Contacts of the strand formed by residues 202 - 208 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106J LEU* 3.4 40.4 - - + -
192J ASN* 4.8 2.5 - - - +
197J GLU* 3.1 27.9 + - - -
200J LYS* 4.7 17.1 + - + +
201J LEU* 1.3 74.7 - - - +
203J CYS* 1.3 54.0 + - - +
204J VAL* 5.5 0.9 - - + -
230J TYR* 3.7 16.8 - - + +
259J PHE* 3.3 32.5 - + + -
264J LYS* 3.5 33.8 + - + -
265J HIS 2.9 19.1 + - - +
266J ALA* 3.1 7.2 - - + -
267J LEU* 2.6 34.5 + - - +
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Residues in contact with CYS 203 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106J LEU* 4.8 0.3 - - - +
185J ILE* 3.8 44.0 - - + -
188J GLN* 4.4 9.0 - - - -
201J LEU* 3.9 9.9 - - - -
202J TYR* 1.3 79.6 - - - +
204J VAL* 1.3 60.3 + - - +
205J TYR 4.2 0.4 - - - -
230J TYR* 3.1 15.3 + - + +
231J SER* 3.2 8.2 - - - -
232J ILE* 2.8 32.7 + - - +
267J LEU* 3.3 31.0 - - + +
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Residues in contact with VAL 204 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185J ILE* 5.9 1.1 - - - -
202J TYR* 5.5 1.1 - - + -
203J CYS* 1.3 81.7 - - - +
205J TYR* 1.3 60.5 + - - +
206J VAL* 4.4 2.7 - - + -
232J ILE* 3.3 29.8 - - + +
234J VAL* 4.5 8.5 - - + -
252J ALA* 3.9 19.1 - - + +
255J ILE* 5.1 1.3 - - + -
256J GLY* 4.3 25.1 - - - +
259J PHE* 5.4 1.8 - - + -
266J ALA* 5.4 3.4 - - + -
267J LEU 2.6 16.6 + - - +
268J ILE* 3.1 25.8 - - + +
269J VAL* 2.8 28.4 + - - +
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Residues in contact with TYR 205 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178J THR* 3.4 19.4 - - + +
181J ALA* 5.3 3.6 - - + -
182J LEU* 5.8 3.8 - - + -
185J ILE* 4.4 21.1 - - + -
203J CYS* 4.2 0.6 - - - +
204J VAL* 1.3 72.3 - - - +
206J VAL* 1.3 68.5 + - - +
207J ALA* 3.7 22.2 + - + -
210J GLN* 3.3 15.3 + - - -
215J VAL* 6.3 0.7 - - + -
218J LEU* 3.3 35.1 - - + +
222J LEU* 5.7 0.9 - - + -
231J SER* 5.9 1.0 - - - -
232J ILE 2.8 9.1 + - - +
233J ILE* 3.6 25.1 - - + +
234J VAL 3.1 23.6 + - - -
269J VAL* 4.0 29.4 - - + -
271J ASP* 3.0 26.6 + - + -
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Residues in contact with VAL 206 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204J VAL* 4.4 0.4 - - + -
205J TYR* 1.3 75.2 - - - +
207J ALA* 1.3 59.6 + - - +
208J VAL* 3.8 20.9 - - + -
234J VAL* 3.6 9.9 - - + +
248J ALA* 4.2 6.1 - - + +
249J PRO* 4.0 22.7 - - + -
252J ALA* 3.6 25.6 - - + -
268J ILE* 3.8 17.7 - - + -
269J VAL 2.9 18.4 + - - +
270J TYR* 3.8 17.3 - - + -
271J ASP* 3.0 30.0 + - - +
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Residues in contact with ALA 207 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205J TYR* 3.7 15.7 + - + -
206J VAL* 1.3 69.8 - - - +
208J VAL* 1.3 62.8 + - - +
210J GLN* 4.0 12.6 - - + +
215J VAL* 3.8 31.4 - - + -
233J ILE* 5.3 2.0 - - + -
234J VAL 3.0 14.3 + - - +
235J ALA* 4.4 7.2 - - + -
236J ALA 3.0 28.2 + - - +
237J THR* 4.4 1.5 + - + -
271J ASP 3.7 3.4 - - - -
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Residues in contact with VAL 208 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206J VAL* 3.8 24.0 - - + +
207J ALA* 1.3 79.2 - - - +
209J GLY* 1.3 61.5 + - - +
210J GLN* 3.2 10.3 + - - +
236J ALA* 3.7 2.9 - - + -
245J GLN* 4.0 27.1 - - + +
248J ALA* 4.1 16.6 - - + -
249J PRO* 4.3 10.1 - - + -
271J ASP 3.0 19.5 + - - +
272J ASP 3.6 11.5 + - - +
275J LYS* 3.4 20.0 - - - +
276J GLN* 4.2 23.6 - - - +
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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