Contacts of the strand formed by residues 313 - 320 (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 ASN 313 (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* 4.7 5.2 + - - -
287L TYR* 3.2 18.6 - - - +
288L ASN* 4.3 9.6 - - + +
311L CYS* 3.4 4.1 - - - -
312L ASP* 1.3 85.7 - - - +
314L PHE* 1.3 76.3 + - - +
315L ASN* 5.5 2.4 + - - -
331L THR* 3.0 18.8 + - - +
332L ALA* 3.3 30.0 + - - +
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Residues in contact with PHE 314 (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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284L PHE 3.5 12.1 - - - -
285L GLY 3.5 8.7 - - - -
286L SER* 3.3 1.4 - - - -
287L TYR* 2.9 75.7 + + + +
299L ILE* 5.2 0.9 - - + -
301L LEU* 3.7 22.7 - - + -
302L LEU* 3.9 13.9 - - + -
305L ILE* 5.0 3.1 - - + -
311L CYS* 4.1 11.9 - - - -
313L ASN* 1.3 86.6 - - - +
315L ASN* 1.3 65.3 - - - +
316L HIS* 3.3 35.9 - + - -
329L PHE* 4.3 10.1 - + + -
330L SER 3.3 15.7 - - - +
331L THR* 3.5 9.4 - - - +
342L LEU* 5.9 2.9 - - + -
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Residues in contact with ASN 315 (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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285L GLY 3.8 2.5 - - - -
286L SER* 3.3 21.8 - - - +
313L ASN* 5.5 2.3 + - - -
314L PHE* 1.3 74.9 - - - +
316L HIS* 1.3 67.8 + - - +
317L PHE* 4.1 17.5 - - - +
329L PHE* 3.3 1.6 - - - -
330L SER* 2.9 51.1 + - - +
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Residues in contact with HIS 316 (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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281L ALA* 3.5 26.7 - - + +
284L PHE* 3.3 30.7 - + + +
285L GLY* 2.9 31.5 + - - +
286L SER* 4.6 4.5 + - - -
301L LEU* 4.7 2.2 - - - +
314L PHE* 3.3 27.6 - + - -
315L ASN* 1.3 77.9 + - - +
317L PHE* 1.3 61.1 + - - +
327L TRP* 4.7 4.6 - - + -
328L GLY 3.5 7.1 + - - +
329L PHE* 3.7 22.1 - + + +
346L THR* 4.3 7.2 - - + +
350L TRP* 3.0 33.9 + + - -
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Residues in contact with PHE 317 (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* 4.2 21.1 - - + -
163L LEU* 5.1 2.7 - - + -
262L LEU 4.3 2.2 - - - -
263L ALA* 4.1 14.1 - - + -
281L ALA* 3.7 11.9 - - - +
315L ASN* 4.1 15.3 - - - +
316L HIS* 1.3 73.9 - - - +
318L SER* 1.3 63.1 + - - +
319L LEU* 3.7 27.6 - - + -
326L LEU* 3.3 31.4 - - + -
327L TRP* 3.7 4.2 + - - -
328L GLY 3.0 36.5 + - - +
329L PHE* 3.5 20.4 - - - -
330L SER* 3.4 25.6 - - - -
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Residues in contact with SER 318 (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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266L GLY* 6.2 0.2 - - - -
267L GLU* 5.6 3.8 + - - +
274L TYR 4.8 1.7 + - - -
277L ALA* 3.9 36.2 - - - +
278L LYS* 3.8 39.5 + - - +
281L ALA* 4.4 2.9 - - - +
317L PHE* 1.3 75.5 - - - +
319L LEU* 1.3 68.2 + - - +
320L SER* 3.3 12.6 + - - -
326L LEU 3.7 5.6 - - - -
327L TRP* 4.0 7.4 - - - +
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Residues in contact with LEU 319 (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* 4.7 15.5 - - + -
164L HIS* 3.5 32.8 - - + +
267L GLU 4.0 2.3 + - - +
317L PHE* 3.7 38.6 - - + -
318L SER* 1.3 74.5 - - - +
320L SER* 1.3 62.5 + - - +
321L TYR* 3.6 20.4 - - + +
325L GLY* 3.1 6.1 - - - -
326L LEU* 2.9 39.9 + - + +
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Residues in contact with SER 320 (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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267L GLU* 2.7 23.7 + - - +
269L VAL* 3.5 27.6 - - - +
274L TYR* 3.6 25.0 + - - -
278L LYS* 5.2 0.6 - - - -
318L SER* 3.3 14.2 + - - -
319L LEU* 1.3 73.3 + - - +
321L TYR* 1.3 77.2 + - - +
324L SER 4.1 0.7 - - - -
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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