Contacts of the strand formed by residues 149 - 159 (chain A) in PDB entry 5ON2
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 VAL 149 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140A PHE* 3.6 39.0 - - + +
143A LEU* 3.7 13.4 + - + -
144A TYR* 3.7 48.4 - - + +
147A GLY* 3.4 9.6 - - - +
148A LEU* 1.3 84.5 - - - +
150A TYR* 1.3 68.8 + - - +
191A TRP* 4.0 17.7 - - + -
192A PHE 3.4 13.2 - - - +
193A ILE* 4.4 6.5 - - + -
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Residues in contact with TYR 150 (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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144A TYR* 5.6 1.1 - - - -
149A VAL* 1.3 76.4 - - - +
151A LYS* 1.3 68.1 + - - +
152A LYS* 2.7 45.4 + - + -
191A TRP* 4.2 7.2 - - - -
192A PHE* 2.9 50.2 + - + +
194A LYS* 3.6 44.9 - - + -
419A ASP* 2.7 26.6 + - - -
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Residues in contact with LYS 151 (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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150A TYR* 1.3 79.0 - - - +
152A LYS* 1.3 63.3 + - - +
189A PRO* 4.2 33.1 + - + +
190A GLN* 3.4 20.6 - - - +
191A TRP* 3.8 43.5 - - + +
436A THR* 5.8 1.8 + - - -
442A VAL* 5.6 8.0 - - + +
486A GLU* 3.9 18.0 + - - -
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Residues in contact with LYS 152 (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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150A TYR* 2.7 44.7 + - + -
151A LYS* 1.3 77.3 - - - +
153A THR* 1.3 73.9 + - - +
154A SER 3.7 0.5 + - - -
189A PRO* 4.1 4.7 - - - -
190A GLN* 2.9 31.7 + - - +
192A PHE* 3.7 39.6 - - + -
329A GLU* 4.2 14.6 - - - -
419A ASP* 4.4 4.9 + - - +
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Residues in contact with THR 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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152A LYS* 1.3 89.7 - - - +
154A SER* 1.3 59.0 + - - +
187A GLU* 3.5 26.2 - - + +
188A ILE* 3.4 32.5 - - - +
189A PRO* 4.1 8.1 - - + +
329A GLU* 4.9 1.4 - - - +
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Residues in contact with SER 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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153A THR* 1.3 76.8 - - - +
155A ALA* 1.3 70.9 + - - +
156A VAL* 3.7 0.7 + - - +
187A GLU* 3.7 7.0 - - - -
188A ILE* 3.0 33.1 + - - +
190A GLN* 3.7 15.2 + - - -
192A PHE* 3.6 30.3 - - - -
329A GLU* 3.6 18.6 + - - -
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Residues in contact with ALA 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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154A SER* 1.3 79.9 + - - +
156A VAL* 1.3 65.1 + - - +
185A ARG* 3.5 38.6 - - + +
186A LYS 3.9 5.8 - - - -
187A GLU* 3.8 17.8 + - - +
290A VAL* 4.3 20.9 - - + +
329A GLU* 5.2 3.0 + - - -
74B C 6.0 0.2 - - - -
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Residues in contact with VAL 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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155A ALA* 1.3 82.6 - - - +
157A ASN* 1.3 70.3 + - - +
158A TRP* 3.6 2.0 + - + -
165A VAL* 3.3 43.5 - - + -
166A LEU 5.0 0.2 - - - +
184A GLU 3.5 2.4 - - - +
185A ARG* 3.7 1.4 - - - -
186A LYS* 3.0 37.6 + - + +
188A ILE* 3.3 25.8 - - + -
190A GLN* 3.4 17.0 - - - +
290A VAL* 4.4 6.0 - - - +
74B C 3.9 16.8 - - + +
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Residues in contact with ASN 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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156A VAL* 1.3 83.6 - - - +
158A TRP* 1.3 58.2 + - - +
159A CYS 4.4 0.2 - - - -
165A VAL* 3.5 1.9 - - - -
166A LEU* 3.2 34.8 + - + +
167A ALA 4.1 3.8 + - - -
168A ASN* 2.9 39.8 + - - +
171A VAL* 4.3 13.0 - - + +
183A VAL* 3.9 14.8 - - + +
184A GLU 3.9 5.3 - - - +
185A ARG* 5.6 1.0 - - - +
289A LYS* 4.3 10.5 - - - +
290A VAL* 3.4 31.0 + - - +
74B C 4.6 0.2 + - - -
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Residues in contact with TRP 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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156A VAL* 4.1 1.8 - - + +
157A ASN* 1.3 75.1 - - - +
159A CYS* 1.3 58.2 + - - +
160A PRO* 3.3 20.3 + - + +
163A GLN* 3.4 40.7 - - + +
164A THR* 3.6 15.5 - - - -
165A VAL* 3.7 29.6 - - + -
183A VAL* 3.5 6.1 - - - +
184A GLU* 3.0 62.6 + - - +
186A LYS* 3.7 53.2 - - + +
188A ILE* 5.0 6.3 - - + -
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Residues in contact with CYS 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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158A TRP* 1.3 70.7 - - - +
160A PRO* 1.4 67.6 - - - +
161A ASN* 3.4 5.2 - - - -
162A ASP* 4.0 12.8 - - + +
163A GLN* 3.0 27.7 + - - -
164A THR* 3.4 10.1 + - - +
166A LEU* 3.9 24.5 - - + +
176A CYS* 4.0 6.5 - - + -
181A THR* 3.2 21.1 - - - -
183A VAL* 4.7 4.5 - - - +
900A ZN 2.4 36.6 - - - -
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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