Contacts of the strand formed by residues 159 - 168 (chain B) in PDB entry 1WZ9
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 ILE 159 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B ALA* 6.2 2.2 - - + -
92B LEU* 3.8 36.3 - - + -
93B TYR 3.3 5.4 - - - +
94B VAL* 4.1 6.7 - - + -
98B LEU* 3.9 9.0 - - + -
157B THR* 4.0 2.7 - - - -
158B LYS* 1.3 86.0 - - + +
160B LEU* 1.3 61.6 + - - +
304B PHE* 4.4 12.3 - - + -
307B MET* 3.9 29.4 - - + -
313B VAL* 3.9 21.8 - - + -
314B ALA 3.6 12.8 - - - +
315B LEU* 3.7 13.7 - - + +
316B SER* 2.8 35.3 + - - -
317B ASN 3.5 1.4 + - - -
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Residues in contact with LEU 160 (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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91B ARG 3.7 1.0 - - - +
92B LEU* 3.6 3.1 - - - +
93B TYR* 2.8 50.9 + - + +
121B PHE* 3.9 21.1 - - + -
132B ILE* 4.2 3.4 - - + -
148B LEU* 3.9 18.6 - - + -
153B VAL* 4.8 11.2 - - + +
157B THR* 3.9 14.6 - - + +
159B ILE* 1.3 75.1 - - - +
161B VAL* 1.3 64.7 + - - +
162B VAL* 3.8 20.4 + - + -
317B ASN* 3.4 29.4 - - + +
319B ILE* 3.9 23.1 - - + -
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Residues in contact with VAL 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B LEU* 4.9 2.9 - - + -
38B SER* 3.8 29.8 - - - +
39B LEU* 4.7 5.8 - - + -
42B ALA* 6.0 0.7 - - + -
91B ARG 3.6 3.6 - - - +
92B LEU* 3.5 22.2 - - + -
160B LEU* 1.3 73.0 - - - +
162B VAL* 1.3 61.3 + - - +
163B ASN* 3.9 11.7 - - - +
315B LEU* 3.4 30.2 - - + +
317B ASN 2.9 7.6 + - - +
318B VAL* 3.4 26.6 - - + -
319B ILE 2.7 31.5 + - - -
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Residues in contact with VAL 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B ILE 3.7 1.3 - - - +
90B LYS* 3.5 1.7 - - - -
91B ARG* 2.9 38.7 + - + +
93B TYR* 3.7 27.4 - - + -
132B ILE* 4.8 4.5 - - + -
136B ILE* 4.1 23.8 - - + -
147B ILE* 4.1 28.3 - - + -
148B LEU* 4.8 1.6 - - + -
160B LEU* 3.8 20.6 + - + -
161B VAL* 1.3 78.1 - - - +
163B ASN* 1.3 72.1 + - - +
164B ALA 4.7 0.2 - - - +
319B ILE* 3.4 14.4 - - + +
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Residues in contact with ASN 163 (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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34B CYS* 3.6 20.6 + - + +
35B LEU* 3.3 26.5 + - - +
38B SER* 2.9 25.5 + - - -
89B ILE 3.3 2.5 - - - -
90B LYS* 4.0 5.1 - - - +
147B ILE* 4.2 4.0 - - - +
161B VAL* 3.9 6.8 - - - +
162B VAL* 1.3 81.3 + - - +
164B ALA* 1.3 61.6 + - - +
165B ALA* 6.3 0.2 - - + -
318B VAL* 5.1 0.2 - - - +
319B ILE 2.7 11.5 + - - +
320B HIS* 2.8 37.9 + - + +
321B LYS 2.9 26.4 + - - -
322B VAL* 6.1 0.2 - - + -
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Residues in contact with ALA 164 (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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34B CYS* 5.5 0.4 - - - -
87B LYS 3.9 0.9 - - - +
89B ILE* 2.8 43.4 + - + +
136B ILE* 3.9 8.5 - - + -
140B THR* 3.9 22.6 - - + +
144B PHE* 3.9 7.6 - - + -
147B ILE* 3.6 24.5 - - + -
162B VAL* 4.2 2.4 - - + -
163B ASN* 1.3 74.4 - - - +
165B ALA* 1.3 60.8 + - - +
321B LYS 3.4 4.7 - - - -
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Residues in contact with ALA 165 (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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31B SER* 4.2 6.3 - - - -
34B CYS* 4.4 3.6 - - - -
87B LYS 3.1 4.3 - - - +
88B LEU* 3.5 29.8 - - + -
140B THR* 5.7 0.2 - - - -
144B PHE* 3.3 8.8 - - - -
163B ASN* 6.3 0.4 - - + -
164B ALA* 1.3 75.0 - - - +
166B TYR* 1.3 62.3 + - - +
321B LYS 3.0 7.7 + - - -
322B VAL* 3.1 18.2 - - + -
323B CME 2.8 23.3 + - - -
368B PHE* 4.0 11.2 - - + -
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Residues in contact with TYR 166 (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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85B SER* 3.7 30.4 + - - -
86B LEU* 3.5 6.2 + - - +
87B LYS* 2.9 61.4 + - + +
140B THR* 3.2 32.5 - - + -
141B ASP* 2.6 26.9 + - + +
143B HIS* 4.3 17.3 - + + +
144B PHE* 4.3 5.2 - + + -
165B ALA* 1.3 76.7 - - - +
167B PHE* 1.3 71.7 + - - +
168B VAL* 4.4 9.2 - - + -
323B CME 3.1 24.5 - - + +
368B PHE* 4.1 3.6 - - - -
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Residues in contact with PHE 167 (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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84B TYR* 3.6 28.7 - + + -
85B SER 3.4 17.0 - - - -
86B LEU* 3.8 13.2 - - + -
166B TYR* 1.3 77.2 - - - +
168B VAL* 1.3 75.9 + - - +
169B GLY* 3.7 11.4 - - - -
170B LYS* 4.4 2.7 - - + -
221B PHE* 3.8 38.4 - + - -
226B LEU* 3.7 22.2 - - + -
323B CME 3.0 6.7 + - - +
324B LEU* 3.5 26.4 - - + +
325B GLU 2.9 25.5 + - - -
358B ILE* 4.1 4.9 - - + -
368B PHE* 3.4 26.2 - + + -
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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
----------------------------------------------------------
85B SER* 3.0 38.8 + - - +
166B TYR* 4.4 11.4 - - + -
167B PHE* 1.3 83.5 - - - +
169B GLY* 1.3 69.8 + - - +
170B LYS* 3.6 4.9 + - - +
325B GLU* 3.6 36.8 - - + +
327B THR* 5.4 4.7 - - - +
329B ASP* 6.1 0.4 - - - +
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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