Contacts of the strand formed by residues 178 - 188 (chain A) in PDB entry 5W30
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 ASP 178 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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158A LYS* 4.9 14.1 - - + +
159A ILE 3.6 4.0 - - - +
160A LYS* 3.9 21.0 - - - +
176A SER* 2.9 23.1 + - - +
177A ASP* 1.3 83.7 + - - +
179A ILE* 1.3 65.7 + - - +
180A ASN* 4.2 4.4 + - - +
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Residues in contact with ILE 179 (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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125A ILE* 5.7 2.5 - - + -
158A LYS* 3.3 3.9 - - - -
159A ILE* 2.8 56.4 + - + +
161A ARG* 3.9 33.7 - - + +
166A PHE* 4.9 5.2 - - + -
176A SER 5.4 0.4 - - - +
178A ASP* 1.3 76.6 - - - +
180A ASN* 1.3 67.9 + - - +
181A LEU* 3.8 18.1 + - + -
301A UNL 3.7 46.7 - - + -
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Residues in contact with ASN 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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157A GLY 3.7 3.1 - - - +
158A LYS* 3.5 23.7 - - - +
178A ASP* 4.2 5.5 + - - +
179A ILE* 1.3 78.8 - - - +
181A LEU* 1.3 63.7 + - - +
182A ASN* 3.7 3.0 + - + +
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Residues in contact with LEU 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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123A LEU* 4.7 0.7 - - + -
132A ILE* 4.1 8.1 - - + -
134A LEU* 3.9 25.1 - - + -
155A LEU 4.2 0.4 - - - +
156A ASN* 3.2 25.1 - - - +
157A GLY 2.8 22.4 + - - +
159A ILE* 3.9 39.9 - - + -
179A ILE* 4.1 6.5 - - + -
180A ASN* 1.3 76.4 - - - +
182A ASN* 1.3 59.0 + - - +
183A ILE* 4.0 12.8 - - + -
301A UNL 3.6 48.7 - - + -
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Residues in contact with ASN 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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154A SER* 5.1 0.6 - - - -
155A LEU 3.7 1.8 - - - -
156A ASN* 2.9 26.1 + - - +
180A ASN* 3.7 4.2 + - + +
181A LEU* 1.3 75.2 - - - +
183A ILE* 1.3 65.2 + - - +
184A GLU* 3.9 27.1 + - - +
304A 9UM 5.4 9.6 - - + +
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Residues in contact with ILE 183 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70A VAL* 6.4 2.5 - - + -
134A LEU* 5.3 3.8 - - + -
153A PHE 4.1 0.2 - - - +
154A SER* 3.2 7.1 - - - -
155A LEU* 2.8 63.2 + - + +
181A LEU* 4.7 10.1 - - + -
182A ASN* 1.3 77.4 - - - +
184A GLU* 1.3 60.9 + - - +
185A VAL* 3.8 22.6 + - + +
301A UNL 3.8 36.3 - - + -
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Residues in contact with GLU 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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153A PHE 3.8 8.0 + - - +
154A SER* 3.4 26.2 - - - -
182A ASN* 3.9 22.6 + - - +
183A ILE* 1.3 73.7 - - - +
185A VAL* 1.3 65.1 + - - +
186A GLU 4.3 0.7 + - - -
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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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56A ILE* 4.5 8.1 - - + -
151A ILE 5.3 0.2 - - - +
152A GLY* 3.2 3.8 - - - -
153A PHE* 2.9 78.4 + - + +
183A ILE* 3.8 22.7 - - + +
184A GLU* 1.3 80.0 - - - +
186A GLU* 1.3 75.6 + - - +
187A ALA* 4.0 9.2 - - + -
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Residues in contact with GLU 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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151A ILE 3.7 6.7 - - - +
152A GLY* 4.4 2.9 - - - -
184A GLU 4.3 0.6 + - - -
185A VAL* 1.3 77.0 - - - +
187A ALA* 1.3 66.1 + - - +
188A ASN* 5.5 0.9 - - - -
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Residues in contact with ALA 187 (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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56A ILE* 4.3 17.3 - - + -
150A LYS* 3.3 5.1 - - - +
151A ILE* 3.0 48.2 + - + +
185A VAL* 4.0 14.8 - - + -
186A GLU* 1.3 77.5 - - - +
188A ASN* 1.3 70.1 + - - +
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Residues in contact with ASN 188 (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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149A GLU 3.5 7.3 - - - +
150A LYS* 3.8 22.0 - - - +
186A GLU 5.5 0.4 - - - -
187A ALA* 1.3 81.7 - - - +
189A GLU* 1.3 70.0 + - - +
190A LYS* 4.8 1.2 - - - +
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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