Contacts of the strand formed by residues 154 - 160 (chain B) in PDB entry 4SBV
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 LYS 154 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134B GLY 4.1 0.2 - - - -
135B PHE* 3.2 33.3 + - + +
137B TYR* 3.1 29.4 - - + +
153B LEU* 1.3 70.6 - - - +
155B GLY* 1.3 67.0 + - - +
186B ALA 5.8 2.9 - - - +
188B ASP* 3.7 29.6 - - + +
65C ASP* 3.0 36.5 + - + -
251C ILE 5.0 1.8 - - - +
252C GLU* 4.2 21.3 - - + +
253C PRO* 3.8 15.4 + - + +
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Residues in contact with GLY 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B MET 3.9 3.0 - - - +
134B GLY* 4.5 0.4 - - - -
135B PHE* 5.6 0.9 - - - -
153B LEU 3.0 2.0 + - - -
154B LYS* 1.3 87.3 - - - +
156B TYR* 1.3 60.0 + - - +
157B VAL* 2.9 21.7 + - - +
185B ILE* 3.8 22.7 - - - +
186B ALA 6.1 0.7 - - - -
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Residues in contact with TYR 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B HIS* 2.8 34.6 + - + -
133B MET 3.3 7.6 - - - -
134B GLY* 4.5 1.5 - - - -
147B VAL* 4.6 2.0 - - - +
150B LEU* 3.3 17.3 - - + +
151B SER* 3.1 55.0 - - - +
153B LEU 3.3 13.7 + - - +
154B LYS 3.6 0.2 - - - -
155B GLY* 1.3 70.1 - - - +
157B VAL* 1.3 77.4 - - - +
158B THR* 2.6 27.4 + - - -
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Residues in contact with VAL 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B ILE 3.4 1.0 - - - +
132B HIS* 3.2 5.7 - - - -
133B MET* 3.2 31.4 + - + +
155B GLY 2.9 14.6 - - - +
156B TYR* 1.3 95.5 - - - +
158B THR* 1.3 66.5 + - - +
182B ALA 5.0 2.2 - - - +
183B ILE* 3.9 26.7 - - + +
184B THR 3.6 29.4 - - - +
185B ILE* 4.9 2.0 - - + -
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Residues in contact with THR 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B ALA* 3.5 13.7 - - + -
131B ILE* 2.5 27.4 - - - +
132B HIS* 3.2 26.7 + - + +
156B TYR* 2.6 34.8 + - - -
157B VAL* 1.3 74.4 - - - +
159B GLY* 1.3 67.3 - - - +
183B ILE* 4.6 8.8 - - - +
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Residues in contact with GLY 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B ALA* 3.3 4.3 - - - -
131B ILE* 3.0 31.9 + - - +
158B THR* 1.3 81.5 - - - +
160B PRO* 1.3 78.8 - - - +
183B ILE* 3.8 15.5 - - - -
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Residues in contact with PRO 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B GLY 3.2 13.9 - - - +
130B ALA* 5.0 0.2 - - + -
159B GLY* 1.3 85.9 - - - +
161B VAL* 1.3 55.0 + - - +
162B TRP* 2.8 46.1 + - + +
163B GLU* 3.0 41.5 + - + +
183B ILE* 4.1 2.9 - - - +
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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
------------------------------------------------------------
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