Contacts of the helix formed by residues 141 - 157 (chain B) in PDB entry 5J3V
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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795A ARG* 3.8 29.0 + - - -
834A PHE* 5.9 0.3 - - - -
139B SER* 3.1 8.5 + - - +
140B GLU* 1.3 76.1 - - - +
142B TYR* 1.3 64.1 + - - +
143B ASN* 3.4 1.8 - - + +
144B THR* 3.0 36.0 + - + +
145B CYS* 3.0 13.2 + - - +
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Residues in contact with TYR 142 (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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107B ARG* 5.3 4.7 - - - -
140B GLU 3.2 7.4 + - - +
141B ASP* 1.3 71.2 - - - +
143B ASN* 1.3 70.4 + - - +
145B CYS* 2.9 5.5 + - + -
146B GLU* 2.6 55.8 + - + +
185B HIS* 4.6 7.9 - + - -
187B SER* 3.2 36.9 + - - -
189B LYS* 3.3 23.9 - - - +
190B ILE* 3.6 22.2 - - + -
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Residues in contact with ASN 143 (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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99B ILE 3.8 5.5 - - - +
100B GLY* 3.2 19.2 - - - -
101B ASP 3.3 17.9 - - - +
102B SER* 4.6 6.3 + - - +
107B ARG* 2.9 41.8 + - - +
141B ASP* 3.4 1.5 - - + +
142B TYR* 1.3 90.4 - - - +
144B THR* 1.3 62.5 + - + +
146B GLU* 4.3 1.8 - - - -
147B GLY* 3.8 9.5 + - - -
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Residues in contact with THR 144 (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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97B ASN 6.1 0.4 - - - +
99B ILE* 4.6 7.0 - - + +
100B GLY* 3.7 27.8 - - - +
136B LEU* 3.3 28.6 - - + +
139B SER* 3.3 19.1 + - - -
141B ASP* 3.0 23.4 + - + +
143B ASN* 1.3 79.2 - - + +
145B CYS* 1.3 58.9 + - - +
148B ALA* 3.3 17.1 + - - +
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Residues in contact with CYS 145 (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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136B LEU 3.8 5.6 - - - -
137B LEU* 3.2 28.6 - - - +
139B SER 3.3 13.2 - - - +
140B GLU 5.0 0.9 - - - +
141B ASP 3.0 16.2 + - - +
142B TYR* 2.9 7.7 + - - +
144B THR* 1.3 80.8 - - - +
146B GLU* 1.3 60.8 + - - +
147B GLY 3.4 0.2 - - - -
148B ALA* 3.9 1.6 - - - +
149B PHE* 3.0 29.2 + - - +
182B PHE* 4.0 18.8 - - - -
185B HIS* 5.1 5.2 - - - -
190B ILE* 4.1 15.3 - - + -
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Residues in contact with GLU 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B ARG* 2.3 44.7 + - - -
142B TYR* 2.6 50.9 + - + +
143B ASN* 5.0 0.7 - - - -
145B CYS* 1.3 73.1 - - - +
147B GLY* 1.3 59.6 + - - +
149B PHE* 3.3 1.9 + - - +
150B GLY* 2.6 35.0 + - - -
189B LYS* 4.9 9.9 - - + -
190B ILE* 3.8 14.1 - - + +
193B HIS* 4.8 11.2 + - + +
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Residues in contact with GLY 147 (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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99B ILE* 3.3 36.1 - - - +
107B ARG* 4.6 8.5 - - - -
111B GLY* 5.6 2.2 - - - -
143B ASN 3.8 9.7 + - - -
145B CYS 3.4 0.2 - - - -
146B GLU* 1.3 87.9 + - - +
148B ALA* 1.3 57.4 + - - +
150B GLY* 3.7 1.9 - - - -
151B ALA* 3.1 22.3 + - - +
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Residues in contact with ALA 148 (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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99B ILE* 3.6 9.6 - - + +
133B LEU* 4.3 12.1 - - + +
136B LEU* 3.6 37.9 - - + +
137B LEU* 4.2 5.2 - - + -
144B THR 3.3 22.1 + - - +
145B CYS 3.7 2.8 + - - +
146B GLU 3.3 0.2 - - - -
147B GLY* 1.3 76.8 - - - +
149B PHE* 1.3 61.3 + - - +
151B ALA* 3.6 3.2 + - - +
152B LEU* 3.4 27.5 + - - +
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Residues in contact with PHE 149 (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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137B LEU* 3.6 18.8 - - + +
145B CYS 3.0 17.6 + - - +
146B GLU* 3.8 5.2 - - - +
148B ALA* 1.3 76.0 - - - +
150B GLY* 1.3 63.5 + - - +
151B ALA 3.2 0.7 - - - -
152B LEU* 3.9 5.6 - - + -
153B GLN* 3.5 13.7 + - - +
179B PHE* 3.5 40.6 - + - -
182B PHE* 4.1 24.7 - + + -
190B ILE* 3.8 35.4 - - + -
193B HIS* 3.3 35.5 + - + -
194B ALA* 3.6 22.0 - - + -
197B CYS* 4.1 3.8 - - - -
