Contacts of the strand formed by residues 246 - 252 (chain B) in PDB entry 2W8D
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 ASN 246 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244B GLY 3.7 1.8 + - - -
245B LYS* 1.3 73.4 - - - +
247B VAL* 1.3 55.6 + - - +
337B TYR* 4.2 2.2 - - - -
400B GLN* 3.3 29.7 + - - +
401B PRO* 3.4 10.9 - - - +
402B PHE* 3.1 52.7 + - + +
460B LEU* 4.7 2.4 + - - +
463B LYS* 3.1 22.4 + - - +
464B SER* 3.1 24.5 + - - +
465B ILE* 2.5 36.2 + - - +
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Residues in contact with VAL 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B LYS 3.8 0.9 + - - +
246B ASN* 1.3 76.8 - - - +
248B ILE* 1.3 65.9 + - - +
249B TYR* 3.6 35.7 - - + -
337B TYR* 4.7 3.6 - - + -
402B PHE* 3.0 8.7 + - - +
403B TYR* 3.4 26.0 - - + -
404B THR* 3.0 26.9 + - - +
465B ILE* 3.4 10.8 - - + +
467B VAL* 4.9 3.1 - - + -
530B ILE* 4.0 15.7 - - + -
534B LEU* 4.0 33.0 - - + -
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Residues in contact with ILE 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B VAL* 1.3 76.5 - - - +
249B TYR* 1.3 60.5 + - - +
250B VAL* 4.5 2.0 - - + -
395B LEU* 4.3 7.4 - - + -
402B PHE* 3.9 16.2 - - + -
404B THR* 3.4 20.2 - - - +
406B PHE* 3.9 20.4 - - + -
451B PHE* 4.0 15.7 - - + -
455B LEU* 3.8 35.4 - - + -
460B LEU* 5.5 1.8 - - + +
464B SER* 4.2 21.1 - - - +
465B ILE 2.8 11.6 + - - +
466B ILE* 3.2 11.7 - - + +
467B VAL 2.8 32.3 + - - +
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Residues in contact with TYR 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B VAL* 3.6 30.7 - - + -
248B ILE* 1.3 72.8 - - - +
250B VAL* 1.3 63.4 + - - +
304B MSE 3.5 44.4 + - + -
305B GLU* 4.8 2.2 - - - -
328B VAL* 5.7 1.7 - - - +
403B TYR* 3.4 30.8 + + - -
404B THR 2.9 16.1 + - - +
405B LYS* 3.4 14.8 - - + -
406B PHE* 2.8 29.3 + - - +
467B VAL* 3.2 21.5 - - + -
469B TYR* 3.8 21.8 - + + +
526B VAL* 3.7 7.0 - - + +
527B ALA* 4.5 4.7 - - - -
530B ILE* 3.6 25.5 - - + +
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Residues in contact with VAL 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248B ILE* 4.5 4.5 - - + -
249B TYR* 1.3 79.6 - - - +
251B SER* 1.3 60.8 + - - +
252B LEU* 3.5 20.5 + - + -
388B PHE* 4.0 10.1 - - + -
406B PHE* 3.4 13.5 - - + +
408B THR* 3.7 17.3 - - + -
448B ILE* 5.1 1.6 - - + -
451B PHE* 3.8 30.1 - - + -
466B ILE* 4.8 2.7 - - + -
467B VAL 2.8 10.3 + - - +
468B MSE 3.3 28.9 - - + +
469B TYR* 3.0 31.7 + - - +
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Residues in contact with SER 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249B TYR* 4.2 0.8 - - - +
250B VAL* 1.3 70.8 - - - +
252B LEU* 1.3 53.8 + - - +
253B GLU* 3.5 1.4 + - - -
297B TPO 4.4 7.4 + - - +
301B GLU* 5.9 0.2 - - - +
406B PHE 3.1 6.3 + - - -
407B ILE* 4.0 25.1 - - - +
408B THR* 2.6 37.4 + - - +
469B TYR* 3.5 29.2 + - - -
471B ASP* 3.6 29.3 + - - +
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Residues in contact with LEU 252 (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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250B VAL* 3.7 26.7 - - + +
251B SER* 1.3 68.3 + - - +
253B GLU* 1.3 66.9 + - - +
254B SER 3.2 2.9 + - - -
255B LEU* 3.4 33.5 + - + -
273B LEU* 4.7 4.7 - - + -
408B THR* 3.7 2.2 - - - -
444B LEU* 4.1 9.4 - - + -
448B ILE* 3.6 29.8 - - + -
468B MSE 3.8 24.7 - - + -
469B TYR 2.7 25.6 + - - +
470B GLY* 3.3 17.4 - - - +
471B ASP* 3.4 2.9 + - - -
504B PRO* 4.7 1.6 - - + -
506B PHE* 4.6 14.4 - - + -
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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
------------------------------------------------------------
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