Contacts of the strand formed by residues 186 - 199 (chain A) in PDB entry 6D6U
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 PHE 186 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50A VAL* 3.5 28.7 - - + -
52A GLU* 3.6 19.7 - - + -
138A MET* 5.0 2.0 - - + -
148A GLN* 4.7 10.8 - - + -
182A GLU* 4.4 4.2 - - - +
183A LEU* 3.5 41.6 + - + +
185A GLN* 1.3 99.8 - - + +
187A SER* 1.3 64.6 + - - +
214A LEU* 3.6 38.8 - - + -
215A LYS 3.3 10.3 - - - +
216A ARG* 3.3 47.6 - - + -
217A ASN* 4.0 6.3 + - - -
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Residues in contact with SER 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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182A GLU* 5.2 10.1 - - - +
183A LEU* 5.5 2.9 - - - +
186A PHE* 1.3 79.6 - - - +
188A ILE* 1.3 63.5 + - - +
189A VAL* 3.2 13.0 + - - +
214A LEU* 4.0 2.8 - - - -
215A LYS* 3.1 35.7 + - - +
216A ARG 5.5 0.3 + - - -
217A ASN* 4.7 10.9 + - - -
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Residues in contact with ILE 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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47A ILE* 4.5 8.3 - - + -
178A VAL* 3.7 29.6 - - + +
181A ILE* 4.1 30.7 + - + +
183A LEU* 4.5 11.4 - - + +
187A SER* 1.3 70.0 - - - +
189A VAL* 1.3 65.4 + - - +
190A ASP* 4.5 7.9 - - - +
191A TYR* 5.3 0.2 - - + -
212A PHE* 3.6 36.1 - - + -
213A LYS 4.0 1.8 - - - +
214A LEU* 3.5 27.8 - - + -
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Residues in contact with VAL 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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187A SER* 3.2 16.8 + - - +
188A ILE* 1.3 76.3 - - - +
190A ASP* 1.3 71.0 + - + +
213A LYS* 3.7 28.6 + - + +
215A LYS* 3.9 29.8 - - + +
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Residues in contact with ASP 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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188A ILE* 3.7 2.6 - - - +
189A VAL* 1.3 89.2 - - + +
191A TYR* 1.3 93.6 + - - +
192A LYS* 4.4 17.7 - - - +
212A PHE* 3.2 3.7 - - - +
213A LYS* 2.9 34.3 + - + +
1F NAG 4.1 5.9 - - + +
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Residues in contact with TYR 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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172A ASP 4.7 8.7 + - - -
175A VAL* 3.8 31.3 + - + -
178A VAL* 3.8 38.9 - - + +
179A THR* 6.4 1.1 - - + -
188A ILE* 5.3 0.7 - - + -
190A ASP* 1.3 93.8 + - - +
192A LYS* 1.3 70.4 + - - +
193A LEU* 5.0 11.0 - - + -
210A LEU* 4.6 18.8 - - + -
211A SER 3.2 7.0 - - - +
212A PHE* 3.5 19.7 - - + -
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Residues in contact with LYS 192 (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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190A ASP* 4.4 15.5 - - - +
191A TYR* 1.3 79.0 - - - +
193A LEU* 1.3 74.4 + - - +
194A ILE* 5.1 4.7 - - + +
209A SER 4.3 0.3 - - - +
210A LEU* 3.9 2.4 - - - +
211A SER* 2.9 31.9 + - - +
1F NAG 4.1 29.6 + - + +
2F NAG 3.5 29.1 + - - +
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Residues in contact with LEU 193 (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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168A TRP* 4.0 34.3 - - + +
171A ASP* 3.6 27.8 - - + +
174A ALA* 3.8 18.2 - - + -
175A VAL* 4.2 10.3 - - + +
191A TYR* 5.0 10.3 - - + -
192A LYS* 1.3 78.7 - - - +
194A ILE* 1.3 68.2 + - - +
209A SER 4.0 1.8 - - - +
210A LEU* 3.6 30.3 - - + -
2F NAG 5.4 1.9 + - - -
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Residues in contact with ILE 194 (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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168A TRP* 3.4 14.1 + - - -
192A LYS* 5.1 3.4 - - + -
193A LEU* 1.3 82.4 - - - +
195A THR* 1.3 73.6 + - - +
196A LYS* 3.7 27.6 - - + +
208A LEU* 3.6 1.2 - - - +
209A SER* 3.4 43.5 + - - +
211A SER* 4.6 7.6 - - - +
1F NAG 3.3 34.5 - - - +
2F NAG 3.9 30.3 - - - +
3F BMA 6.5 0.2 - - - -
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Residues in contact with THR 195 (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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166A PHE 4.4 12.3 - - - +
167A TYR* 5.4 2.1 - - + -
168A TRP* 3.9 9.9 + - - -
194A ILE* 1.3 81.4 + - - +
196A LYS* 1.3 73.8 + - - +
207A ARG 3.8 5.4 - - - +
208A LEU* 3.3 21.6 - - + +
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Residues in contact with LYS 196 (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 GLU* 4.4 14.8 + - - -
194A ILE* 3.7 15.4 - - + +
195A THR* 1.3 85.1 - - - +
197A LYS* 1.3 73.4 + - - +
198A VAL* 4.8 4.7 - - + +
206A PRO* 4.0 1.9 - - - +
207A ARG* 3.0 61.5 + - + +
209A SER* 4.9 8.7 + - - -
2F NAG 3.3 39.8 + - + +
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Residues in contact with LYS 197 (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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161A THR* 3.7 28.9 + - + +
165A GLU* 4.7 15.2 + - - -
196A LYS* 1.3 80.0 - - - +
198A VAL* 1.3 63.2 + - - +
199A VAL* 4.2 5.1 + - + +
204A SER* 4.3 13.0 - - - +
205A TYR 3.8 4.9 - - - +
206A PRO* 4.9 7.0 - - + -
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Residues in contact with VAL 198 (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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155A GLU* 4.9 1.6 - - - +
196A LYS* 4.8 9.2 - - + +
197A LYS* 1.3 77.6 - - - +
199A VAL* 1.3 68.2 + - - +
200A PHE* 3.9 29.1 + - + -
204A SER* 3.4 3.1 - - - -
205A TYR* 2.8 40.4 + - - +
207A ARG* 3.4 52.7 - - + +
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Residues in contact with VAL 199 (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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197A LYS 4.2 4.7 + - - +
198A VAL* 1.3 82.9 - - - +
200A PHE* 1.3 79.7 + - - +
203A GLY 3.6 7.6 - - - +
204A SER* 4.2 16.8 - - - +
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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