Contacts of the strand formed by residues 250 - 256 (chain M) in PDB entry 3FKS
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 ASP 250 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149M ARG* 6.1 0.7 - - - -
178M HIS* 3.5 25.0 + - + +
179M GLY 3.6 11.5 - - - +
180M GLY* 4.0 1.6 - - - -
181M PHE 3.4 18.6 + - - +
249M GLN* 1.3 78.4 - - - +
251M VAL* 1.3 62.1 + - - +
302M GLY* 5.6 0.5 - - - -
303M SER* 3.4 24.5 + - - +
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Residues in contact with VAL 251 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178M HIS* 4.5 2.2 - - - -
181M PHE 3.8 5.8 - - - +
182M SER* 5.1 0.2 - - - -
183M VAL* 4.5 11.4 - - + -
240M ALA* 3.6 35.7 - - + +
243M PHE* 3.5 33.2 - - + -
244M ARG* 3.7 15.0 - - + +
249M GLN* 3.8 6.3 - - + +
250M ASP* 1.3 74.1 - - - +
252M LEU* 1.3 69.7 + - - +
253M LEU* 3.9 4.9 - - + +
303M SER 3.1 10.3 + - - +
304M VAL* 3.6 9.6 - - + -
305M THR* 3.1 27.4 + - - -
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Residues in contact with LEU 252 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174M ILE* 3.6 29.2 - - + -
175M ALA* 3.9 14.4 - - - -
178M HIS* 4.0 24.5 - - + +
181M PHE 3.2 8.4 + - - +
182M SER* 3.2 23.4 - - - +
183M VAL 2.8 23.2 + - - +
251M VAL* 1.3 75.5 - - - +
253M LEU* 1.3 61.5 + - - +
254M PHE* 3.3 36.1 - - + -
305M THR* 3.3 27.8 - - + +
307M VAL* 4.7 4.5 - - + -
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Residues in contact with LEU 253 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183M VAL* 3.1 37.2 - - + +
185M THR* 4.0 12.1 - - - +
236M GLY 4.4 3.4 - - - +
237M LEU* 3.8 14.1 - - + -
240M ALA* 4.1 13.0 - - + -
251M VAL* 3.9 5.2 + - + -
252M LEU* 1.3 74.6 - - - +
254M PHE* 1.3 64.2 + - - +
255M ILE* 3.7 25.4 - - + -
296M ILE* 3.6 28.9 - - + -
304M VAL* 4.1 14.4 - - + -
305M THR 3.1 10.1 + - - +
306M SER* 4.2 3.1 - - - +
307M VAL 3.0 26.3 + - - -
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Residues in contact with PHE 254 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167M ILE* 4.9 7.9 - - + -
170M LEU* 4.4 13.2 - - + -
171M ILE* 3.4 50.0 - - + -
174M ILE* 4.9 4.5 - - + -
175M ALA* 5.0 1.8 - - + -
182M SER* 5.0 6.3 - - - -
183M VAL 2.7 14.4 + - - +
184M PHE* 3.4 25.0 - + + -
185M THR* 2.7 35.7 + - - +
252M LEU* 3.3 48.7 - - + -
253M LEU* 1.3 74.3 - - - +
255M ILE* 1.3 59.4 + - - +
256M ASP* 4.2 0.4 - - + -
307M VAL* 3.8 31.2 - - + +
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Residues in contact with ILE 255 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167M ILE* 5.4 0.2 - - - +
185M THR* 3.8 8.3 - - + +
187M VAL* 4.3 17.3 - - + -
233M ALA* 5.3 8.1 - - + +
237M LEU* 4.5 4.3 - - + -
253M LEU* 3.7 25.4 - - + -
254M PHE* 1.3 77.5 - - - +
256M ASP* 1.3 64.6 + - - +
257M ASN* 4.4 0.2 - - - -
258M ILE* 4.1 26.9 + - + +
296M ILE* 3.6 31.6 - - + -
306M SER* 4.0 0.9 - - - +
307M VAL 3.4 8.5 + - - +
308M GLN* 3.4 24.5 - - + +
309M ALA 3.0 27.4 + - - +
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Residues in contact with ASP 256 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163M LYS* 5.4 0.5 - - - +
164M THR* 4.2 12.5 + - - +
167M ILE* 3.0 36.9 - - + +
184M PHE* 4.6 10.0 - - + -
185M THR 3.1 8.9 + - - +
186M GLY* 3.4 8.5 - - - -
187M VAL 2.7 24.4 + - - -
189M GLU* 2.8 43.5 - - - +
254M PHE 4.2 0.2 - - - -
255M ILE* 1.3 78.9 - - - +
257M ASN* 1.3 67.8 + - - +
309M ALA* 3.5 7.3 - - + +
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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