Contacts of the strand formed by residues 202 - 208 (chain S) 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 TYR 202 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106S LEU* 3.7 20.4 - - + +
192S ASN* 5.2 3.4 - - - -
197S GLU* 3.4 27.0 + - - -
200S LYS* 3.9 23.1 + - + +
201S LEU* 1.3 76.4 - - - +
203S CYS* 1.3 60.4 + - - +
204S VAL* 5.4 0.7 - - + -
230S TYR* 3.6 35.9 - - + +
232S ILE* 5.0 1.8 - - + -
259S PHE* 3.3 44.0 - + + -
264S LYS* 3.9 23.7 + - + -
265S HIS 3.0 14.7 + - - +
266S ALA* 3.1 7.7 - - + -
267S LEU* 2.8 27.2 + - - +
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Residues in contact with CYS 203 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185S ILE* 3.5 49.8 - - + -
188S GLN* 3.9 16.8 - - - -
201S LEU 3.7 11.4 - - - -
202S TYR* 1.3 80.5 - - - +
204S VAL* 1.3 63.6 + - - +
205S TYR 3.9 0.7 - - - -
230S TYR* 3.5 11.1 + - - -
231S SER* 3.1 10.8 - - - -
232S ILE* 2.8 28.8 + - - +
267S LEU* 3.4 16.8 - - - +
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Residues in contact with VAL 204 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185S ILE* 5.9 0.2 - - - -
202S TYR* 5.4 0.7 - - + -
203S CYS* 1.3 76.8 - - - +
205S TYR* 1.3 60.2 + - - +
206S VAL* 4.6 0.2 - - + -
232S ILE* 3.5 31.2 - - + +
234S VAL* 5.1 0.4 - - + -
252S ALA* 3.5 33.7 - - + +
255S ILE* 4.7 4.3 - - + -
256S GLY* 3.7 29.2 - - - +
259S PHE* 5.3 1.6 - - + -
266S ALA* 4.9 7.9 - - + -
267S LEU 2.8 10.8 + - - +
268S ILE* 3.0 22.9 - - + +
269S VAL* 2.9 22.9 + - - -
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Residues in contact with TYR 205 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178S THR* 3.8 21.4 - - + +
181S ALA* 5.5 3.1 - - + -
182S LEU* 6.0 3.8 - - + -
185S ILE* 4.5 21.5 - - + -
203S CYS* 3.9 3.0 + - - +
204S VAL* 1.3 74.5 - - - +
206S VAL* 1.3 95.4 + - - +
207S ALA* 3.5 17.5 - - + -
210S GLN* 3.0 25.9 + - - -
215S VAL* 5.9 1.3 - - + -
218S LEU* 3.8 31.3 - - + +
222S LEU* 6.1 1.1 - - + -
231S SER* 5.7 1.1 - - - -
232S ILE 3.1 8.5 + - - +
233S ILE* 3.6 25.1 - - + -
234S VAL* 3.1 25.3 + - - +
269S VAL* 4.1 21.3 - - + +
271S ASP* 3.7 15.8 + - + -
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Residues in contact with VAL 206 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204S VAL 4.0 0.4 - - - +
205S TYR* 1.3 89.2 - - - +
207S ALA* 1.3 61.3 + - - +
208S VAL* 3.5 23.6 - - + -
234S VAL 3.4 9.0 - - - +
248S ALA* 4.3 22.2 - - + +
249S PRO* 4.4 4.7 - - + -
252S ALA* 3.7 23.1 - - + -
268S ILE* 3.8 20.9 - - + -
269S VAL 3.0 17.6 + - - +
270S TYR* 4.3 10.3 - - + -
271S ASP* 2.8 24.3 + - - +
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Residues in contact with ALA 207 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205S TYR* 3.5 15.2 - - + -
206S VAL* 1.3 70.5 - - - +
208S VAL* 1.3 61.3 + - - +
209S GLY 4.1 0.2 + - - -
210S GLN* 3.4 23.8 - - - +
215S VAL* 3.6 24.0 - - + -
233S ILE* 5.3 0.9 - - + -
234S VAL 3.0 9.6 + - - +
235S ALA* 4.0 10.3 - - + +
236S ALA 2.9 28.2 + - - -
237S THR* 4.0 1.9 + - - -
271S ASP 3.5 3.4 - - - -
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Residues in contact with VAL 208 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206S VAL* 3.5 28.0 - - + -
207S ALA* 1.3 71.9 - - - +
209S GLY* 1.3 61.8 + - - +
210S GLN* 3.0 14.9 + - - +
236S ALA* 3.9 3.1 - - + +
245S GLN* 3.7 40.4 - - + +
248S ALA* 4.2 10.5 - - + -
249S PRO* 4.3 10.5 - - + -
270S TYR* 6.1 0.4 - - - -
271S ASP 2.8 19.9 + - - +
272S ASP 3.7 11.6 + - - +
275S LYS* 3.4 15.4 - - - +
276S GLN* 4.4 17.5 - - + +
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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