Contacts of the strand formed by residues 247 - 251 (chain B) in PDB entry 3HYW
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 247 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B THR* 3.5 23.3 - - + -
132B THR* 4.0 9.2 - - + -
135B LYS* 3.9 45.1 - - + +
136B LEU* 3.6 35.2 - - + -
139B LEU* 4.0 25.8 - - + -
145B PRO 3.2 3.7 + - - +
146B VAL* 3.3 21.9 - - + -
147B VAL 3.0 22.9 + - - -
163B PHE* 3.9 22.2 - + - -
167B LEU* 4.3 2.0 - - + -
245B ALA* 4.2 0.3 - - - +
246B LYS* 1.3 80.7 - - + +
248B THR* 1.3 77.9 + - - +
249B MET* 4.1 0.9 - - + -
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Residues in contact with THR 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119B ASN 4.3 1.6 + - - -
120B SER* 2.6 35.0 + - - -
121B THR* 2.7 29.5 + - - -
135B LYS* 3.7 8.4 + - - +
147B VAL* 3.0 14.8 - - + +
226B ILE* 3.6 10.2 - - + +
227B GLU 5.7 1.3 - - - +
230B LYS 5.6 0.2 - - - +
231B VAL* 3.6 19.1 - - + -
245B ALA* 3.6 23.8 - - + +
246B LYS 5.6 0.2 - - - -
247B PHE* 1.3 87.8 - - - +
249B MET* 1.3 54.9 + - - +
250B PHE* 3.9 7.2 - - - -
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Residues in contact with MET 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B THR* 3.3 24.2 - - - +
122B SER* 3.9 12.6 - - - -
123B ILE* 4.0 18.4 - - + -
132B THR* 4.4 0.2 - - + -
147B VAL 3.2 5.1 + - - -
148B ILE* 3.3 11.7 - - + +
149B GLY 3.2 21.1 + - - -
160B ALA* 4.0 9.2 - - + -
163B PHE* 3.7 54.3 - - + -
247B PHE* 4.1 1.9 - - + -
248B THR* 1.3 75.3 - - - +
250B PHE* 1.3 68.1 + - - +
251B MET* 3.3 33.4 - - + -
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Residues in contact with PHE 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B PHE* 5.3 0.2 - - - -
116B GLN* 3.8 24.4 + - + +
120B SER* 3.4 12.7 + - - +
121B THR 3.0 16.4 + - - +
122B SER* 3.7 8.0 - - - -
147B VAL* 3.6 41.5 - - + -
148B ILE 4.0 0.9 - - - -
149B GLY* 3.3 35.4 - - - -
150B ALA* 3.5 12.1 - - - -
151B ILE* 4.2 7.0 - - + -
185B ILE* 3.7 4.9 - - + -
223B VAL* 3.7 20.4 - - + -
226B ILE* 3.8 24.2 - - + -
231B VAL* 4.1 11.9 - - + -
248B THR* 3.9 7.6 - - - -
249B MET* 1.3 82.3 - - - +
251B MET* 1.3 61.2 + - - +
252B PRO* 3.6 7.1 - - - +
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Residues in contact with MET 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B GLN* 3.5 4.4 + - - -
123B ILE* 3.6 13.2 - - + -
124B CYS* 4.1 20.4 - - - -
149B GLY 3.0 12.2 + - - +
150B ALA* 4.3 2.5 - - + -
151B ILE* 3.4 14.6 + - - +
154B VAL* 3.3 32.1 - - + +
156B CSS 3.6 20.6 - - - +
159B PRO* 3.6 19.1 - - + -
160B ALA* 3.4 35.7 - - + +
249B MET* 3.3 33.6 + - + -
250B PHE* 1.3 69.2 - - - +
252B PRO* 1.3 66.8 - - + +
254B PHE* 6.4 0.2 - - - -
700B H2S 4.6 1.6 - - - -
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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