Contacts of the strand formed by residues 250 - 256 (chain N) 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 N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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134N LEU* 4.4 19.0 - - + +
149N ARG* 2.8 38.0 + - - -
174N ILE* 3.7 21.5 - - - +
178N HIS* 4.3 25.3 + - + +
180N GLY* 3.8 7.9 - - - -
248N GLY 4.8 2.6 - - - +
249N GLN* 1.3 74.4 - - - +
251N VAL* 1.3 65.6 + - - +
252N LEU* 4.7 0.7 - - - +
302N GLY* 4.3 0.9 - - - -
303N SER* 2.7 26.6 + - - +
305N THR* 5.3 0.9 - - - +
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Residues in contact with VAL 251 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181N PHE 3.1 22.9 - - - +
183N VAL* 4.5 6.1 - - + -
240N ALA* 3.4 42.0 - - + +
243N PHE* 3.6 23.8 - - + -
244N ARG 3.8 7.2 - - - +
249N GLN* 3.8 8.7 - - + +
250N ASP* 1.3 77.3 - - - +
252N LEU* 1.3 76.5 + - - +
303N SER 2.8 14.9 + - - +
304N VAL* 3.9 10.1 - - + -
305N THR* 2.9 24.5 + - - +
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Residues in contact with LEU 252 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134N LEU* 4.2 12.6 - - + -
147N TYR* 5.9 2.2 - - + -
170N LEU* 3.7 19.3 - - + +
174N ILE* 3.4 35.9 - - + -
181N PHE 2.9 6.1 + - - -
182N SER* 3.3 25.7 - - - +
183N VAL* 2.6 35.3 + - - +
250N ASP 4.7 0.2 - - - +
251N VAL* 1.3 83.2 - - - +
253N LEU* 1.3 55.5 + - - +
254N PHE* 4.1 17.0 - - + -
304N VAL* 5.2 0.2 - - - -
305N THR* 3.1 27.8 - - + +
306N SER* 5.4 0.2 - - - -
307N VAL* 5.0 13.0 - - + +
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Residues in contact with LEU 253 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183N VAL* 3.2 27.8 - - + +
185N THR* 3.4 18.8 - - - +
236N GLY 4.0 12.1 - - - +
237N LEU* 3.4 41.5 - - + -
240N ALA* 4.5 4.3 - - + -
252N LEU* 1.3 72.8 - - - +
254N PHE* 1.3 60.8 + - - +
255N ILE* 3.5 20.8 + - + +
292N LEU* 6.2 1.1 - - + -
296N ILE* 4.1 6.1 - - + -
304N VAL* 4.3 9.4 - - + -
305N THR 2.9 10.6 + - - +
306N SER* 3.1 39.0 + - - +
307N VAL 3.4 3.2 + - - +
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Residues in contact with PHE 254 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155N LEU* 6.1 0.2 - - + -
167N ILE* 3.7 33.4 - - + -
170N LEU* 3.8 34.3 - - + -
171N ILE* 3.7 23.6 - - + -
182N SER* 4.2 15.7 - - - -
183N VAL 3.1 7.9 + - - -
184N PHE* 3.4 32.5 - + + -
185N THR* 2.7 31.4 + - - +
252N LEU* 4.2 14.8 - - + -
253N LEU* 1.3 71.5 - - - +
255N ILE* 1.3 64.3 + - - +
256N ASP* 6.1 0.2 - - + -
307N VAL* 3.4 40.6 - - + +
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Residues in contact with ILE 255 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185N THR* 3.6 13.2 - - + -
187N VAL* 3.7 21.8 - - + -
233N ALA* 4.7 14.4 - - + +
253N LEU* 3.5 34.3 - - + +
254N PHE* 1.3 81.6 - - - +
256N ASP* 1.3 65.2 + - - +
257N ASN* 4.3 0.7 - - - -
258N ILE* 4.3 26.7 - - + -
261N PHE* 5.5 0.2 - - + -
292N LEU* 5.6 4.0 - - + -
307N VAL 3.5 6.3 + - - +
308N GLN* 3.4 35.6 - - + +
309N ALA 3.0 27.9 + - - +
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Residues in contact with ASP 256 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163N LYS* 3.4 22.5 + - - -
167N ILE* 5.7 2.1 - - + +
184N PHE* 4.4 24.7 - - + -
185N THR 3.2 7.4 + - - +
186N GLY* 3.4 6.6 - - - -
187N VAL 2.7 28.5 + - - +
189N GLU* 3.6 15.0 - - - +
254N PHE* 6.1 0.2 - - + -
255N ILE* 1.3 78.4 - - - +
257N ASN* 1.3 57.0 + - - +
260N ARG* 3.9 1.5 + - - -
309N ALA* 3.2 24.4 - - + +
610N PO4 3.2 22.6 + - - -
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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