Contacts of the strand formed by residues 147 - 155 (chain B) in PDB entry 1JG0
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 HIS 147 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58B GLU* 5.7 3.1 - - - -
62B PHE* 3.9 20.9 - + - -
80B TRP* 6.1 0.2 - + - -
94B TYR* 3.0 57.7 + + - -
98B TRP* 5.6 0.5 + - - -
132B ALA* 4.3 2.3 - - - +
146B CYS* 1.3 74.7 - - - +
148B ALA* 1.3 59.2 + - - +
149B PHE 3.6 2.8 + - - -
150B PHE* 5.6 1.4 - - - -
163B LEU* 3.5 26.2 - - + +
164B TYR 3.9 6.3 - - - -
165B GLN* 4.3 6.9 - - + +
177B ASN* 4.6 10.0 + - - -
180B SER* 6.2 0.8 - - - -
181B TYR* 2.6 39.6 + + + +
305B UMP 3.7 24.8 + + - -
306B DDT 5.7 2.9 - - - -
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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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149A PHE* 4.2 22.2 - - + -
131B SER* 3.6 1.4 + - - -
132B ALA* 3.0 25.6 + - - -
133B TRP* 3.5 33.2 + - + +
145B PRO* 4.4 9.4 - - - +
146B CYS 3.0 10.6 + - - +
147B HIS* 1.3 72.7 - - - +
149B PHE* 1.3 62.4 + - + +
150B PHE* 5.6 0.2 - - - -
164B TYR* 3.2 10.0 + - + +
166B ARG* 5.2 3.4 - - + -
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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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133A TRP* 4.0 22.7 - + + -
148A ALA* 4.5 11.4 - - + -
149A PHE* 4.7 21.5 - + + -
164A TYR* 3.6 41.3 - + - -
166A ARG* 5.3 0.2 - - + -
129B ILE* 3.6 39.9 - - + -
130B VAL 3.4 7.9 - - - -
131B SER* 3.9 19.5 - - - +
147B HIS 3.6 2.6 + - - -
148B ALA* 1.3 86.1 - - + +
150B PHE* 1.3 74.8 + - - +
151B GLN* 4.7 0.2 - - + -
162B GLN 4.1 0.6 - - - +
163B LEU* 3.6 2.1 - - - +
164B TYR* 2.9 40.6 + - + -
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Residues in contact with PHE 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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98B TRP* 3.7 36.6 - + - -
112B ILE* 4.6 4.0 - - + -
129B ILE* 3.4 3.6 - - - +
130B VAL* 2.9 76.2 + - + -
132B ALA* 6.1 0.9 - - + -
147B HIS 5.6 1.1 - - - -
149B PHE* 1.3 84.7 - - - +
151B GLN* 1.3 60.3 + - - +
152B PHE* 3.6 35.2 - + - -
161B CYS* 4.1 10.5 - - - -
162B GLN 3.1 12.8 - - - +
163B LEU* 4.1 10.8 - - + -
181B TYR* 3.7 19.7 - + + -
184B LEU* 3.8 18.2 - - + -
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Residues in contact with GLN 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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30A PHE* 3.4 15.6 - - + -
164A TYR* 2.6 49.4 + - + +
166A ARG* 3.1 33.0 + - - +
204A GLY* 3.7 4.9 - - - -
205A ASP* 4.2 2.1 + - - +
126B ARG* 3.3 19.6 - - - +
128B ILE 3.3 13.7 - - - +
129B ILE* 3.9 12.5 - - + +
149B PHE* 4.7 1.1 - - + -
150B PHE* 1.3 75.7 - - - +
152B PHE* 1.3 75.4 - - - +
161B CYS* 3.2 3.7 - - - -
162B GLN 2.8 36.3 + - - -
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Residues in contact with PHE 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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30A PHE* 4.2 0.7 - - - -
115B VAL* 3.6 27.6 - - + -
119B LEU* 4.2 7.2 - - + -
125B SER 4.7 3.3 - - - +
126B ARG 6.0 0.2 - - - -
128B ILE* 2.9 38.4 + - + +
130B VAL* 4.7 3.1 - - + -
150B PHE* 3.6 38.6 - + - -
151B GLN* 1.3 88.5 - - - +
153B TYR* 1.3 63.8 + - - +
159B LEU* 3.8 26.0 - - + -
160B SER 3.3 16.6 - - - -
161B CYS* 3.7 18.6 - - + -
184B LEU* 4.8 6.3 - - + -
185B VAL* 4.5 6.7 - - + -
188B MET* 4.1 28.9 - - + -
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Residues in contact with TYR 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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16A THR* 4.5 3.3 + - - -
18A LYS* 4.0 12.4 - - - -
28A SER* 3.0 37.5 + - - -
29A ILE* 4.1 3.4 - - - -
30A PHE* 3.4 53.6 - + + -
205A ASP* 3.3 30.7 - - + -
123B PRO 5.3 1.3 - - - -
125B SER 5.6 3.8 - - - -
128B ILE* 5.4 1.8 - - - -
152B PHE* 1.3 77.9 - - - +
154B VAL* 1.3 71.3 + - - +
155B ALA* 3.6 29.9 - - + +
158B LYS 5.4 0.2 - - - -
159B LEU* 3.6 1.0 - - - +
160B SER* 2.8 43.2 + - - +
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Residues in contact with VAL 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A LYS* 2.8 29.8 + - - +
119B LEU* 3.5 28.7 - - + -
123B PRO* 3.5 32.6 + - + +
124B ASP* 4.3 2.3 - - - +
153B TYR* 1.3 85.4 - - - +
155B ALA* 1.3 66.4 + - - +
156B ASP 5.1 0.2 - - - +
157B GLY* 4.6 4.9 - - - +
158B LYS 3.4 11.9 - - - +
159B LEU* 3.9 8.1 - - + -
194B LEU* 4.0 27.8 - - + -
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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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16A THR* 4.4 20.4 - - + +
18A LYS* 4.6 5.4 - - - +
153B TYR* 3.6 28.2 - - + +
154B VAL* 1.3 75.6 - - - +
156B ASP* 1.3 75.8 + - - +
157B GLY 3.2 1.3 - - - -
158B LYS* 3.0 27.7 + - - +
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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