Contacts of the strand formed by residues 290 - 298 (chain S) in PDB entry 5K0Y
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 290 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275S PHE 4.2 2.0 - - - -
276S ASP* 4.5 7.9 - - - -
289S GLY* 1.4 72.3 - - - -
291S VAL* 1.3 60.8 + - - -
354S THR* 2.9 36.5 + - - +
356S ILE* 3.1 17.1 + - - -
357S ASP 5.4 1.6 - - - -
361S CYS* 3.7 21.5 - - - -
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Residues in contact with VAL 291 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75N A 3.3 42.0 - - + +
275S PHE* 2.8 62.8 + - + +
277S VAL* 3.7 35.0 - - + -
289S GLY 4.4 1.3 - - - +
290S GLY* 1.3 75.8 - - - -
292S ALA* 1.3 65.6 + - - +
351S GLY* 4.3 1.3 - - - -
352S VAL 3.6 7.0 - - - +
353S GLY* 3.9 11.7 - - - -
356S ILE* 5.6 0.2 - - - -
361S CYS* 3.9 0.4 - - - -
366S MET* 3.7 8.0 - - - +
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Residues in contact with ALA 292 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269S LEU* 4.9 2.7 - - + -
271S VAL* 3.6 33.2 - - + -
273S ARG 3.8 4.9 - - - -
290S GLY 4.2 0.6 + - - -
291S VAL* 1.3 73.7 - - - +
293S GLY* 1.3 58.7 + - - +
294S GLY 3.6 1.1 + - - +
350S ILE 3.6 1.7 - - - +
351S GLY* 3.4 2.9 - - - -
352S VAL* 2.8 43.9 + - + +
354S THR* 5.4 5.6 - - + +
356S ILE* 5.9 1.3 - - + -
366S MET* 4.0 10.5 - - + -
371S LEU* 5.2 4.9 - - + -
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Residues in contact with GLY 293 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271S VAL* 3.7 1.1 - - - +
272S ILE* 3.1 12.2 + - - +
273S ARG* 2.9 39.2 + - - +
275S PHE* 3.5 26.8 - - - -
292S ALA* 1.3 68.5 - - - +
294S GLY* 1.4 58.5 + - - -
349S LEU* 4.2 11.7 - - - -
350S ILE 3.9 5.4 - - - -
351S GLY* 4.7 1.1 - - - -
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Residues in contact with GLY 294 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269S LEU* 3.7 15.7 - - - +
270S ILE 3.0 15.9 - - - -
271S VAL* 3.8 4.7 - - - -
272S ILE* 4.4 2.0 - - - -
292S ALA 3.6 3.2 + - - -
293S GLY* 1.4 76.5 - - - +
295S SER* 1.4 59.9 + - - -
349S LEU* 3.5 7.2 - - - +
350S ILE 2.8 34.4 + - - +
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Residues in contact with SER 295 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56S ASN* 3.3 19.7 + - - -
164S VAL* 3.9 32.4 + - - +
269S LEU* 3.6 0.7 - - - +
270S ILE* 2.9 33.4 + - - +
272S ILE* 5.1 2.6 - - - +
294S GLY* 1.4 73.9 - - - -
296S ILE* 1.4 69.9 + - - +
297S LEU* 4.2 2.5 + - - +
348S GLY 3.2 15.3 + - - -
349S LEU* 4.0 14.0 - - - +
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Residues in contact with ILE 296 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261S ARG* 4.5 0.9 + - - -
267S PRO* 5.5 0.2 - - + -
268S ARG 3.4 18.4 - - - +
269S LEU* 3.6 24.5 - - + -
294S GLY 5.3 0.2 - - - +
295S SER* 1.4 81.9 + - - +
297S LEU* 1.4 59.2 + - - +
298S LYS 3.5 8.1 - - - +
299S GLY 3.2 24.0 - - - +
301S LEU* 3.8 21.1 - - + -
344S ALA* 3.5 39.3 - - + +
345S ALA 4.5 0.2 - - - +
346S PRO* 3.8 10.3 - - + -
347S GLY* 3.0 23.6 + - - -
348S GLY 3.3 8.0 + - - +
350S ILE* 4.1 10.5 - - + -
352S VAL* 5.2 0.7 - - + -
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Residues in contact with LEU 297 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164S VAL* 5.8 6.7 - - + +
194S LYS* 5.9 5.6 - - - +
261S ARG* 3.5 34.5 + - - +
262S ASP* 5.4 3.1 + - - +
268S ARG* 3.5 31.0 - - + +
270S ILE* 3.8 35.7 - - + -
295S SER* 5.1 1.6 - - - +
296S ILE* 1.4 73.5 - - - +
298S LYS* 1.4 67.1 + - + +
346S PRO* 4.2 6.1 - - - -
449S GLU* 5.6 9.6 - - + +
452S GLU* 5.5 6.7 - - - +
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Residues in contact with LYS 298 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262S ASP* 4.2 16.4 - - + +
265S SER* 3.7 24.9 - - - -
266S GLU* 3.6 17.9 - - + +
267S PRO* 3.3 0.2 - - - +
268S ARG* 2.9 39.4 + - - +
296S ILE* 3.5 4.4 - - - +
297S LEU* 1.4 94.3 - - + +
299S GLY* 1.4 66.3 + - - +
346S PRO* 3.8 4.4 - - - +
449S GLU* 3.4 33.4 + - - -
450S VAL* 6.0 0.4 - - - +
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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