Contacts of the helix formed by residues 144 - 158 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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139A ILE* 3.8 12.6 - - + +
140A ASN 5.7 0.6 + - - +
141A SER* 3.1 23.5 + - - +
143A LYS* 1.3 110.5 + - - +
145A ILE* 1.3 52.1 + - - +
146A PRO* 3.4 2.7 - - - -
147A ILE* 3.5 13.7 + - + +
148A GLY* 2.8 34.3 + - - -
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Residues in contact with ILE 145 (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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12A GLY* 3.7 25.6 - - - +
15A VAL* 3.8 14.8 - - + +
16A LEU* 3.6 41.3 - - + +
19A ALA* 3.9 8.1 - - + -
139A ILE* 3.7 22.3 - - + +
141A SER 4.0 0.7 - - - +
142A ILE* 3.2 28.0 + - - +
144A ASP* 1.3 77.1 - - - +
146A PRO* 1.4 65.6 - - + +
148A GLY* 3.6 0.5 - - - -
149A ILE* 2.9 29.5 + - + +
172A LEU* 4.0 17.3 - - + -
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Residues in contact with PRO 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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15A VAL* 4.5 8.7 - - + -
19A ALA* 4.2 11.0 - - + -
23A ASN* 5.1 3.2 + - - +
142A ILE 4.3 2.0 - - - +
143A LYS* 3.7 12.8 - - - +
144A ASP 3.6 2.2 - - - -
145A ILE* 1.4 92.6 - - + +
147A ILE* 1.3 59.8 + - - +
149A ILE* 4.1 0.9 - - - +
150A ALA* 3.0 29.1 + - - +
182A ALA 5.4 0.2 - - - +
185A LEU* 3.5 38.6 - - + +
186A LEU* 4.1 23.1 - - + +
187A PHE* 3.7 14.2 - - + +
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Residues in contact with ILE 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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143A LYS 5.7 0.9 - - - +
144A ASP* 3.5 17.8 + - + +
145A ILE 3.4 0.2 - - - -
146A PRO* 1.3 79.2 - - - +
148A GLY* 1.3 59.0 + - - +
150A ALA* 3.3 4.3 + - + +
151A ARG* 2.8 49.9 + - + +
187A PHE* 3.5 28.9 - - + -
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Residues in contact with GLY 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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137A PHE* 4.9 6.3 - - - +
139A ILE* 4.0 20.1 - - - +
144A ASP 2.8 22.2 + - - -
145A ILE 3.6 1.6 - - - -
147A ILE* 1.3 76.4 - - - +
149A ILE* 1.3 56.6 + - - +
151A ARG* 3.5 7.8 + - - +
152A ALA* 3.1 26.0 + - - +
166A VAL* 4.9 3.5 - - - +
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Residues in contact with ILE 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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16A LEU* 3.6 32.1 - - + -
19A ALA* 4.0 17.9 - - + +
20A LEU* 4.1 22.4 - - + -
23A ASN* 3.5 26.0 - - + +
102A ILE* 5.7 2.5 - - + -
104A LEU* 4.3 15.0 - - + -
139A ILE* 4.3 11.4 - - + -
145A ILE 2.9 23.0 + - - +
146A PRO 4.2 3.1 - - - +
148A GLY* 1.3 70.5 - - - +
150A ALA* 1.3 60.2 + - - +
152A ALA* 3.1 8.4 + - + +
153A VAL* 2.8 37.1 + - + +
166A VAL* 4.9 2.5 - - + -
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Residues in contact with ALA 150 (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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23A ASN* 4.4 4.0 - - - +
146A PRO 3.0 19.3 + - - +
147A ILE* 3.4 6.5 - - + +
149A ILE* 1.3 77.1 - - - +
151A ARG* 1.3 56.6 + - + +
153A VAL* 3.3 1.3 + - - +
154A ARG* 2.9 40.1 + - - +
187A PHE* 3.5 24.0 - - + -
189A PRO* 3.6 24.2 - - + -
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Residues in contact with ARG 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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137A PHE* 4.0 38.4 - - + -
147A ILE* 2.8 39.1 + - + +
148A GLY* 3.7 7.9 - - - +
150A ALA* 1.3 72.5 - - + +
