Contacts of the strand formed by residues 166 - 171 (chain B) in PDB entry 5WN0
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 166 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159B VAL* 3.8 26.2 - - + -
160B ALA 3.6 11.7 - - - +
161B GLU* 3.9 15.3 - - + +
165B PHE* 1.3 77.6 - - - +
167B LEU* 1.3 63.2 + - - +
199B LEU* 4.4 19.5 - - + +
202B ARG* 5.6 2.5 - - - +
203B LYS* 4.0 20.6 - - + +
204B PRO 2.9 13.2 + - - +
205B LEU* 3.4 19.0 - - + +
206B VAL 2.9 24.3 + - - -
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Residues in contact with LEU 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B ILE* 4.2 12.1 - - + -
91B ILE* 3.9 40.6 - - + -
93B CYS* 4.2 11.2 - - - -
133B LEU* 4.2 10.8 - - + +
158B ILE 3.7 1.0 - - - +
159B VAL* 3.6 1.7 - - - +
160B ALA* 2.8 46.1 + - + +
162B PHE* 4.3 4.7 - - + -
165B PHE* 3.7 13.2 - - + -
166B VAL* 1.3 73.4 - - - +
168B VAL* 1.3 72.0 + - - +
169B THR* 4.6 0.4 - - - +
206B VAL* 3.2 37.2 - - + +
208B CYS* 4.4 12.6 - - - -
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Residues in contact with VAL 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157B VAL* 4.0 14.8 - - + -
158B ILE 3.3 6.5 - - - +
159B VAL* 4.0 12.3 - - + -
167B LEU* 1.3 79.7 - - - +
169B THR* 1.3 75.1 + - - +
192B PHE* 4.1 13.5 - - + -
195B PHE* 5.0 0.4 - - + -
196B LEU* 4.0 7.4 - - + -
199B LEU* 3.5 31.9 - - + -
205B LEU* 3.9 11.0 - - + -
206B VAL 2.8 9.4 + - - +
207B LEU* 3.3 21.7 - - + -
208B CYS 3.0 24.8 + - - -
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Residues in contact with THR 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93B CYS* 2.8 39.0 - - + -
94B LEU 4.6 4.3 - - - +
95B GLN* 2.6 38.8 - - + +
131B VAL* 5.0 5.5 - - + +
132B GLY 5.3 2.7 - - - +
133B LEU* 4.5 8.4 - - - +
156B ARG 3.5 0.6 - - - +
157B VAL* 3.2 6.6 - - - -
158B ILE* 3.0 37.3 + - - +
167B LEU* 4.6 0.7 - - - +
168B VAL* 1.3 75.0 - - - +
170B ALA* 1.3 62.9 + - - +
208B CYS* 3.1 12.5 - - - +
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Residues in contact with ALA 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B GLN* 3.0 19.0 - - - +
156B ARG 3.2 6.5 - - - -
157B VAL* 4.1 7.4 - - + -
169B THR* 1.3 76.7 - - - +
171B TYR* 1.3 60.6 + - - +
172B VAL* 3.8 13.5 - - + +
188B TRP* 4.5 1.3 - - + -
192B PHE* 3.7 33.2 - - + -
207B LEU* 4.1 8.1 - - + -
208B CYS 3.0 6.0 + - - +
209B GLY* 3.3 1.7 - - - -
210B ASP 3.2 14.8 + - - -
211B LEU* 4.9 2.5 - - + -
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Residues in contact with TYR 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B ASN* 3.5 15.3 - - - -
95B GLN* 3.6 17.3 - - + -
96B GLU* 2.9 46.6 + - + +
128B TYR* 5.3 7.8 + + - -
129B SER* 3.5 23.8 - - - -
130B GLY 4.8 0.4 - - - -
131B VAL* 3.8 10.3 - - + -
156B ARG* 2.5 75.9 + - - +
170B ALA* 1.3 72.9 - - - +
172B VAL* 1.3 53.5 + - - +
174B ASN* 5.5 6.7 + - - +
188B TRP* 5.2 0.2 - - - -
210B ASP* 3.5 32.1 - - + -
212B ASN* 3.9 13.4 + - - -
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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