Contacts of the strand formed by residues 156 - 163 (chain S) in PDB entry 5JBA
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 GLN 156 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16S ILE* 3.6 23.9 - - + +
19S GLY* 3.8 5.0 + - - +
20S GLU* 3.3 23.5 + - - +
21S ASP* 2.9 27.0 + - - +
22S ALA* 5.1 0.2 - - - -
139S SER* 3.1 6.9 - - - -
140S GLY 3.0 36.7 + - - +
144S VAL* 4.2 13.8 - - + +
152S ALA* 3.8 17.5 - - + -
154S VAL 2.9 22.3 + - - +
155S LEU* 1.3 79.6 + - - +
157S TYR* 1.3 60.8 + - - +
303S DMS 3.6 13.7 - - - +
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Residues in contact with TYR 157 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16S ILE* 4.3 1.3 - - - -
19S GLY* 3.2 4.3 - - - -
20S GLU* 2.9 80.0 + - + +
21S ASP 3.5 12.8 - - - -
22S ALA 3.7 6.5 - - - -
26S GLN* 3.7 27.2 + - - -
27S PHE* 3.5 38.8 - + + -
137S TYR* 3.8 26.5 - + + -
138S VAL 3.2 11.7 - - - +
139S SER* 4.1 2.9 - - - -
156S GLN* 1.3 77.0 - - - +
158S LEU* 1.3 67.6 + - - +
159S ARG 5.5 0.4 - - - -
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Residues in contact with LEU 158 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16S ILE* 3.7 13.0 - - + -
17S VAL 3.9 5.4 - - - +
18S GLY 3.7 22.4 - - - +
19S GLY* 4.2 2.0 - - - -
137S TYR* 3.4 6.0 - - - -
138S VAL* 2.9 38.2 + - + +
157S TYR* 1.3 80.8 - - - +
159S ARG* 1.3 73.6 + - - +
160S VAL* 3.6 19.1 - - + -
184S PHE* 5.3 0.2 - - - +
188S ARG* 3.6 20.9 - - + +
189S ASP* 3.3 39.3 - - - +
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Residues in contact with ARG 159 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135S SER* 3.0 40.3 + - - +
136S GLY 3.3 9.4 - - - +
137S TYR* 3.6 36.4 - - + -
157S TYR* 5.0 0.6 - - - -
158S LEU* 1.3 77.6 - - - +
160S VAL* 1.3 61.2 + - - +
161S PRO* 4.0 21.4 - - - +
184S PHE* 3.4 51.7 + - - +
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Residues in contact with VAL 160 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135S SER* 3.7 0.5 - - - -
136S GLY 2.9 33.6 + - - +
138S VAL* 4.1 18.6 - - + -
158S LEU* 3.6 26.2 - - + -
159S ARG* 1.3 81.4 - - - +
161S PRO* 1.3 66.4 - - + +
162S LEU 3.7 0.3 + - - -
183S ALA* 3.8 23.6 - - + +
184S GLY* 4.1 17.5 - - + +
188S ARG 4.9 2.7 - - - +
189S ASP* 5.2 2.5 - - - -
199S HIS* 4.1 18.1 + - + -
228S TYR* 4.4 7.2 - - - +
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Residues in contact with PRO 161 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134S GLY 3.3 10.8 - - - +
159S ARG* 4.0 13.9 - - - +
160S VAL* 1.3 86.2 - - + +
162S LEU* 1.3 69.3 + - - +
163S VAL* 5.6 0.4 - - + -
183S ALA* 3.2 4.1 - - - -
184S GLY* 2.9 84.3 + - + +
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Residues in contact with LEU 162 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131S LEU* 3.7 34.3 - - + +
132S LYS* 4.1 20.4 - - + +
134S GLY* 2.8 28.9 + - - +
160S VAL 3.7 0.6 + - - -
161S PRO* 1.3 78.6 - - - +
163S VAL* 1.3 70.9 + - - +
164S ASP* 4.3 1.0 + - - -
181S PHE* 3.7 26.2 - - + -
182S CYS 3.5 18.4 - - - +
183S ALA* 4.4 2.5 - - - -
199S HIS* 6.0 1.5 + - - +
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Residues in contact with VAL 163 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161S PRO* 5.6 0.2 - - + -
162S LEU* 1.3 90.3 - - - +
164S ASP* 1.3 77.4 + - - +
165S ARG* 3.6 2.1 + - - -
167S THR* 3.8 24.7 - - + -
168S CYS* 4.1 5.6 - - - +
181S PHE* 5.8 0.2 - - - +
182S CYS* 3.1 31.8 + - + +
183S ALA* 4.1 1.1 - - - -
184S GLY 3.6 22.4 - - - +
185S HIS* 4.5 11.7 - - + -
225S TYR* 3.6 32.5 - - + -
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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