Contacts of the helix formed by residues 144 - 156 (chain B) in PDB entry 2JG1
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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142B ASN* 2.8 31.1 + - - +
143B GLN* 1.3 77.5 - - - +
145B TYR* 1.3 59.1 + - - +
146B TYR 3.4 2.5 - - - -
147B ALA* 3.1 16.5 + - + +
148B GLN* 2.4 62.7 + - - +
171B THR* 4.7 6.7 - - + -
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Residues in contact with TYR 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B LEU* 3.9 10.5 - - + -
58B PHE* 3.8 3.8 - + - -
114B ALA* 2.7 45.0 + - + -
117B PHE* 3.3 28.6 - + - +
118B ILE* 3.5 16.6 - - + +
137B LEU* 4.0 11.2 - - + +
141B LEU* 3.5 36.1 - - + -
142B ASN* 3.1 18.4 + - + +
143B GLN 3.3 2.4 + - - -
144B ASP* 1.3 80.8 + - - +
146B TYR* 1.3 57.1 + - - +
148B GLN* 3.2 21.6 + - - +
149B ILE* 3.0 53.8 + - + +
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Residues in contact with TYR 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B LEU* 5.4 0.4 - - + -
7B LEU* 3.6 30.1 - - + +
133B ILE* 3.3 31.8 - - + +
134B SER 3.7 9.5 + - - -
135B GLY 2.8 31.9 + - - -
136B SER 3.8 7.1 + - - -
137B LEU* 3.7 22.3 - - + +
143B GLN 5.0 1.3 + - - +
144B ASP 3.4 0.6 - - - -
145B TYR* 1.3 74.6 - - - +
147B ALA* 1.3 61.1 + - - +
149B ILE* 3.2 15.1 + - + +
150B ILE* 2.9 42.0 + - + +
162B LEU* 4.7 2.0 - - + -
164B CYS* 4.6 11.0 - - + -
168B THR* 3.7 26.5 - - + -
172B VAL* 3.9 16.8 - - + -
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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
----------------------------------------------------------
144B ASP* 3.1 20.7 + - + +
146B TYR* 1.3 77.9 - - - +
148B GLN* 1.3 56.8 + - + +
150B ILE* 3.4 5.6 + - - +
151B GLU* 3.0 30.1 + - - +
171B THR* 5.2 6.5 - - + +
172B VAL* 4.5 6.1 - - + +
175B ASN* 3.5 39.6 - - + +
177B TYR* 4.2 5.4 - - - +
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Residues in contact with GLN 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B ILE* 4.1 21.8 - - + +
142B ASN* 4.4 7.5 - - - +
144B ASP* 2.4 54.9 + - - +
145B TYR* 3.2 22.6 + - - +
147B ALA* 1.3 75.2 - - + +
149B ILE* 1.3 61.7 + - - +
151B GLU* 3.4 7.3 - - - +
152B ARG* 2.9 49.9 + - - +
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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
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5B LEU* 4.0 13.0 - - + -
7B LEU* 4.2 3.8 - - + -
117B PHE* 3.9 17.7 - - + -
118B ILE* 3.8 17.0 - - + -
121B PHE* 3.5 27.5 - - + -
133B ILE* 3.8 21.3 - - + -
145B TYR* 3.0 42.5 + - + +
146B TYR* 3.2 21.7 + - + +
148B GLN* 1.3 74.8 - - - +
150B ILE* 1.3 66.0 + - - +
152B ARG* 3.1 17.7 + - - +
153B CYS* 3.2 13.8 + - - -
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Residues in contact with ILE 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B ILE* 4.3 7.9 - - + -
146B TYR* 2.9 30.6 + - + +
147B ALA* 4.0 3.1 - - - +
149B ILE* 1.3 68.3 - - - +
151B GLU* 1.3 55.3 + - - +
153B CYS* 3.2 6.8 + - + +
154B GLN* 2.8 35.9 + - - +
160B VAL* 4.2 27.6 - - + -
162B LEU* 4.5 11.2 - - + -
172B VAL* 3.8 31.0 - - + -
177B TYR* 3.4 19.1 - - + +
178B LYS 3.4 26.5 - - - +
179B PRO* 4.0 9.0 - - + -
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Residues in contact with GLU 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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147B ALA 3.0 13.9 + - - +
148B GLN* 3.4 14.8 - - - +
149B ILE 3.2 0.2 - - - -
150B ILE* 1.3 76.5 - - - +
152B ARG* 1.3 72.7 + - - +
154B GLN* 3.3 1.0 + - - +
155B ASN* 2.9 50.7 + - - +
177B TYR* 3.6 52.8 + - + +
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Residues in contact with ARG 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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118B ILE* 3.6 25.5 - - + +
119B LYS* 5.4 3.0 - - - +
121B PHE* 4.0 19.3 - - + -
122B GLU* 2.8 39.4 + - + -
125B MSE 4.1 9.3 - - + +
148B GLN* 2.9 50.7 + - - +
149B ILE* 3.1 8.1 + - - +
151B GLU* 1.3 93.9 + - - +
153B CYS* 1.3 63.3 + - - +
155B ASN* 3.7 15.7 + - - +
156B LYS* 3.5 24.3 + - - +
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Residues in contact with CYS 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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121B PHE* 3.5 26.7 - - - -
125B MSE 4.1 9.6 - - - -
131B VAL* 3.9 13.5 - - - -
149B ILE* 3.2 15.7 + - - -
150B ILE* 3.2 6.9 + - + +
152B ARG* 1.3 73.1 - - - +
154B GLN* 1.3 60.4 + - - +
156B LYS* 3.0 4.3 + - - -
157B GLY 2.9 24.4 + - - -
158B VAL* 3.0 28.9 + - + +
160B VAL* 3.4 26.0 - - + -
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Residues in contact with GLN 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 ILE* 2.8 21.5 + - - +
151B GLU 3.7 4.3 - - - +
153B CYS* 1.3 73.3 - - - +
155B ASN* 1.3 63.8 + - - +
156B LYS 3.0 0.9 + - - -
157B GLY* 3.1 14.2 + - - +
158B VAL 5.1 1.3 - - - +
177B TYR* 4.3 24.0 - - + -
178B LYS* 3.3 33.9 + - - +
180B THR* 5.6 3.0 + - - -
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Residues in contact with ASN 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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151B GLU* 2.9 43.9 + - - +
152B ARG* 3.8 17.0 - - - +
153B CYS 3.3 0.2 - - - -
154B GLN* 1.3 74.7 - - - +
156B LYS* 1.3 68.6 + - + +
157B GLY 3.5 0.4 + - - -
177B TYR* 4.9 5.0 - - - -
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Residues in contact with LYS 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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122B GLU 5.8 1.3 - - - -
125B MSE 3.8 31.9 - - + +
126B GLU* 6.4 0.2 - - - -
152B ARG 3.5 15.7 + - - +
153B CYS 3.0 4.6 + - - +
155B ASN* 1.3 87.3 - - + +
157B GLY* 1.3 63.2 + - - +
158B VAL* 3.4 11.8 + - + +
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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