Contacts of the strand formed by residues 156 - 160 (chain A) in PDB entry 2R8J
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 GLU 156 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A HIS* 3.2 28.5 + - + +
29A ILE 3.3 5.2 - - - -
30A ASP* 2.9 13.5 - - - +
151A ARG* 3.7 0.5 - - - -
152A ALA* 3.1 30.5 + - + +
153A SER* 3.0 32.6 + - - +
154A ILE 3.7 0.2 - - - -
155A ASP* 1.3 90.8 - - - +
157A VAL* 1.3 73.3 + - - +
272A LYS* 3.6 12.6 + - - -
1501A CA 2.6 27.9 - - - -
2001A DCP 4.3 0.7 + - - -
13Q G 3.6 14.1 + - - +
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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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27A ALA 3.6 0.5 - - - +
28A HIS* 3.3 4.7 - - - -
29A ILE* 2.9 39.7 + - + +
139A LEU* 4.3 9.2 - - + -
142A PHE* 3.7 48.9 - - + -
149A VAL* 3.9 15.3 - - + -
150A GLU 3.1 12.3 - - - +
151A ARG* 4.2 10.1 - - + -
152A ALA 4.3 0.7 - - - +
155A ASP 5.5 0.2 - - - -
156A GLU* 1.3 87.1 - - - +
158A PHE* 1.3 63.9 + - - +
159A LEU* 4.6 7.4 - - + -
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Residues in contact with PHE 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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26A ILE* 4.2 5.4 - - + -
27A ALA 3.0 10.5 - - - -
28A HIS* 3.2 35.7 - + + -
148A LEU 3.8 0.7 - - - +
149A VAL* 3.3 7.3 - - - +
150A GLU* 2.8 57.5 + - + +
152A ALA* 3.7 22.9 - - + -
157A VAL* 1.3 75.0 - - - +
159A LEU* 1.3 64.8 + - - +
268A LYS* 3.5 52.3 - - + -
271A CYS* 4.8 0.2 - - + -
272A LYS* 4.3 9.6 - - + -
386A LEU* 3.9 17.1 - - + +
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Residues in contact with LEU 159 (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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26A ILE* 3.3 8.5 - - - +
27A ALA* 2.7 40.6 + - + +
29A ILE* 3.9 25.6 - - + -
142A PHE* 4.5 12.8 - - + +
146A CYS* 4.0 11.0 - - + -
148A LEU 3.7 0.9 - - - -
149A VAL* 3.3 38.1 - - + -
157A VAL* 4.6 9.4 - - + -
158A PHE* 1.3 79.5 - - - +
160A ASP* 1.3 60.3 + - - +
161A LEU* 3.5 19.7 + - + +
245A CYS* 5.2 2.2 - - - -
248A ILE* 4.1 25.1 - - + -
386A LEU* 3.7 4.0 - - - -
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Residues in contact with ASP 160 (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 PRO 5.0 0.7 - - - +
18A ALA* 3.9 15.6 - - - +
19A TYR* 4.2 7.1 + - - +
25A CYS 4.1 4.5 + - - +
26A ILE* 4.1 16.9 - - - +
146A CYS* 3.4 13.7 - - - -
147A ASP* 4.4 3.3 - - - +
148A LEU* 3.5 37.2 + - + +
159A LEU* 1.3 71.4 - - - +
161A LEU* 1.3 58.5 + - - +
162A GLY* 2.9 21.8 + - - -
163A ARG* 3.3 27.6 + - - +
164A ILE* 5.5 0.3 - - - +
386A LEU* 3.7 12.6 - - + +
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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