Contacts of the strand formed by residues 159 - 168 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A ALA* 6.2 1.8 - - + -
92A LEU* 3.8 33.7 - - + -
93A TYR 3.5 4.5 - - - +
94A VAL* 4.3 4.9 - - + -
98A LEU* 3.8 12.3 - - + -
157A THR* 4.3 0.9 - - - -
158A LYS* 1.3 82.3 - - - +
160A LEU* 1.3 62.6 + - - +
304A PHE* 4.4 14.6 - - + -
307A MET* 4.0 23.6 - - + -
313A VAL* 3.6 23.6 - - + -
314A ALA 3.4 17.7 - - - +
315A LEU* 3.8 13.9 - - + +
316A SER* 2.8 36.0 + - - -
317A ASN 3.5 2.6 + - - +
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Residues in contact with LEU 160 (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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91A ARG 3.6 1.0 - - - +
92A LEU* 3.4 4.0 - - - -
93A TYR* 2.7 55.0 + - + +
121A PHE* 4.1 9.9 - - + -
132A ILE* 4.4 2.7 - - + -
148A LEU* 4.0 8.3 - - + -
153A VAL* 3.5 28.7 - - + -
157A THR* 4.0 11.0 - - + -
159A ILE* 1.3 77.7 - - - +
161A VAL* 1.3 68.6 + - - +
162A VAL* 3.9 21.7 + - + -
317A ASN* 3.5 35.9 - - + +
319A ILE* 4.1 13.9 - - + -
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Residues in contact with VAL 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A LEU* 4.9 2.0 - - + -
38A SER* 3.6 34.1 - - - +
39A LEU* 4.7 8.7 - - + -
42A ALA* 5.9 0.9 - - + -
91A ARG 3.5 3.8 - - - +
92A LEU* 3.5 27.4 - - + -
160A LEU* 1.3 73.7 - - - +
162A VAL* 1.3 62.6 + - - +
163A ASN* 3.8 11.4 - - - +
315A LEU* 3.7 16.8 - - + -
317A ASN 3.1 7.1 + - - -
318A VAL* 3.5 28.7 - - + -
319A ILE 2.8 30.8 + - - -
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Residues in contact with VAL 162 (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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89A ILE* 3.6 1.0 - - - +
90A LYS* 3.4 1.6 - - - -
91A ARG* 2.9 34.6 + - + +
93A TYR* 3.8 26.7 - - + -
132A ILE* 4.8 1.8 - - + -
136A ILE* 3.9 23.8 - - + -
147A ILE* 3.9 22.9 - - + -
148A LEU* 4.5 10.3 - - + -
160A LEU* 3.9 18.8 - - + -
161A VAL* 1.3 78.3 - - - +
163A ASN* 1.3 75.0 + - - +
164A ALA* 4.5 1.8 - - + +
319A ILE* 3.5 12.3 - - + +
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Residues in contact with ASN 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A CYS* 3.7 21.3 + - + -
35A LEU* 3.4 27.0 + - - +
38A SER* 2.9 26.3 + - - -
89A ILE 3.3 2.9 - - - -
90A LYS* 3.8 8.3 - - - +
147A ILE* 4.6 1.7 - - - +
161A VAL* 3.8 4.4 - - - +
162A VAL* 1.3 86.3 + - - +
164A ALA* 1.3 61.9 + - - +
165A ALA* 6.2 0.4 - - + -
319A ILE 2.7 14.5 + - - +
320A HIS* 3.0 34.5 + - + +
321A LYS* 3.0 25.6 + - - +
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Residues in contact with ALA 164 (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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34A CYS* 5.6 0.2 - - - -
87A LYS 3.9 0.3 - - - +
88A LEU* 3.9 0.2 - - - -
89A ILE* 2.8 42.6 + - + +
136A ILE* 3.9 28.3 - - + -
140A THR* 4.0 6.4 - - + +
144A PHE* 3.9 18.2 - - + -
147A ILE* 4.0 11.0 - - + -
162A VAL* 4.5 2.4 - - + +
163A ASN* 1.3 75.1 - - - +
165A ALA* 1.3 60.6 + - - +
321A LYS 3.5 5.4 - - - -
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Residues in contact with ALA 165 (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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31A SER* 4.3 13.0 - - - +
34A CYS* 4.5 4.3 - - - -
87A LYS 3.1 12.1 - - - +
88A LEU* 3.6 22.4 - - + -
144A PHE* 3.3 9.6 - - - -
163A ASN* 5.7 0.4 - - + -
164A ALA* 1.3 75.5 - - - +
166A TYR* 1.3 60.9 + - - +
321A LYS 3.1 8.9 + - - +
322A VAL* 3.2 7.2 - - + -
323A CME 3.0 22.9 + - - -
368A PHE* 4.0 11.9 - - + -
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Residues in contact with TYR 166 (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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85A SER* 3.7 24.4 - - - -
86A LEU* 3.3 11.3 + - - +
87A LYS* 2.9 64.2 + - + +
140A THR* 3.4 30.7 - - + -
141A ASP* 2.7 26.7 + - - +
143A HIS* 3.5 32.6 + + + -
144A PHE* 4.2 9.2 - + + -
165A ALA* 1.3 76.5 - - - +
167A PHE* 1.3 65.8 + - - +
168A VAL* 4.3 5.2 - - + -
323A CME 3.1 31.2 - - + +
368A PHE* 4.3 3.8 - - - -
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Residues in contact with PHE 167 (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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84A TYR* 4.0 28.9 - + + -
85A SER 3.3 13.9 - - - -
86A LEU* 3.8 13.2 - - + -
166A TYR* 1.3 76.8 - - - +
168A VAL* 1.3 75.2 + - - +
169A GLY* 3.9 6.7 - - - -
170A LYS 4.5 1.8 - - - -
221A PHE* 3.7 50.7 - + + -
226A LEU* 3.9 17.9 - - + -
323A CME 3.0 8.1 + - - +
324A LEU* 3.5 25.0 - - + +
325A GLU 2.9 25.3 + - - -
358A ILE* 4.1 3.6 - - + -
368A PHE* 3.5 26.9 - + + -
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Residues in contact with VAL 168 (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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85A SER* 2.9 35.9 + - - +
143A HIS* 4.7 2.7 - - + +
166A TYR* 4.4 11.4 - - + -
167A PHE* 1.3 76.1 - - - +
169A GLY* 1.3 69.3 + - - +
170A LYS* 3.6 3.3 + - - +
323A CME 3.6 35.4 - - + +
325A GLU* 3.7 26.5 - - + +
327A THR* 5.4 4.9 - - - +
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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
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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