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Residues in contact with GLY 150 (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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111B GLY* 5.1 3.3 - - - +
115B THR* 4.5 4.9 - - - +
146B GLU* 2.6 23.2 + - - -
147B GLY* 3.3 4.5 + - - -
148B ALA 3.3 0.4 - - - -
149B PHE* 1.3 75.5 - - - +
151B ALA* 1.3 59.3 + - - +
153B GLN* 4.2 6.1 + - - +
154B LYS* 4.3 8.3 + - - +
193B HIS* 3.5 21.0 + - - -
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Residues in contact with ALA 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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99B ILE* 4.9 1.3 - - + -
111B GLY* 4.8 4.9 - - - +
114B ILE* 3.9 35.2 - - + -
115B THR* 3.4 16.6 - - + +
133B LEU* 4.2 8.7 - - + -
147B GLY 3.1 15.0 + - - +
148B ALA* 3.9 5.2 - - - +
149B PHE 3.2 0.2 - - - -
150B GLY* 1.3 76.9 - - - +
152B LEU* 1.3 64.7 + - - +
153B GLN 3.3 1.3 + - - -
154B LYS 3.5 0.5 + - - -
155B ILE* 3.1 27.5 + - - +
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Residues in contact with LEU 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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130B LEU* 3.8 26.9 - - + -
133B LEU* 3.7 35.9 - - + +
134B CYS* 4.9 0.9 - - - +
137B LEU* 3.7 35.7 - - + -
148B ALA 3.4 18.9 + - - +
149B PHE* 4.0 10.1 - - + +
150B GLY 3.5 0.4 - - - -
151B ALA* 1.3 79.4 - - - +
153B GLN* 1.3 56.3 + - - +
155B ILE* 3.3 5.9 + - + +
156B CYS* 2.8 37.5 + - - -
175B MET* 5.0 8.5 - - + -
179B PHE* 4.0 18.8 - - + -
197B CYS* 4.4 0.4 - - - -
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Residues in contact with GLN 153 (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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149B PHE 3.5 12.2 + - - +
150B GLY 4.4 5.4 - - - +
151B ALA 3.3 1.0 - - - -
152B LEU* 1.3 78.8 - - - +
154B LYS* 1.3 63.4 + - - +
156B CYS* 3.2 11.1 + - - +
157B GLU* 3.2 39.8 + - - +
192B SER 4.7 0.4 + - - +
193B HIS* 3.2 37.3 + - - +
196B ALA* 3.4 31.3 - - + +
197B CYS* 3.6 17.9 - - - -
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Residues in contact with LYS 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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112B ILE* 3.4 26.2 - - + +
115B THR* 3.6 37.9 - - + +
116B THR* 5.3 4.0 - - + -
150B GLY 4.3 4.8 + - - +
151B ALA 3.5 2.0 + - - -
152B LEU 3.4 0.2 - - - -
153B GLN* 1.3 80.0 - - - +
155B ILE* 1.3 60.6 + - - +
157B GLU* 3.3 12.3 + - + +
158B ASP* 3.1 42.4 + - - +
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Residues in contact with ILE 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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114B ILE* 3.9 22.2 - - + +
115B THR* 4.3 15.3 - - + +
118B ALA* 4.1 4.3 - - + -
119B SER* 6.6 0.2 - - - -
123B LEU* 3.0 34.8 - - + +
129B LEU* 3.8 26.0 - - + -
130B LEU* 4.7 15.5 - - + -
133B LEU* 4.5 6.1 - - + -
151B ALA 3.1 20.6 - - - +
152B LEU* 3.3 11.2 + - + +
153B GLN 3.2 0.6 - - - -
154B LYS* 1.3 76.1 - - - +
156B CYS* 1.3 62.0 + - - +
157B GLU 3.2 2.0 - - - -
158B ASP* 3.5 4.5 + - - +
159B SER* 3.3 23.7 + - - -
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Residues in contact with CYS 156 (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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130B LEU* 5.8 3.6 - - - -
152B LEU* 2.8 30.1 + - - +
153B GLN* 3.2 8.7 + - - +
155B ILE* 1.3 77.6 - - - +
157B GLU* 1.3 58.4 + - - +
158B ASP 3.4 0.4 - - - -
159B SER 4.2 3.1 - - - +
160B ALA* 3.4 26.1 + - - +
175B MET* 5.4 5.4 - - - -
179B PHE* 4.4 16.4 - - - -
197B CYS* 4.3 18.6 - - + -
200B GLN* 3.4 14.5 - - + +
201B PHE* 4.4 21.7 - - + -
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Residues in contact with GLU 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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153B GLN* 3.2 46.0 + - + +
154B LYS* 3.3 11.6 + - + +
155B ILE 3.2 0.8 - - - -
156B CYS* 1.3 78.8 - - - +
158B ASP* 1.3 68.7 + - - +
159B SER 3.5 0.9 - - - -
160B ALA* 4.7 2.5 - - - +
196B ALA* 4.3 6.5 - - - +
200B GLN* 3.3 35.4 + - + +
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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