Contacts of the strand formed by residues 153 - 160 (chain B) in PDB entry 2JG8
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 LEU 153 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B LEU* 6.0 1.6 - - + -
113B ILE* 5.9 3.1 - - + -
145B TYR* 5.6 2.5 - - + +
147B ALA* 3.8 28.7 - - + -
149B SER* 4.1 13.7 - - - +
152B ASN* 1.3 76.6 - - - +
154B CYS* 1.3 74.2 + - - +
155B VAL* 5.1 7.2 - - + +
170B PHE 3.9 0.7 - - - +
171B CYS* 3.3 1.9 - - - +
172B ASP* 2.8 42.7 + - - +
173B TYR* 4.3 0.6 - - - -
179B GLN* 4.3 1.3 - - - +
181B THR* 4.2 14.1 - - + +
202B LYS 3.6 13.9 - - - +
203B ASN* 4.2 4.3 - - - -
204B SER 3.5 28.9 - - - +
205B LEU* 3.9 18.8 - - + -
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Residues in contact with CYS 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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209A GLU* 5.9 0.2 - - - -
153B LEU* 1.3 78.4 - - - +
155B VAL* 1.3 60.3 + - - +
169B THR* 4.4 3.6 - - + -
170B PHE 3.2 4.5 - - - -
171B CYS* 2.1 47.8 - - - -
173B TYR* 3.8 20.0 - - - -
199B ALA* 4.4 1.7 - - - -
200B THR* 2.9 43.8 + - + +
202B LYS* 3.0 22.4 + - + +
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Residues in contact with VAL 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B ILE* 3.6 25.4 - - + -
145B TYR* 3.0 43.1 - - + +
153B LEU* 5.1 8.9 - - + +
154B CYS* 1.3 75.7 - - - +
156B ASN* 1.3 68.6 + - - +
157B LEU 4.0 0.3 + - - -
168B VAL 3.9 0.3 - - - +
169B THR* 3.3 2.6 - - - -
170B PHE* 2.9 39.4 + - + +
197B LEU* 3.7 24.2 - - + -
198B GLN 3.5 12.8 - - - +
200B THR* 4.6 0.2 - - - -
205B LEU* 6.4 0.9 - - + -
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Residues in contact with ASN 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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110B ASP* 5.4 1.4 + - - -
155B VAL* 1.3 74.7 - - - +
157B LEU* 1.3 60.3 - - - +
158B MET* 3.5 20.0 + - - +
166B LYS* 4.0 14.8 - - + +
168B VAL 3.5 4.9 - - - +
169B THR* 2.6 33.4 + - - +
197B LEU* 3.5 4.4 - - - -
198B GLN* 2.9 58.4 + - - +
199B ALA 4.7 0.6 + - - -
200B THR* 3.9 19.6 - - - +
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Residues in contact with LEU 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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143B PHE* 5.0 9.4 - - + -
155B VAL* 4.0 1.6 + - - +
156B ASN* 1.3 69.8 - - - +
158B MET* 1.3 59.1 + - - +
166B LYS* 3.5 1.9 - - - -
167B VAL* 2.7 42.8 + - + +
168B VAL* 2.9 32.1 + - + -
170B PHE* 4.8 8.3 - - + -
184B GLY 5.4 0.7 - - - -
185B MET* 3.5 37.7 - - + -
187B LEU* 4.3 9.6 - - + -
195B VAL* 4.0 24.7 - - + -
196B PHE 3.9 2.7 - - - +
197B LEU* 3.8 23.7 - - + +
215B PHE* 5.2 2.2 - - + -
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Residues in contact with MET 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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156B ASN* 3.7 10.3 - - - +
157B LEU* 1.3 74.8 - - - +
159B ARG* 1.3 60.2 + - - +
164B ALA* 3.9 27.8 - - + +
165B GLN 3.5 1.6 - - - -
166B LYS* 3.5 31.0 - - + +
167B VAL* 4.3 0.9 - - - -
194B ASN 4.5 0.2 - - - -
195B VAL* 3.4 10.4 - - - +
196B PHE* 3.0 62.1 + - + +
198B GLN* 3.6 47.1 - - + +
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Residues in contact with ARG 159 (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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115A ILE* 4.4 13.3 + - - +
116A THR* 5.1 1.4 + - - -
158B MET* 1.3 76.2 - - - +
160B GLY* 1.3 62.4 + - - +
164B ALA* 4.0 2.9 - - - -
165B GLN* 2.8 42.7 + - - +
167B VAL* 3.6 27.8 - - + +
187B LEU* 3.3 37.3 - - + +
188B LYS 4.1 15.6 + - - +
189B LEU* 3.8 19.3 - - + -
193B GLU* 3.5 22.9 - - + +
194B ASN 3.4 7.9 - - - +
195B VAL* 4.5 4.7 - - + -
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Residues in contact with GLY 160 (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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159B ARG* 1.3 82.2 - - - +
161B ARG* 1.3 58.4 + - - -
163B ARG 3.9 10.5 - - - -
164B ALA* 4.0 2.5 - - - -
165B GLN* 5.9 0.4 - - - -
193B GLU* 4.3 8.3 - - - -
194B ASN* 2.6 54.3 + - - +
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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