152A ALA* 1.3 55.3 + - - +
154A ARG* 4.2 4.2 - - - +
155A THR* 2.7 41.8 + - - -
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Residues in contact with ALA 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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102A ILE* 3.8 16.9 - - + +
137A PHE* 4.3 2.0 - - + -
148A GLY 3.1 14.8 + - - +
149A ILE* 3.1 12.3 + - + +
151A ARG* 1.3 74.1 - - - +
153A VAL* 1.3 63.9 + - - +
156A ALA* 3.1 25.6 + - - +
164A VAL* 3.5 19.9 - - + +
166A VAL* 3.7 26.2 - - + -
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Residues in contact with VAL 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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20A LEU* 6.2 0.2 - - + -
23A ASN* 3.7 39.5 - - + +
25A ILE* 5.6 4.9 - - + -
73A PRO* 4.3 20.4 - - + -
102A ILE* 4.0 19.5 - - + -
149A ILE* 2.8 27.3 + - + +
150A ALA 3.9 2.5 - - - +
152A ALA* 1.3 71.0 - - - +
154A ARG* 1.3 59.9 + - - +
156A ALA* 3.4 0.9 + - - +
157A VAL* 2.9 42.8 + - + +
189A PRO* 5.6 1.1 - - + -
192A PRO* 4.5 15.3 - - + -
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Residues in contact with ARG 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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150A ALA* 2.9 23.2 + - - +
151A ARG* 4.2 4.5 - - - +
153A VAL* 1.3 73.3 - - - +
155A THR* 1.3 58.0 + - - +
157A VAL* 4.1 5.6 - - - -
158A SER* 2.4 42.8 + - - +
187A PHE* 6.0 1.0 - - - -
189A PRO* 3.8 16.8 - - + +
190A ILE* 2.9 45.4 + - - +
191A ASP 3.3 13.9 + - - -
192A PRO* 3.6 19.5 + - + +
194A PRO* 5.8 0.8 - - - +
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Residues in contact with THR 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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134A LYS* 2.5 58.0 + - + +
135A ALA* 3.8 15.7 - - + -
137A PHE* 3.9 12.3 - - - -
151A ARG* 2.7 28.4 + - - -
154A ARG* 1.3 76.3 - - - +
156A ALA* 1.3 58.8 + - - +
158A SER* 4.3 2.9 - - - -
164A VAL* 3.7 19.7 - - + -
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Residues in contact with ALA 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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73A PRO* 3.8 21.1 - - + -
100A PRO* 3.6 2.9 - - - +
101A MET 4.0 11.2 - - - +
102A ILE* 4.5 1.1 - - + -
152A ALA 3.1 18.4 + - - +
153A VAL 3.8 3.1 - - - +
155A THR* 1.3 78.9 - - - +
157A VAL* 1.3 59.3 + - - +
161A PRO* 3.0 10.4 - - - +
162A GLY 3.0 43.9 + - - +
164A VAL* 3.5 7.1 - - + +
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Residues in contact with VAL 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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71A GLY 4.1 15.7 - - - +
72A LYS* 4.3 0.4 - - + -
73A PRO* 3.6 34.5 - - + -
100A PRO* 4.0 9.9 - - + -
153A VAL* 2.9 29.7 + - + +
154A ARG 4.0 0.2 - - - +
156A ALA* 1.3 77.6 - - - +
158A SER* 1.3 64.1 + - - +
159A GLY 4.3 1.4 - - - +
161A PRO* 4.1 15.9 - - - +
192A PRO* 3.4 33.4 - - + +
193A ALA* 3.7 20.2 - - + +
226A TYR* 4.9 4.7 + - - +
1570A PGE 5.7 1.4 - - - -
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Residues in contact with SER 158 (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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134A LYS* 2.7 30.6 + - - -
154A ARG* 2.4 31.1 + - - +
155A THR* 4.2 2.6 + - - -
157A VAL* 1.3 76.8 - - - +
159A GLY* 1.3 64.3 + - - +
160A ARG 3.4 2.4 - - - +
192A PRO 3.5 17.3 - - - -
193A ALA* 4.7 3.1 - - - +
194A PRO* 4.4 12.1 - - - -
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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