Contacts of the helix formed by residues 144 - 158 (chain B) in PDB entry 2JI8
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
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Residue Dist Surf HB Arom Phob DC
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139B ILE* 4.0 11.6 - - + +
140B ASN 5.7 0.7 + - - +
141B SER* 3.1 20.7 + - - +
143B LYS* 1.3 113.7 + - - +
145B ILE* 1.3 52.3 + - - +
146B PRO 3.5 1.3 - - - -
147B ILE* 3.3 11.9 + - + +
148B GLY* 2.7 34.5 + - - -
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Residues in contact with ILE 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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12B GLY* 3.9 22.7 - - - +
15B VAL* 3.9 12.3 - - + -
16B LEU* 3.7 37.0 - - + +
19B ALA* 3.8 12.1 - - + -
139B ILE* 3.6 25.4 - - + -
141B SER 4.1 0.9 - - - +
142B ILE* 3.4 27.1 + - + +
144B ASP* 1.3 73.8 - - - +
146B PRO* 1.3 76.8 - - + +
148B GLY 4.4 0.2 - - - +
149B ILE* 2.9 25.2 + - + +
172B LEU* 4.1 18.4 - - + -
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Residues in contact with PRO 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B VAL* 4.1 9.9 - - + -
19B ALA* 4.2 9.9 - - + -
23B ASN* 5.2 2.8 + - - -
142B ILE 4.2 1.8 - - - +
143B LYS 3.8 10.1 - - - +
144B ASP 3.7 2.5 - - - -
145B ILE* 1.3 94.1 - - + +
147B ILE* 1.3 61.3 + - + +
149B ILE* 4.0 1.6 - - - +
150B ALA* 3.1 22.3 + - - +
185B LEU* 3.3 42.2 - - + +
186B LEU* 3.9 25.6 - - + +
187B PHE* 3.7 13.7 - - + +
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Residues in contact with ILE 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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143B LYS 5.3 1.3 + - - +
144B ASP* 3.3 14.6 + - + +
145B ILE 3.3 0.2 - - - -
146B PRO* 1.3 76.7 - - + +
148B GLY* 1.3 67.5 + - - +
150B ALA* 3.3 4.4 + - + +
151B ARG* 3.0 39.8 + - + +
185B LEU 6.0 0.2 - - - +
187B PHE* 3.6 27.8 - - + -
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Residues in contact with GLY 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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137B PHE* 5.0 6.8 - - - +
139B ILE* 4.0 21.9 - - - +
144B ASP 2.7 21.8 + - - -
145B ILE 3.7 1.3 - - - -
147B ILE* 1.3 76.1 - - - +
149B ILE* 1.3 60.0 + - - +
151B ARG* 3.6 8.1 + - - +
152B ALA* 3.2 21.7 + - - +
166B VAL* 5.0 2.1 - - - +
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Residues in contact with ILE 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B LEU* 3.9 30.3 - - + -
19B ALA* 4.1 13.2 - - + +
20B LEU* 4.1 24.7 - - + -
23B ASN* 3.8 20.0 - - + +
102B ILE* 5.7 2.9 - - + -
104B LEU* 4.7 13.9 - - + -
139B ILE* 4.1 15.5 - - + -
145B ILE* 2.9 24.9 + - + +
146B PRO 4.1 2.5 - - - +
148B GLY* 1.3 74.4 - - - +
150B ALA* 1.3 65.4 + - - +
152B ALA* 3.3 5.5 + - + +
153B VAL* 3.0 32.7 + - + +
166B VAL* 4.7 5.8 - - + -
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Residues in contact with ALA 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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23B ASN* 4.3 5.2 + - - +
146B PRO 3.1 8.2 + - - +
147B ILE* 3.5 10.1 - - + +
149B ILE* 1.3 77.2 - - - +
151B ARG* 1.3 57.6 + - + +
153B VAL* 3.5 1.2 + - - +
154B ARG* 3.0 41.6 + - - +
187B PHE* 3.5 31.6 - - + -
189B PRO* 3.6 23.1 - - + +
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Residues in contact with ARG 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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137B PHE* 3.9 39.8 - - + -
147B ILE* 3.0 35.8 + - + +
148B GLY* 3.7 8.1 - - - +
