Contacts of the helix formed by residues 159 - 165 (chain B) in PDB entry 2WP9
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 CYS 159 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155B CYS 3.3 7.3 + - - +
156B SER 3.2 12.1 + - - +
157B THR 3.5 0.6 - - - -
158B SER* 1.3 76.2 - - - +
160B PRO* 1.3 72.8 - - - +
161B SER* 3.4 24.7 - - - -
162B PHE* 2.9 22.4 + - + +
163B TRP* 3.0 14.6 + - - -
169B PHE* 3.6 15.5 - - - -
172B PRO* 4.1 13.2 - - + -
206B CYS* 5.9 1.8 - - - -
209B ILE* 5.2 5.4 - - - -
211B ASN* 4.8 3.8 - - + -
212B CYS* 5.8 5.4 - - - +
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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
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158B SER 3.5 10.3 - - - +
159B CYS* 1.3 82.9 - - - +
161B SER* 1.3 61.2 + - - +
163B TRP* 3.1 29.9 + - + +
164B TRP* 3.0 45.2 + - + +
209B ILE* 3.7 42.0 - - + -
211B ASN* 4.4 4.3 - - - +
20C PHE* 5.1 6.1 - - + -
24C ALA* 5.9 1.1 - - + -
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Residues in contact with SER 161 (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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159B CYS* 3.2 15.0 - - - -
160B PRO* 1.3 77.5 - - - +
162B PHE* 1.3 62.8 + - - +
164B TRP* 3.4 9.3 + - - +
165B ASN* 3.1 25.5 + - - +
169B PHE* 3.7 16.9 - - - +
205B ARG* 2.6 36.3 + - - +
206B CYS* 4.6 1.2 - - - -
207B THR* 4.8 2.6 + - - +
209B ILE* 4.4 10.3 - - - +
82D ASP* 5.2 5.7 + - - -
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Residues in contact with PHE 162 (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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96B GLY 6.4 0.9 - - - -
97B LEU* 4.3 19.7 - - + -
109B GLN* 4.7 1.1 - - + -
110B PHE* 4.4 25.4 - + - -
113B GLN* 4.0 6.1 - - + -
156B SER* 3.3 45.1 - - - +
157B THR* 4.8 4.9 - - + -
159B CYS* 2.9 12.5 + - + +
161B SER* 1.3 77.5 - - - +
163B TRP* 1.3 70.2 + + - +
165B ASN 4.7 0.7 - - - +
166B PRO* 3.1 61.1 - - + +
169B PHE* 3.5 14.3 - + + -
170B ILE 4.0 14.8 - - - -
171B GLY* 3.8 17.7 - - - -
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Residues in contact with TRP 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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95B PRO* 3.9 17.9 + - + +
96B GLY* 4.1 17.5 - - - -
156B SER 4.5 2.5 - - - -
157B THR* 2.8 36.3 + - - -
158B SER* 4.0 15.0 - - - -
159B CYS 3.0 10.8 + - - -
160B PRO* 3.1 26.7 + - + +
162B PHE* 1.3 80.5 - + - +
164B TRP* 1.3 92.8 + + + +
166B PRO* 3.5 10.0 - - - +
211B ASN* 5.4 0.2 - - - -
13C LEU* 3.6 23.2 - - + +
15C LEU* 3.9 18.6 - - + -
18C ILE* 4.1 13.2 - - + -
20C PHE* 3.9 29.2 - + - -
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Residues in contact with TRP 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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160B PRO* 3.0 33.4 + - + +
161B SER* 4.1 3.8 - - - +
163B TRP* 1.3 109.2 - + + +
165B ASN* 1.3 56.6 + - - +
166B PRO* 3.6 3.7 - - - +
13C LEU* 4.2 18.4 - - + -
15C LEU* 5.2 14.8 - - + -
31C ARG* 4.7 0.4 - - - +
82D ASP* 3.5 52.5 - - + +
83D TYR* 3.5 34.3 + + - -
85D LYS* 2.6 34.3 + - - +
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Residues in contact with ASN 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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161B SER 3.1 12.2 + - - +
162B PHE 3.6 2.5 - - - -
164B TRP* 1.3 79.9 - - - +
166B PRO* 1.3 57.3 - - - +
167B ASP* 3.0 12.0 + - - +
168B LYS* 3.7 30.6 + - + -
169B PHE* 2.9 32.6 + - + +
201B PHE* 4.0 13.1 - - + -
205B ARG* 3.8 10.5 - - + +
81D THR 3.5 13.3 + - - +
82D ASP* 2.9 28.3 + - - -
85D LYS* 3.0 19.5 + - - +
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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