Contacts of the strand formed by residues 152 - 158 (chain A) in PDB entry 5V5W
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 THR 152 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138A GLN* 3.4 7.1 - - - +
139A THR* 3.0 46.6 + - - +
140A VAL* 6.3 0.4 - - - -
151A LYS* 1.3 76.1 - - - +
153A VAL* 1.3 67.5 + - - +
154A PHE* 3.6 17.6 - - + -
200A LYS* 5.1 2.7 - - + -
201A LEU 3.3 8.3 - - - -
202A LYS* 3.6 46.7 - - + +
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Residues in contact with VAL 153 (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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136A VAL* 4.0 18.6 - - + -
137A HIS 3.7 2.9 - - - -
138A GLN* 4.0 18.8 - - + +
152A THR* 1.3 80.1 - - - +
154A PHE* 1.3 64.1 + - - +
155A LEU* 3.4 22.4 - - + +
199A LEU 3.4 1.7 - - - +
200A LYS* 3.3 4.7 - - - +
201A LEU* 2.8 45.2 + - + +
204A LEU* 3.7 32.1 - - + -
233A LEU* 4.1 20.6 - - + -
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Residues in contact with PHE 154 (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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135A THR 3.9 0.7 - - - +
136A VAL* 3.4 6.2 - - - +
137A HIS* 2.8 62.1 + - + +
138A GLN 5.0 0.2 - - - -
139A THR* 3.9 17.0 - - + -
152A THR* 3.6 24.7 - - + -
153A VAL* 1.3 74.5 - - - +
155A LEU* 1.3 60.8 + - - +
156A ARG* 4.1 3.0 + - + +
187A TYR* 3.4 20.6 - - - -
198A VAL* 4.2 10.8 - - + -
199A LEU 3.4 2.7 - - - -
200A LYS* 3.4 36.6 - - + -
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Residues in contact with LEU 155 (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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134A LEU* 4.1 6.3 - - + -
135A THR 3.7 3.6 - - - -
136A VAL* 4.5 7.9 - - + -
153A VAL* 3.4 29.4 - - + +
154A PHE* 1.3 73.5 - - - +
156A ARG* 1.3 59.4 + - - +
169A TRP* 3.5 26.6 - - + -
198A VAL* 3.2 4.5 - - - -
199A LEU* 2.7 61.7 + - + +
201A LEU* 4.2 6.7 - - + -
212A TYR* 3.8 32.1 - - + -
231A PHE* 4.3 24.9 - - + -
233A LEU* 5.6 1.6 - - + -
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Residues in contact with ARG 156 (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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133A MET 3.6 1.4 - - - +
134A LEU* 3.2 6.5 - - - +
135A THR* 2.8 55.5 + - - +
154A PHE* 5.4 2.7 - - + +
155A LEU* 1.3 71.7 - - - +
157A CYS* 1.3 57.8 + - - +
158A THR* 3.8 18.1 + - + +
189A PRO* 4.2 8.1 - - - +
191A TYR* 2.9 31.7 + - - -
192A THR* 3.7 13.7 - - - +
193A GLN* 4.4 6.3 - - - +
196A THR* 3.7 27.8 + - + +
197A LYS 3.7 2.2 - - - -
198A VAL* 3.9 13.9 - - + -
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Residues in contact with CYS 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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132A PRO* 3.9 16.2 - - - -
133A MET 3.2 10.1 - - - -
134A LEU* 4.0 2.2 - - + -
155A LEU 4.0 0.2 + - - -
156A ARG* 1.3 73.1 - - - +
158A THR* 1.3 63.5 + - - +
167A PHE* 3.6 12.8 - - + -
169A TRP* 3.5 17.5 - - + -
196A THR* 3.2 4.5 - - - +
197A LYS 2.8 38.2 + - - +
214A CYS* 2.0 50.7 - - + -
229A ILE* 4.4 1.6 - - - -
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Residues in contact with THR 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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132A PRO* 3.1 5.6 - - - +
133A MET* 2.7 59.8 + - - +
156A ARG* 3.8 20.0 - - + +
157A CYS* 1.3 76.6 - - - +
159A VAL* 1.3 60.9 + - - +
167A PHE* 4.6 0.7 - - - -
193A GLN 6.2 0.2 - - - +
194A GLY 5.5 1.8 - - - +
195A GLU 3.2 7.6 - - - -
196A THR* 3.2 33.7 - - + +
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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