Contacts of the strand formed by residues 290 - 297 (chain A) in PDB entry 6HKP
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 THR 290 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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188A LEU 3.6 0.8 - - - +
189A ILE* 3.2 7.6 - - - +
190A GLY* 3.0 31.3 + - - -
209A GLN* 4.1 2.7 - - - -
211A LYS 3.1 6.1 - - - -
212A GLY* 4.2 0.4 - - - -
213A TYR 3.5 29.8 - - - +
214A LYS* 3.6 16.7 - - + -
283A SER* 2.8 39.5 + - - +
284A LEU 4.9 0.9 - - - +
287A GLY 5.6 0.4 - - - +
288A GLY 4.1 5.8 - - - +
289A ILE* 1.3 78.4 - - - +
291A ILE* 1.3 66.5 + - - +
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Residues in contact with ILE 291 (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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76A TRP* 4.0 19.5 - - + +
77A ASP* 4.4 6.3 - - - -
78A LEU* 5.1 0.7 - - + +
81A LEU* 4.2 20.4 - - + -
187A LEU* 4.0 23.3 - - + -
188A LEU 3.3 3.8 - - - +
189A ILE* 4.1 15.5 - - + -
209A GLN* 3.6 3.1 + - - -
210A ILE* 2.9 43.9 + - + -
211A LYS* 2.9 41.7 + - + +
289A ILE* 4.4 7.9 - - + -
290A THR* 1.3 78.3 - - - +
292A THR* 1.3 67.3 + - - +
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Residues in contact with THR 292 (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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186A LEU 3.7 0.4 - - - +
187A LEU* 3.6 2.1 - - - +
188A LEU* 2.9 38.5 + - + +
207A PHE* 3.6 35.4 - - + -
208A ALA 3.3 18.8 - - - +
209A GLN* 2.7 19.6 + - - +
210A ILE* 4.2 2.2 - - - -
214A LYS* 2.9 27.8 + - - -
291A ILE* 1.3 72.3 - - - +
293A VAL* 1.3 78.2 + - - +
294A ASN 4.3 0.9 - - - +
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Residues in contact with VAL 293 (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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70A VAL* 4.9 3.4 - - + -
76A TRP* 4.0 13.0 - - + -
150A LEU* 4.3 10.3 - - + -
165A PHE* 4.7 7.2 - - + -
185A ASN* 4.0 17.5 - - + +
186A LEU 3.3 7.6 - - - +
187A LEU* 3.9 19.5 - - + -
208A ALA* 2.9 35.8 + - - +
210A ILE* 3.4 24.6 - - + +
292A THR* 1.3 78.8 - - - +
294A ASN* 1.3 73.3 + - - +
295A PHE* 4.0 14.3 - - + -
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Residues in contact with ASN 294 (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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184A SER 4.2 0.3 - - - +
185A ASN* 2.9 27.4 + - - +
186A LEU* 2.9 41.1 + - - +
188A LEU* 4.4 3.8 - - + +
205A ASN* 3.5 15.3 - - - +
206A PHE 3.4 4.7 - - - -
207A PHE* 4.4 8.7 - - + +
292A THR* 4.3 0.4 - - - +
293A VAL* 1.3 72.1 - - - +
295A PHE* 1.3 66.0 + - - +
296A TRP* 3.3 41.6 - - - -
412A OGA 3.1 25.7 + - - +
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Residues in contact with PHE 295 (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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69A LEU* 3.8 26.9 - - + -
70A VAL* 3.8 21.3 - - + -
165A PHE* 3.6 25.8 - + + -
167A TRP* 3.8 29.6 - + - -
170A ILE* 3.6 17.5 - - + -
182A LEU* 4.1 3.4 - - + -
184A SER 4.0 0.2 - - - -
185A ASN* 3.2 24.2 - - - +
204A GLN 3.4 1.2 - - - +
205A ASN* 3.4 5.0 - - - -
206A PHE* 2.9 38.8 + - + +
208A ALA* 4.0 1.1 - - + -
293A VAL* 4.0 13.7 - - + -
294A ASN* 1.3 78.7 - - - +
296A TRP* 1.3 62.4 + - - +
297A TYR* 3.7 21.9 - - + -
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Residues in contact with TRP 296 (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 LEU* 3.4 6.3 - - - +
183A THR* 2.8 38.4 + - - +
184A SER* 3.2 27.1 + - - +
186A LEU* 3.8 26.5 - - + -
201A ASP* 4.0 12.8 - - - +
203A GLN* 3.4 26.5 - - + +
204A GLN 3.5 13.2 - - - -
205A ASN* 3.5 24.6 - - + +
294A ASN* 3.3 29.6 - - - -
295A PHE* 1.3 72.5 - - - +
297A TYR* 1.3 55.1 + - - +
412A OGA 3.2 23.4 + - - -
413A ZN 4.4 0.4 - - - -
985S VAL* 3.4 45.0 - - + +
986S ASN* 4.3 10.3 - - + -
987S ALA* 4.1 7.6 - - + -
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Residues in contact with TYR 297 (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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167A TRP* 4.6 4.2 - - - -
170A ILE* 3.4 40.7 + - + +
171A ASN* 4.7 3.0 + - - -
174A GLN* 3.7 29.2 - - + -
179A TRP* 3.7 32.8 - + + -
180A GLY 3.7 12.1 - - - +
181A GLN 3.4 3.6 - - - +
182A LEU* 3.5 49.0 - - + +
203A GLN* 3.1 9.1 - - - +
204A GLN* 2.8 38.4 + - + +
206A PHE* 4.6 1.8 - + - -
295A PHE* 3.7 22.6 - - + -
296A TRP* 1.3 76.1 - - - +
298A LYS* 1.3 66.6 + - - +
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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