Contacts of the strand formed by residues 265 - 271 (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 HIS 265 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146J GLU* 3.2 32.3 + - - -
163J ARG* 3.0 25.4 + - - +
197J GLU 3.9 5.7 + - - -
198J SER* 3.4 31.1 + - - -
200J LYS 3.5 14.6 + - - +
201J LEU* 3.5 11.1 - - + -
202J TYR* 2.9 32.6 + - - -
259J PHE* 4.6 0.9 - - - -
263J GLY 6.2 0.2 - - - -
264J LYS* 1.3 84.7 + - - +
266J ALA* 1.3 60.3 + - - +
320J SER 3.7 20.0 - - - -
321J GLY* 4.5 0.2 - - - -
322J SER* 2.9 25.6 + - - +
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Residues in contact with ALA 266 (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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201J LEU* 3.5 6.4 - - - +
202J TYR* 3.1 10.3 - - + +
204J VAL* 5.4 2.0 - - + -
256J GLY* 3.7 16.8 - - - +
259J PHE* 3.7 29.6 - - + -
265J HIS* 1.3 76.2 - - - +
267J LEU* 1.3 61.6 + - - +
322J SER* 3.3 8.4 + - - +
323J LEU* 3.2 14.3 - - + +
324J THR* 2.9 24.6 + - - -
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Residues in contact with LEU 267 (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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148J VAL* 4.7 10.1 - - + -
184J THR* 4.0 20.2 - - + +
185J ILE* 4.7 3.6 - - + -
201J LEU* 3.5 17.0 - - + +
202J TYR 2.6 13.8 + - - +
203J CYS* 3.3 23.4 - - + -
204J VAL* 2.6 35.4 + - - +
266J ALA* 1.3 74.7 - - - +
268J ILE* 1.3 58.5 + - - +
269J VAL* 4.5 7.6 - - + -
323J LEU* 4.7 0.7 - - - -
324J THR* 3.5 36.3 - - + +
326J LEU* 3.7 36.6 - - + -
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Residues in contact with ILE 268 (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* 3.1 20.4 - - + +
206J VAL* 3.8 7.4 - - + -
252J ALA* 3.8 37.5 - - + +
253J ALA* 3.9 3.1 - - - +
256J GLY* 5.9 0.4 - - - -
267J LEU* 1.3 76.8 - - - +
269J VAL* 1.3 60.4 + - - +
270J TYR* 3.5 41.3 + - + +
311J ALA* 5.5 0.2 - - + -
323J LEU* 4.1 20.2 - - + -
324J THR 2.8 21.0 + - - +
325J ALA* 3.9 9.6 - - + +
326J LEU* 2.7 32.7 + - - +
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Residues in contact with VAL 269 (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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181J ALA* 3.9 28.9 - - + +
185J ILE* 5.0 7.4 - - + -
204J VAL 2.8 10.5 + - - +
205J TYR* 4.1 26.3 - - + -
206J VAL* 2.9 31.0 + - - +
267J LEU* 4.5 9.2 - - + -
268J ILE* 1.3 75.6 - - - +
270J TYR* 1.3 62.7 + - - +
271J ASP* 3.4 2.2 + - + +
326J LEU* 3.2 40.4 - - + +
328J VAL* 4.2 13.7 - - + -
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Residues in contact with TYR 270 (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 16.2 - - + -
249J PRO* 3.5 25.8 - - + -
253J ALA* 3.8 7.3 - - - +
268J ILE* 3.5 45.9 - - + +
269J VAL* 1.3 69.6 - - - +
271J ASP* 1.3 58.9 + - - +
272J ASP* 3.5 4.4 - - - -
273J LEU* 3.5 24.0 - - + -
307J LEU* 3.3 44.3 + - + +
308J LEU* 4.7 6.5 - - + -
311J ALA* 5.7 1.6 - - - +
323J LEU* 5.5 2.1 - - - +
325J ALA* 4.2 14.0 - - + +
326J LEU 3.1 6.3 + - - -
327J PRO* 4.0 22.4 - - + -
328J VAL* 2.7 33.9 + - - +
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Residues in contact with ASP 271 (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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177J LYS* 5.5 1.4 + - - -
178J THR* 3.1 25.4 + - - +
205J TYR* 3.0 29.9 + - + +
206J VAL* 3.0 17.5 + - - +
208J VAL* 3.0 27.8 + - - +
210J GLN* 3.3 22.9 + - - +
269J VAL* 3.4 1.7 + - + +
270J TYR* 1.3 74.5 - - - +
272J ASP* 1.3 66.8 + - - +
275J LYS* 5.0 0.7 + - - -
328J VAL* 4.0 22.2 - - + +
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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