* 2.9 37.0 + - + +
153B ALA 2.9 10.8 + - - +
154B ASN 3.6 4.3 - - - +
156B VAL* 1.3 77.9 - - - +
158B GLY* 1.3 57.9 + - - +
160B VAL* 4.6 0.7 - - - -
161B THR* 2.9 40.9 + - - -
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Residues in contact with GLY 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A ASN 3.3 20.4 - - - -
158A GLY* 3.5 16.6 - - - -
154B ASN 2.8 10.5 + - - -
155B ALA 2.9 5.3 + - - -
157B ASN* 1.3 76.9 - - - +
159B ILE* 1.3 62.3 + - - +
162B PHE* 2.9 36.2 + - - +
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Residues in contact with ILE 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A ILE* 4.3 16.8 - - + +
154A ASN* 4.0 17.9 - - + -
155A ALA* 4.1 4.9 - - + +
87B LEU* 4.9 2.5 - - + -
155B ALA 2.9 13.0 + - - +
156B VAL 3.0 4.9 + - - +
158B GLY* 1.3 77.8 - - - +
160B VAL* 1.3 61.8 + - - +
163B THR* 2.8 39.8 + - + +
171B ARG* 5.1 4.9 - - + +
174B LEU* 5.1 6.3 - - + -
175B MET* 3.7 31.4 - - + +
178B PHE* 3.6 46.2 - - + -
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Residues in contact with VAL 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B SER* 3.7 41.1 - - - +
87B LEU* 3.9 20.9 - - + +
93B TYR* 4.0 29.6 - - + +
156B VAL* 2.9 20.1 + - + +
157B ASN 4.0 2.7 - - - +
159B ILE* 1.3 78.1 - - - +
161B THR* 1.3 65.2 + - - +
163B THR* 4.0 2.1 + - - -
164B HIS* 4.3 4.4 + - - +
171B ARG* 3.3 20.6 + - - +
175B MET* 3.8 12.8 - - + -
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Residues in contact with THR 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162A PHE* 3.6 20.1 - - + -
201A DEQ 3.0 31.1 + - - +
93B TYR 5.0 0.5 + - - -
96B GLN* 3.6 15.8 - - + +
97B ASN* 3.8 16.6 + - - +
100B ILE* 4.6 1.6 - - + -
157B ASN* 2.9 37.1 + - - -
158B GLY 4.2 0.2 - - - -
160B VAL* 1.3 80.6 - - - +
162B PHE* 1.3 66.1 + - + +
163B THR 3.6 0.7 + - - -
164B HIS* 3.7 14.5 - - - +
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Residues in contact with PHE 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A GLU* 5.3 3.5 - - - +
154A ASN* 3.2 24.2 + - - +
157A ASN* 3.6 38.6 - - + +
158A GLY 3.9 0.2 - - - -
161A THR* 3.5 31.0 - - + -
162A PHE* 3.9 15.7 - + - -
201A DEQ 3.2 71.7 - + + +
100B ILE* 4.7 1.3 - - + -
158B GLY* 2.9 42.2 + - - +
161B THR* 1.3 72.2 - - + +
163B THR* 1.3 61.1 + - - +
164B HIS 3.5 2.7 - - - -
166B GLN* 4.7 1.6 - - - +
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Residues in contact with THR 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A ASN* 3.3 30.7 - - + +
87B LEU* 4.8 0.2 - - - +
159B ILE* 2.8 31.8 + - + +
160B VAL* 4.0 0.3 + - - -
161B THR 3.4 0.4 - - - -
162B PHE* 1.3 77.1 - - - +
164B HIS* 1.3 55.5 + - - +
165B GLU* 2.9 10.4 + - - -
166B GLN* 3.3 36.4 - - - +
171B ARG* 2.9 40.4 + - - +
174B LEU* 5.1 7.6 - - + -
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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