Contacts of the strand formed by residues 181 - 191 (chain A) in PDB entry 2PWP
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 LEU 181 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150A THR* 4.1 6.3 - - - +
151A TYR 3.5 12.1 - - - +
152A ASP 4.0 2.2 - - - +
154A ILE* 3.8 20.9 - - + +
177A ILE* 3.4 27.1 - - + +
178A TYR* 3.2 8.4 + - - +
179A ASN 4.1 4.9 - - - +
180A ALA* 1.3 81.3 - - - +
182A LYS* 1.3 71.6 + - - +
183A PRO* 3.8 1.2 - - - +
185A GLY* 3.8 4.3 - - - +
186A TYR 3.3 37.2 - - - +
187A CYS* 4.1 7.4 - - + -
212A PHE* 3.7 30.7 - - + -
237A LYS* 3.0 15.1 + - - +
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Residues in contact with LYS 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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79A LYS* 6.1 1.4 - - - +
80A ASN* 5.2 4.6 - - - +
150A THR* 2.9 39.5 + - - +
151A TYR 2.8 22.3 + - - +
152A ASP* 3.6 28.3 + - - +
181A LEU* 1.3 77.0 - - - +
183A PRO* 1.3 74.0 - - + +
184A ASN* 3.1 14.6 - - - +
185A GLY* 2.9 20.8 + - - +
237A LYS* 3.1 8.5 + - - +
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Residues in contact with PRO 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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181A LEU 4.4 0.9 - - - +
182A LYS* 1.3 92.9 - - + +
184A ASN* 1.3 59.3 + - + +
185A GLY 3.4 0.7 - - - -
237A LYS* 3.1 33.0 - - + +
238A THR* 5.2 1.7 - - - +
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Residues in contact with ASN 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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75A SER* 5.3 2.1 + - - -
76A LYS* 6.1 4.8 - - - +
152A ASP* 4.8 3.1 + - - +
182A LYS* 3.6 16.3 - - - +
183A PRO* 1.3 77.3 - - - +
185A GLY* 1.3 60.1 + - - +
186A TYR* 3.9 20.8 - - - +
237A LYS* 4.5 3.6 - - - -
238A THR* 4.7 18.2 - - + -
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Residues in contact with GLY 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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151A TYR 4.4 0.2 - - - -
152A ASP* 3.3 15.9 - - - -
181A LEU* 3.8 13.3 - - - +
182A LYS* 2.9 22.0 + - - -
183A PRO 3.4 1.0 + - - -
184A ASN* 1.3 81.3 - - - +
186A TYR* 1.3 61.3 + - - -
212A PHE* 5.1 0.2 - - - -
235A CYS 4.4 0.9 - - - +
237A LYS* 3.7 26.5 + - - +
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Residues in contact with TYR 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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71A PRO* 4.6 6.3 - - + -
74A VAL* 3.7 22.1 + - + +
75A SER* 3.8 39.5 - - - -
152A ASP 3.0 8.3 + - - +
153A VAL* 3.3 10.5 - - + +
154A ILE 2.9 24.3 + - - +
181A LEU* 3.3 7.2 - - - +
184A ASN* 3.9 15.7 + - - +
185A GLY* 1.3 79.3 - - - -
187A CYS* 1.3 60.1 - - - +
235A CYS 3.6 5.2 - - - +
236A SER* 3.2 34.1 - - - -
237A LYS 4.9 0.4 - - - -
238A THR* 3.6 20.0 + - - +
240A THR* 4.4 5.7 + - - -
241A GLY 4.4 3.3 + - - -
242A LEU* 3.8 25.6 - - + -
246A ASN* 5.6 0.3 + - - -
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Residues in contact with CYS 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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71A PRO* 5.8 0.2 - - - -
154A ILE* 3.2 14.4 - - + +
156A VAL* 3.9 17.0 - - - -
174A TYR* 4.8 11.0 - - - -
177A ILE* 3.7 33.2 - - + -
181A LEU* 4.1 6.8 - - + +
186A TYR* 1.3 75.0 - - - +
188A VAL* 1.3 78.4 + - - +
189A ALA* 4.6 3.8 - - - -
233A LEU 3.9 0.4 - - - +
235A CYS* 2.8 46.1 + - + +
242A LEU* 4.2 1.0 - - - +
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Residues in contact with VAL 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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67A MET* 3.5 26.0 - - + +
70A VAL* 4.9 0.9 - - + -
71A PRO* 3.9 28.7 - - + +
154A ILE 3.0 3.5 + - - +
155A ILE* 3.7 25.0 - - + +
156A VAL 2.9 23.9 + - - -
187A CYS* 1.3 81.5 - - - +
189A ALA* 1.3 63.6 + - - +
232A ILE* 3.7 14.4 - - + -
233A LEU 3.2 5.2 - - - -
234A CYS* 3.9 21.8 - - - -
242A LEU* 4.4 7.2 - - + -
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Residues in contact with ALA 189 (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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67A MET* 4.3 4.0 - - - -
156A VAL* 3.6 23.6 - - + -
158A SER* 5.7 0.2 - - - -
174A TYR* 3.3 28.0 - - + +
187A CYS* 4.7 2.5 - - - -
188A VAL* 1.3 78.4 - - - +
190A GLN* 1.3 67.7 + - - +
191A CYS 3.1 0.5 + - - -
232A ILE* 3.5 3.9 - - - -
233A LEU* 2.8 41.7 + - + +
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Residues in contact with GLN 190 (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 TYR* 3.4 25.0 + - + +
67A MET* 3.8 7.9 - - - +
156A VAL 3.1 15.2 + - - +
158A SER* 4.0 13.9 + - - +
159A SER 3.3 20.1 - - - +
160A ASP* 3.8 8.0 - - - +
169A PHE* 4.4 12.1 - - - -
189A ALA* 1.3 74.5 - - - +
191A CYS* 1.3 61.9 + - - +
192A GLU* 3.4 22.9 - - - +
230A ILE* 3.7 28.3 - - + +
231A GLY 3.8 4.3 - - - +
401A SPD 3.1 36.9 + - - +
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Residues in contact with CYS 191 (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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169A PHE* 5.5 2.2 - - - -
189A ALA 3.1 0.6 + - - +
190A GLN* 1.3 75.2 - - - +
192A GLU* 1.3 66.5 + - - +
200A THR* 5.4 1.3 - - - -
201A ILE* 4.3 13.0 - - - -
204A MET* 3.9 34.1 - - - -
217A TYR* 3.9 21.8 - - + -
230A ILE* 3.4 5.4 - - - +
231A GLY 2.8 34.3 + - - +
233A LEU* 3.7 31.6 - - + +
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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