Contacts of the strand formed by residues 156 - 161 (chain C) in PDB entry 2WUB
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 ARG 156 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C ILE* 4.2 23.7 + - + +
18C GLY* 3.0 25.4 + - - +
19C GLY 3.4 5.7 + - - -
20C SER* 2.5 39.8 + - - +
21C SER* 2.9 15.2 + - - +
22C SER 4.6 0.4 - - - +
139C ALA* 3.5 1.4 - - - +
140C GLY 3.3 37.4 + - - +
142C GLY 5.4 2.5 - - - +
152C SER* 3.7 25.6 - - - +
154C SER 3.1 6.3 + - - +
155C LEU* 1.3 83.3 - - - +
157C GLU* 1.3 65.3 + - - +
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Residues in contact with GLU 157 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C ILE* 4.1 7.1 - - - +
18C GLY 4.1 1.4 - - - +
19C GLY* 3.8 1.7 - - - -
20C SER* 3.0 35.3 + - - +
21C SER 3.0 29.8 - - - +
22C SER* 3.3 15.9 + - - -
26C SER* 4.1 6.9 + - - -
27C HIS* 2.9 31.4 + - + +
137C GLN* 3.7 17.7 + - - +
138C ILE 3.6 11.9 - - - +
139C ALA* 4.2 0.9 - - + +
156C ARG* 1.3 77.9 - - - +
158C ALA* 1.3 66.3 + - - +
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Residues in contact with ALA 158 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C ILE* 3.5 22.0 - - + -
19C GLY* 3.9 19.7 - - - +
20C SER* 4.8 2.5 - - - +
137C GLN* 3.2 8.4 - - - +
138C ILE* 3.1 36.4 + - + +
157C GLU* 1.3 83.2 - - - +
159C LEU* 1.3 67.5 + - - +
160C VAL* 5.3 0.4 - - + -
188C SER* 4.7 10.5 - - + +
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Residues in contact with LEU 159 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135C LYS* 4.6 28.7 - - + +
136C CYS 3.5 16.2 - - - +
137C GLN* 3.7 29.4 - - + +
158C ALA* 1.3 75.2 - - - +
160C VAL* 1.3 67.8 + - - +
161C PRO* 4.5 0.2 - - - -
184C TYR* 3.0 23.4 + - - -
188C SER* 4.5 4.7 - - - +
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Residues in contact with VAL 160 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135C LYS* 4.7 1.8 - - - -
136C CYS* 2.8 38.8 + - - +
138C ILE* 3.7 31.4 - - + -
158C ALA* 5.1 1.1 - - + -
159C LEU* 1.3 81.0 - - - +
161C PRO* 1.3 68.4 - - + +
183C ALA* 4.0 20.3 - - + +
184C GLY* 4.2 7.0 - - + -
188C SER 4.3 15.9 - - - +
189C ASP* 5.5 3.4 - - - +
199C LEU* 3.6 31.2 - - + -
228C TYR* 4.3 4.7 - - - +
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Residues in contact with PRO 161 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133C GLY* 3.8 17.3 - - - +
134C HIS 3.4 8.5 - - - +
135C LYS* 4.5 4.7 - - + -
160C VAL* 1.3 87.1 - - + +
162C LEU* 1.3 66.3 + - - +
163C VAL* 5.8 0.2 - - + -
183C ALA* 3.3 3.3 - - - -
184C GLY* 2.9 81.2 + - + +
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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