Contacts of the strand formed by residues 258 - 265 (chain L) in PDB entry 1KYO
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 ALA 258 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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257L LYS* 1.3 76.5 - - - +
259L TRP* 1.3 63.8 + - - +
260L ILE* 4.0 3.1 + - + +
331L THR 4.0 0.7 - - - +
332L ALA* 3.6 1.2 - - - -
333L THR* 3.0 44.7 + - + +
336L VAL* 4.6 3.4 - - + -
339L ILE* 4.1 7.4 - - + -
435L THR 3.5 6.3 - - - -
437L GLN 3.3 30.3 - - - +
438L ILE* 3.9 9.4 - - + -
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Residues in contact with TRP 259 (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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155L HIS* 3.9 28.5 - + + -
156L PRO* 4.0 32.1 - - + +
159L VAL* 4.0 18.2 - - + +
255L LEU* 3.8 21.5 - - + -
256L PRO* 4.3 14.1 - - + -
257L LYS* 3.2 57.8 - - + +
258L ALA* 1.3 71.4 - - - +
260L ILE* 1.3 67.1 + - - +
331L THR 3.3 6.5 - - - +
332L ALA* 3.5 23.2 - - + +
434L GLY* 3.4 1.6 - - - -
435L THR* 3.0 43.1 + - + +
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Residues in contact with ILE 260 (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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159L VAL* 4.2 2.0 - - - -
258L ALA* 4.1 8.7 - - + +
259L TRP* 1.3 83.4 - - - +
261L SER* 1.3 67.7 + - - +
262L LEU* 5.1 5.2 - - + -
329L PHE* 5.0 2.2 - - + -
330L SER* 3.4 1.0 - - - -
331L THR* 2.6 57.6 + - + +
333L THR* 5.5 2.5 - - + -
339L ILE* 5.2 10.3 - - + -
342L LEU* 5.4 2.7 - - + -
343L ILE* 3.4 33.4 - - + -
432L ILE* 5.3 2.5 - - + -
433L ALA 3.4 11.7 - - - +
434L GLY* 4.6 1.1 - - - -
438L ILE* 4.1 19.5 - - + -
441L LEU* 3.8 23.6 - - + -
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Residues in contact with SER 261 (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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156L PRO 4.6 2.3 + - - -
159L VAL* 3.6 19.1 - - - +
160L LEU* 4.2 14.1 + - - +
163L LEU* 3.8 19.1 - - - +
260L ILE* 1.3 75.0 - - - +
262L LEU* 1.3 64.4 + - - +
317L PHE* 5.1 0.9 - - - -
329L PHE* 3.3 6.5 - - - -
330L SER* 2.9 28.7 + - - -
432L ILE* 3.8 3.1 - - - +
433L ALA 3.1 29.7 + - - +
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Residues in contact with LEU 262 (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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163L LEU* 4.4 2.2 - - - +
260L ILE* 5.1 3.1 - - + -
261L SER* 1.3 77.3 - - - +
263L ALA* 1.3 69.0 + - - +
317L PHE* 4.3 0.8 - - - -
328L GLY* 3.2 1.9 - - - -
329L PHE* 2.8 46.1 + - + +
343L ILE* 4.5 11.0 - - + -
347L LEU* 4.4 13.5 - - + -
350L TRP* 3.5 30.1 - - + -
430L ILE* 4.5 16.4 - - + -
431L ALA 3.2 12.3 - - - +
432L ILE* 4.3 16.6 - - + -
447L ILE* 3.8 29.4 - - + -
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Residues in contact with ALA 263 (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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163L LEU* 3.9 21.2 - - + +
243L PHE* 4.5 1.8 - - - -
262L LEU* 1.3 81.9 - - - +
264L VAL* 1.3 68.5 + - - +
317L PHE* 4.1 9.6 - - + -
326L LEU* 4.1 4.9 - - + -
327L TRP 3.4 22.9 - - - +
328L GLY* 3.9 1.8 - - - +
350L TRP* 5.2 0.2 - - - -
430L ILE* 3.4 4.0 - - - +
431L ALA* 2.7 41.7 + - - +
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Residues in contact with VAL 264 (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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243L PHE* 3.7 10.3 - - - -
263L ALA* 1.3 73.2 - - - +
265L GLU* 1.3 72.4 + - - +
266L GLY 3.1 0.9 + - - -
326L LEU* 3.3 9.4 - - - +
327L TRP* 2.9 42.6 + - + +
350L TRP* 5.1 4.5 - - + -
424L ARG* 3.6 18.6 - - + +
425L LEU* 3.6 31.0 - - + -
428L GLN* 5.0 3.4 - - + +
429L ASP 3.7 8.1 - - - +
430L ILE* 3.6 28.0 - - + -
451L MET* 4.6 7.9 - - + -
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Residues in contact with GLU 265 (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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242L ALA* 5.1 1.0 - - - -
243L PHE* 3.4 49.2 + - + +
264L VAL* 1.3 77.6 - - - +
266L GLY* 1.3 70.4 + - - +
324L SER* 3.4 24.5 + - - +
325L GLY 3.8 4.5 - - - -
424L ARG* 3.6 40.3 + - - +
429L ASP 5.0 0.2 + - - -
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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