Contacts of the strand formed by residues 265 - 271 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146L GLU* 3.3 25.8 + - - -
163L ARG* 3.2 15.4 + - - -
197L GLU 4.7 2.5 + - - -
198L SER* 2.9 38.9 + - - -
200L LYS 3.6 14.8 + - - +
201L LEU* 3.7 13.0 - - + -
202L TYR* 3.1 28.3 + - - -
259L PHE* 4.4 1.0 - - - +
263L GLY 5.0 4.6 + - - -
264L LYS* 1.3 76.9 - - - +
266L ALA* 1.3 61.4 + - - +
313L LYS* 4.1 0.9 - - - -
320L SER* 3.2 25.8 - - - -
321L GLY* 4.5 0.9 - - - -
322L SER* 2.7 28.7 + - - +
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Residues in contact with ALA 266 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201L LEU* 3.6 6.2 - - - +
202L TYR 3.1 12.8 - - - +
204L VAL* 5.3 2.0 - - + -
256L GLY* 3.8 15.9 - - - +
259L PHE* 3.8 27.8 - - + -
265L HIS* 1.3 76.0 - - - +
267L LEU* 1.3 54.4 + - - +
322L SER* 2.9 8.0 + - - +
323L LEU* 3.3 12.6 - - + +
324L THR* 2.7 34.0 + - - -
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Residues in contact with LEU 267 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148L VAL* 3.9 27.6 - - + -
161L ILE* 5.9 0.7 - - + -
184L THR* 4.0 10.3 - - + -
185L ILE* 4.4 15.9 - - + -
188L GLN* 5.5 0.2 - - - +
201L LEU* 3.7 20.3 - - + +
202L TYR 2.8 8.0 + - - +
203L CYS* 3.3 10.1 - - + -
204L VAL* 2.7 33.9 + - - +
266L ALA* 1.3 75.2 - - - +
268L ILE* 1.3 58.1 + - - +
269L VAL* 3.7 27.1 - - + -
323L LEU* 4.6 0.4 - - - -
324L THR* 3.5 17.9 - - + +
326L LEU* 3.6 24.7 - - + -
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Residues in contact with ILE 268 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204L VAL* 3.1 28.0 - - + +
206L VAL* 3.4 19.1 - - + -
252L ALA* 4.4 7.6 - - + +
253L ALA* 5.3 1.1 - - - -
256L GLY* 6.0 0.7 - - - -
267L LEU* 1.3 76.2 - - - +
269L VAL* 1.3 72.4 + - - +
270L TYR* 3.3 56.3 + - + +
311L ALA* 5.6 0.2 - - + -
323L LEU* 4.1 19.7 - - + -
324L THR 2.7 20.4 + - - +
325L ALA* 3.8 5.4 - - + -
326L LEU* 2.7 33.3 + - - +
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Residues in contact with VAL 269 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181L ALA* 3.9 25.8 - - + +
185L ILE* 4.3 14.4 - - + -
204L VAL 3.0 9.1 + - - +
205L TYR* 3.9 24.5 - - + -
206L VAL* 2.9 30.8 + - - +
267L LEU* 3.7 20.2 - - + -
268L ILE* 1.3 78.6 - - - +
270L TYR* 1.3 60.6 + - - +
271L ASP* 3.4 5.7 + - + +
326L LEU* 3.7 27.1 - - + +
328L VAL* 4.0 11.4 - - + -
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Residues in contact with TYR 270 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206L VAL* 4.3 6.5 - - + -
208L VAL* 6.2 0.2 - - - -
249L PRO* 3.2 41.5 - - + -
253L ALA* 3.4 23.1 - - + +
268L ILE* 3.3 44.9 - - + +
269L VAL* 1.3 69.5 - - - +
271L ASP* 1.3 58.2 + - - +
272L ASP* 4.2 0.9 - - - -
273L LEU* 3.5 25.6 + - + -
307L LEU* 3.6 22.3 + - + +
308L LEU* 4.1 23.3 - - + -
323L LEU* 5.1 4.0 - - - +
325L ALA* 4.2 3.8 - - + -
326L LEU 3.5 4.6 + - - -
327L PRO* 3.8 18.2 - - + -
328L VAL* 2.7 34.1 + - - +
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Residues in contact with ASP 271 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178L THR* 3.3 23.7 + - - +
205L TYR* 3.2 21.3 + - + +
206L VAL* 2.8 23.8 + - - +
207L ALA* 3.2 2.3 - - - -
208L VAL* 2.7 28.4 + - - -
210L GLN* 3.2 18.8 + - - +
269L VAL* 3.4 9.2 + - + +
270L TYR* 1.3 73.4 - - - +
272L ASP* 1.3 71.0 + - - +
275L LYS* 5.0 0.7 + - - -
328L VAL* 4.2 23.4 - - + +
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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