Contacts of the strand formed by residues 325 - 333 (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 GLY 325 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168L PHE* 3.4 8.1 - - - -
265L GLU* 3.8 3.3 - - - -
266L GLY* 2.8 23.6 + - - +
267L GLU 4.1 6.7 - - - -
319L LEU 3.1 13.9 - - - -
321L TYR* 4.1 9.6 - - - -
324L SER* 1.3 81.0 + - - +
326L LEU* 1.3 73.3 + - - +
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Residues in contact with LEU 326 (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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160L LEU* 5.9 0.4 - - + -
163L LEU* 3.4 24.7 - - + -
164L HIS* 3.7 35.9 - - + +
167L ALA* 3.9 11.0 - - + -
168L PHE* 3.8 11.2 - - + -
243L PHE* 3.6 24.2 - - + -
263L ALA* 4.1 13.7 - - + -
264L VAL 3.3 13.2 - - - +
266L GLY* 3.8 2.4 - - - +
317L PHE* 3.3 14.9 - - + -
318L SER* 3.7 0.4 - - - -
319L LEU* 2.9 41.0 + - + +
321L TYR* 5.5 0.4 - - + -
325L GLY* 1.3 81.5 - - - +
327L TRP* 1.3 59.1 + - - +
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Residues in contact with TRP 327 (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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263L ALA* 3.4 2.4 - - - -
264L VAL* 2.9 43.1 + - + +
266L GLY* 4.1 9.9 - - - -
277L ALA* 3.0 27.1 + - + -
280L ALA* 3.7 28.2 - - + +
281L ALA* 3.6 13.7 - - + +
284L PHE* 4.1 7.2 - + - -
316L HIS* 4.7 3.4 - - - -
317L PHE 3.7 10.8 - - - -
318L SER* 4.0 10.3 - - - +
326L LEU* 1.3 73.3 - - - +
328L GLY* 1.3 63.5 + - - +
350L TRP* 3.6 41.2 - + - -
353L LEU* 4.1 2.7 - - + -
420L TRP* 3.1 33.6 - + + -
425L LEU* 3.5 35.9 - - + -
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Residues in contact with GLY 328 (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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262L LEU 3.2 13.2 - - - -
263L ALA* 3.9 1.3 - - - -
316L HIS* 3.5 5.2 + - - +
317L PHE* 3.0 36.2 + - - +
327L TRP* 1.3 88.4 - - - +
329L PHE* 1.3 63.2 + - - +
350L TRP* 3.8 11.2 - - - -
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Residues in contact with PHE 329 (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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260L ILE* 5.2 1.1 - - + -
261L SER* 3.3 1.0 - - - -
262L LEU* 2.8 60.1 + - + -
314L PHE* 4.3 10.5 - + + -
315L ASN 3.3 13.0 - - - +
316L HIS* 3.7 22.9 - + + +
317L PHE* 3.5 9.6 - - - -
328L GLY* 1.3 74.7 - - - +
330L SER* 1.3 69.1 + - - +
331L THR* 3.3 27.8 - - + -
342L LEU* 4.8 4.9 - - + -
343L ILE* 4.0 18.8 - - + -
346L THR* 3.5 36.8 - - + -
347L LEU* 4.7 1.1 - - + -
350L TRP* 3.6 19.1 - + - -
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Residues in contact with SER 330 (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* 5.6 2.4 + - - -
160L LEU* 4.0 10.2 - - - +
260L ILE 3.4 5.2 - - - -
261L SER* 2.9 21.0 + - - -
314L PHE* 3.3 2.3 - - - +
315L ASN* 2.9 46.2 + - - +
317L PHE* 3.4 18.7 - - - -
329L PHE* 1.3 73.7 - - - +
331L THR* 1.3 70.1 + - - +
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Residues in contact with THR 331 (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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258L ALA 4.0 0.7 - - - +
259L TRP* 3.3 4.2 - - - +
260L ILE* 2.6 61.0 + - + +
311L CYS* 3.8 2.1 - - - +
313L ASN* 3.0 20.4 + - - +
314L PHE* 3.5 8.7 - - - +
329L PHE* 3.3 30.1 - - + -
330L SER* 1.3 82.2 - - - +
332L ALA* 1.3 67.3 + - - +
333L THR* 5.8 0.4 - - - -
342L LEU* 3.6 23.1 - - + +
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Residues in contact with ALA 332 (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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257L LYS* 4.5 12.1 - - + +
258L ALA 3.6 5.8 - - - -
259L TRP* 3.5 28.7 - - + +
311L CYS* 3.3 7.8 - - - +
312L ASP* 3.1 21.7 + - + -
313L ASN* 3.3 29.0 + - - +
331L THR* 1.3 78.7 + - - +
333L THR* 1.3 61.6 + - - +
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Residues in contact with THR 333 (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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257L LYS* 3.5 5.6 - - - +
258L ALA* 3.0 50.1 + - + +
260L ILE* 5.5 3.6 - - + -
310L LEU 2.8 27.6 + - - +
311L CYS* 3.7 8.9 - - - +
312L ASP* 4.0 2.7 - - - +
331L THR* 5.1 0.7 - - - +
332L ALA* 1.3 75.8 - - - +
334L ARG* 1.3 65.2 + - - +
335L ASN 3.0 15.0 + - - +
336L VAL* 4.5 1.6 - - - +
339L ILE* 4.2 20.0 - - + -
342L LEU* 4.6 11.9 - - + -
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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