Contacts of the strand formed by residues 179 - 186 (chain A) in PDB entry 2WA2
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 179 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75A LYS* 4.9 2.0 - - - +
141A ALA 3.7 16.4 - - - +
142A ASP* 3.4 17.5 - - - +
143A THR 4.4 0.4 - - - +
144A VAL* 4.0 9.0 - - - -
173A LEU* 3.5 31.9 - - - -
176A ASN* 3.0 31.2 + - + +
177A GLN 3.3 1.8 + - - -
178A GLY* 1.3 81.1 - - - +
180A GLY* 1.3 68.7 + - - +
181A PHE* 3.5 14.0 - - - -
225A SER* 4.4 1.7 - - - -
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Residues in contact with GLY 180 (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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72A VAL* 4.8 4.3 - - - -
73A GLU* 4.8 9.0 - - - -
75A LYS* 4.6 5.1 - - - +
142A ASP 3.0 12.4 + - - -
143A THR* 3.4 7.7 - - - -
144A VAL 2.8 23.1 + - - -
178A GLY 3.7 1.0 + - - -
179A CYS* 1.3 78.0 - - - +
181A PHE* 1.3 64.3 + - - +
225A SER* 3.3 14.1 - - - -
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Residues in contact with PHE 181 (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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72A VAL* 3.6 10.0 - - - +
144A VAL* 3.1 13.7 - - + +
173A LEU* 3.7 34.8 - - + -
179A CYS 3.5 16.6 - - - -
180A GLY* 1.3 75.2 - - - +
182A CYS* 1.3 64.6 + - - +
183A VAL* 4.5 7.6 - - + -
204A PHE* 3.9 20.0 - - + -
205A GLY 4.0 10.8 - - - -
206A GLY* 4.3 0.4 - - - -
223A PHE* 3.2 49.6 - + - -
224A VAL* 3.4 20.6 - - - -
225A SER* 2.9 49.3 + - - -
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Residues in contact with CYS 182 (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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63A LEU* 4.3 6.7 - - - -
66A ILE* 3.6 36.1 - - - -
72A VAL* 4.1 11.7 - - + -
88A TRP* 3.8 18.3 - - - -
144A VAL 3.0 6.5 + - - -
145A LEU* 3.4 19.1 - - + -
146A CYS 3.0 24.3 + - - +
181A PHE* 1.3 78.6 - - - +
183A VAL* 1.3 60.3 + - - +
222A TYR* 4.1 3.4 - - - -
223A PHE 3.3 5.4 - - - -
224A VAL* 3.9 11.2 - - + -
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Residues in contact with VAL 183 (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 VAL* 4.6 3.4 - - + +
146A CYS* 3.3 7.9 - - + -
165A VAL* 4.0 11.4 - - + -
166A LEU* 4.2 13.5 - - + -
169A ILE* 3.6 50.5 - - + -
181A PHE* 4.5 10.5 - - + -
182A CYS* 1.3 84.7 - - - +
184A LYS* 1.3 77.7 + - - +
185A VAL* 3.7 1.2 - - - +
222A TYR* 3.4 6.0 - - - -
223A PHE* 2.7 49.1 + - + +
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Residues in contact with LYS 184 (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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62A LYS* 5.0 2.0 - - - +
146A CYS 2.8 14.9 + - - +
147A ASP* 3.3 34.6 + - - +
148A ILE 3.8 23.7 - - - +
149A GLY* 2.8 27.8 + - - +
151A SER* 5.5 1.6 + - - +
162A THR* 5.3 1.4 - - - +
165A VAL* 4.3 8.0 - - - +
166A LEU* 5.0 1.2 - - - +
183A VAL* 1.3 83.2 - - - +
185A VAL* 1.3 63.8 + - - +
186A LEU* 3.9 19.7 + - - +
218A THR* 5.3 0.2 + - - -
220A GLU* 3.1 34.9 + - + -
222A TYR* 3.6 22.3 + - + +
1248A SAM 6.3 0.4 - - - +
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Residues in contact with VAL 185 (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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162A THR* 3.5 24.0 - - + -
166A LEU* 4.3 7.6 - - + -
183A VAL 3.7 8.3 - - - +
184A LYS* 1.3 77.2 - - - +
186A LEU* 1.3 65.9 + - - +
188A PRO* 3.7 30.2 - - + +
193A VAL* 3.8 9.2 - - + -
197A LEU* 3.9 19.3 - - + -
208A LEU* 3.7 25.4 - - + -
220A GLU* 3.4 0.5 - - - -
221A MET 2.7 33.3 + - - +
223A PHE* 3.9 5.6 - - + -
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Residues in contact with LEU 186 (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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148A ILE 5.1 0.6 + - - +
149A GLY* 4.0 14.8 - - - +
150A GLU 3.4 29.8 - - - +
151A SER* 3.9 25.8 - - - +
158A GLU* 3.6 41.8 - - + +
161A ARG* 5.0 4.3 - - + -
162A THR* 3.5 13.0 + - - +
184A LYS* 3.9 24.2 + - - +
185A VAL* 1.3 73.6 - - - +
187A ASN* 1.3 58.4 + - - +
188A PRO* 3.5 6.1 - - - +
218A THR* 4.3 8.7 - - - +
219A HIS* 3.8 5.0 + - - +
220A GLU* 3.7 15.7 + - - +
1249A SO4 4.8 2.5 - - - +
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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