150B ALA* 1.3 73.0 - - + +
152B ALA* 1.3 60.3 + - - +
154B ARG* 4.0 5.1 - - - +
155B THR* 2.7 41.0 + - - -
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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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102B ILE* 4.0 16.2 - - + -
137B PHE* 4.2 1.7 - - + -
148B GLY 3.2 9.3 + - - +
149B ILE* 3.3 11.2 + - + +
151B ARG* 1.3 77.7 - - - +
153B VAL* 1.3 59.7 + - - +
155B THR 3.4 0.2 + - - -
156B ALA* 3.0 27.9 + - - +
164B VAL* 3.3 23.8 - - + +
166B VAL* 3.6 31.6 - - + -
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Residues in contact with VAL 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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23B ASN* 3.9 37.0 - - + +
25B ILE* 5.5 5.2 - - + -
73B PRO* 4.2 19.1 - - + -
102B ILE* 3.9 19.7 - - + -
149B ILE* 3.0 22.9 + - + +
150B ALA* 4.0 2.9 - - - +
152B ALA* 1.3 75.5 - - - +
154B ARG* 1.3 62.8 + - + +
156B ALA* 3.4 2.1 + - - +
157B VAL* 2.9 38.7 + - + +
189B PRO* 5.7 0.7 - - + -
192B PRO* 4.5 14.1 - - + -
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Residues in contact with ARG 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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150B ALA* 3.0 25.5 + - - +
151B ARG* 4.1 5.2 - - - +
153B VAL* 1.3 77.3 - - - +
155B THR* 1.3 55.2 + - - +
157B VAL* 4.1 5.8 - - - -
158B SER* 2.3 43.0 + - - +
187B PHE* 6.2 0.8 - - - -
189B PRO* 3.9 16.7 - - + +
190B ILE* 2.8 43.5 + - - +
191B ASP 3.7 11.9 + - - -
192B PRO* 3.8 20.6 + - + +
194B PRO* 5.7 1.8 - - - +
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Residues in contact with THR 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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134B LYS* 2.6 67.0 + - + +
135B ALA* 3.8 15.0 - - + -
137B PHE* 4.1 11.4 - - - -
151B ARG* 2.7 26.6 + - - +
154B ARG* 1.3 74.2 - - - +
156B ALA* 1.3 61.9 + - - +
157B VAL 3.6 0.2 + - - -
158B SER* 4.2 2.7 - - - -
164B VAL* 3.6 15.5 - - + -
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Residues in contact with ALA 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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73B PRO* 3.7 24.5 - - + -
100B PRO* 3.5 3.2 - - + +
101B MET 4.0 14.1 - - - +
102B ILE* 4.5 0.9 - - + -
152B ALA 3.0 17.5 + - - +
153B VAL 3.8 0.4 - - - +
155B THR* 1.3 77.2 - - - +
157B VAL* 1.3 58.0 + - - +
161B PRO* 3.0 9.6 - - - +
162B GLY 3.0 42.8 + - - +
164B VAL* 3.5 8.2 - - + +
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Residues in contact with VAL 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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71B GLY 4.3 7.0 - - - +
72B LYS* 4.1 7.9 - - - -
73B PRO* 3.5 33.0 - - + -
100B PRO* 4.0 9.9 - - + -
153B VAL* 2.9 24.2 + - + +
154B ARG 4.1 0.2 - - - +
156B ALA* 1.3 75.6 - - - +
158B SER* 1.3 66.8 + - - +
159B GLY 4.2 1.4 - - - +
161B PRO* 4.0 16.8 - - - +
192B PRO* 3.4 32.8 - - + +
193B ALA* 3.8 18.6 - - + +
226B TYR* 4.7 4.5 + - - +
1567B PGE 4.9 6.2 - - - +
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Residues in contact with SER 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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134B LYS* 2.7 29.4 + - - -
154B ARG* 2.3 32.2 + - - +
155B THR* 4.2 2.9 + - - -
157B VAL* 1.3 76.9 - - - +
159B GLY* 1.3 65.3 + - - +
160B ARG 3.4 2.6 - - - +
192B PRO 3.5 16.4 - - - -
193B ALA* 4.6 3.1 - - - +
194B PRO* 4.3 12.8 - - - -
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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