Contacts of the strand formed by residues 265 - 271 (chain U) 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 U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146U GLU* 3.8 17.3 + - - -
163U ARG* 3.5 17.3 - - - +
197U GLU 4.4 2.9 + - - -
198U SER* 3.3 38.6 + - - -
200U LYS 3.2 17.7 + - - +
201U LEU* 3.3 9.1 - - + -
202U TYR* 3.1 23.7 + - - -
259U PHE* 4.4 1.6 - - - -
263U GLY 4.2 7.9 + - - -
264U LYS* 1.3 84.5 + - - +
266U ALA* 1.3 60.3 + - - +
313U LYS* 4.1 0.7 - - - -
320U SER 3.1 27.1 - - - -
321U GLY* 3.7 5.2 - - - -
322U SER* 3.3 27.1 + - - +
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Residues in contact with ALA 266 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201U LEU* 3.9 4.1 - - - +
202U TYR* 3.5 11.4 - - + +
204U VAL* 4.9 4.9 - - + -
256U GLY* 3.7 18.2 - - - +
259U PHE* 3.6 36.4 - - + +
265U HIS* 1.3 74.8 - - - +
267U LEU* 1.3 62.0 + - - +
322U SER* 3.3 7.8 + - - -
323U LEU* 3.2 9.8 - - + +
324U THR 3.1 21.3 + - - -
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Residues in contact with LEU 267 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148U VAL* 3.9 28.3 - - + -
161U ILE* 5.7 0.7 - - + -
184U THR* 4.4 9.4 - - + -
185U ILE* 4.1 14.2 - - + +
188U GLN* 5.8 0.7 - - + -
201U LEU* 3.8 18.4 - - + +
202U TYR 2.7 15.4 + - - +
203U CYS* 3.1 9.5 - - - +
204U VAL* 2.8 23.5 + - - -
266U ALA* 1.3 74.0 - - - +
268U ILE* 1.3 64.2 + - - +
269U VAL* 3.7 26.6 + - + -
324U THR* 3.5 28.5 - - + +
326U LEU* 3.9 18.4 - - + -
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Residues in contact with ILE 268 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204U VAL* 3.2 26.2 - - + +
206U VAL* 4.0 11.9 - - + -
252U ALA 3.5 30.1 - - - +
253U ALA* 3.9 4.0 - - - +
256U GLY* 5.4 2.0 - - - -
267U LEU* 1.3 75.1 - - - +
269U VAL* 1.3 63.4 + - - +
270U TYR* 3.4 44.2 + - + +
311U ALA* 5.4 0.4 - - + -
323U LEU* 3.7 24.5 - - + -
324U THR 2.9 18.9 + - - +
325U ALA* 3.5 6.4 - - + +
326U LEU 3.1 22.0 + - - -
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Residues in contact with VAL 269 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181U ALA* 4.1 20.4 - - + -
185U ILE* 4.6 9.9 - - + -
204U VAL 3.0 7.8 + - - +
205U TYR* 4.4 22.4 - - + -
206U VAL* 3.0 29.4 + - - +
267U LEU* 3.7 16.3 + - + -
268U ILE* 1.3 74.6 - - - +
270U TYR* 1.3 66.0 + - - +
271U ASP* 3.7 2.0 + - + -
326U LEU* 3.6 38.1 - - + +
328U VAL* 4.1 16.6 - - + -
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Residues in contact with TYR 270 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206U VAL* 4.0 9.4 - - + -
208U VAL* 6.2 0.7 - - + -
249U PRO* 3.3 46.9 - - + -
253U ALA* 3.4 18.0 - - - +
268U ILE* 3.4 45.4 - - + +
269U VAL* 1.3 73.7 - - - +
271U ASP* 1.3 61.1 + - - +
272U ASP* 4.4 1.8 - - - -
273U LEU* 3.6 24.5 - - + -
307U LEU* 3.5 21.8 + - + +
308U LEU* 4.1 23.7 - - + -
323U LEU* 5.8 1.6 - - - +
325U ALA* 4.5 5.6 - - + -
326U LEU 3.4 3.8 + - - -
327U PRO* 4.4 9.0 - - + -
328U VAL* 3.0 33.4 + - - +
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Residues in contact with ASP 271 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178U THR* 3.3 23.2 + - - +
205U TYR* 3.9 13.3 + - + +
206U VAL* 2.7 26.1 + - - +
207U ALA* 3.2 2.1 - - - -
208U VAL* 2.6 30.6 + - - +
210U GLN* 2.9 24.1 + - - +
269U VAL* 4.7 3.6 - - + -
270U TYR* 1.3 75.8 - - - +
272U ASP* 1.3 69.8 + - - +
328U VAL* 3.8 21.0 - - + +
614U PO4 5.3 1.0 + - - -
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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