Contacts of the strand formed by residues 277 - 284 (chain T) 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 GLU 277 (chain T).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132M THR* 4.2 8.8 - - - +
268T ARG* 3.6 16.1 - - - +
269T PHE 3.4 15.9 - - - +
270T PHE* 3.8 22.4 - - + -
276T GLU* 1.4 71.0 - - - +
278T PHE* 1.4 60.6 + - - +
279T GLY* 3.5 12.7 - - - +
280T ARG* 3.2 58.6 + - - +
323T PHE* 5.4 1.2 - - - +
326T ARG* 3.6 7.2 + - - -
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Residues in contact with PHE 278 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130M PHE 4.0 4.9 - - - -
131M ILE 3.1 23.3 - - - +
132M THR* 3.8 13.6 - - + +
134M LYS* 3.2 14.7 + - - -
241T TYR* 6.0 2.0 - + - -
243T HIS* 3.3 38.4 - + + +
269T PHE* 3.0 10.6 + - + -
276T GLU 3.6 0.6 + - - +
277T GLU* 1.4 72.2 - - - +
279T GLY* 1.3 57.8 + - - +
318T TYR* 3.5 51.4 - + - -
321T PHE 3.2 29.4 - - - -
322T GLU* 3.9 10.3 - - - -
326T ARG* 3.1 27.1 - - - +
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Residues in contact with GLY 279 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132M THR 4.9 6.5 - - - -
134M LYS* 4.0 16.8 - - - -
267T ALA 4.5 0.7 - - - -
268T ARG* 3.5 3.6 - - - -
269T PHE* 3.1 33.9 + - - +
277T GLU* 3.5 13.2 - - - +
278T PHE* 1.3 82.5 - - - +
280T ARG* 1.3 62.2 + - - +
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Residues in contact with ARG 280 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128M MET* 4.8 0.5 - - - +
132M THR 5.4 1.4 + - - -
134M LYS* 3.2 25.4 - - - +
135M GLU* 3.2 56.7 + - + +
229T GLU* 4.9 8.9 + - - -
266T GLU* 4.0 24.7 - - + -
267T ALA 3.4 5.8 - - - -
268T ARG* 3.4 41.0 - - + +
277T GLU* 3.2 40.7 + - - +
279T GLY* 1.3 71.3 - - - +
281T VAL* 1.4 61.3 + - - +
282T LYS* 3.9 3.7 + - + +
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Residues in contact with VAL 281 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128M MET* 4.0 15.5 - - + -
134M LYS* 4.0 7.2 - - + -
1T MET* 3.6 35.0 - - + -
3T PRO* 4.9 3.1 - - + -
265T PHE 4.2 0.3 - - - +
266T GLU* 3.3 4.5 - - - +
267T ALA* 3.0 28.1 + - - +
269T PHE* 4.0 11.4 - - + -
280T ARG* 1.4 76.7 - - - +
282T LYS* 1.4 70.5 + - - +
284T HIS* 4.7 5.5 - - - -
300T TYR* 3.4 26.6 + - - +
312T HIS* 3.9 19.0 + - + +
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Residues in contact with LYS 282 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126M VAL* 5.3 0.2 - - - +
128M MET* 3.4 21.2 - - - +
135M GLU* 4.3 23.1 + - + +
138M ASN* 3.9 31.1 + - + +
139M CYS* 3.6 24.0 - - - +
3T PRO* 4.9 4.2 - - - +
263T GLY 4.5 6.8 + - - +
264T LYS* 3.9 45.4 - - - +
265T PHE 3.6 7.9 - - - +
266T GLU* 4.1 19.3 - - + -
280T ARG* 3.9 3.7 + - + +
281T VAL* 1.4 81.8 - - - +
283T GLY* 1.4 59.3 + - - +
284T HIS* 3.8 2.6 - - - -
310T ARG* 5.1 1.4 - - - -
312T HIS* 5.4 0.5 + - - -
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Residues in contact with GLY 283 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126M VAL* 6.0 3.4 - - - -
3T PRO* 6.1 0.2 - - - -
263T GLY* 4.9 4.4 - - - -
264T LYS 5.1 1.2 - - - +
265T PHE 3.6 0.6 + - - -
282T LYS* 1.4 79.5 - - - +
284T HIS* 1.4 64.6 + - - +
285T PHE* 3.5 24.3 - - - -
310T ARG* 3.1 36.0 + - - -
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Residues in contact with HIS 284 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5T LEU* 5.9 0.8 - - - +
263T GLY* 3.4 1.6 - - - -
264T LYS 3.3 8.1 + - - -
265T PHE* 3.2 36.5 + - + +
267T ALA* 5.7 1.0 - - + +
281T VAL 4.7 7.2 - - - -
282T LYS 5.0 0.4 - - - -
283T GLY* 1.4 81.9 - - - +
285T PHE* 1.4 60.6 + - - +
286T GLY 3.4 16.6 - - - +
288T ILE* 3.6 23.1 - - + +
302T SER* 3.5 43.1 - - - -
303T GLY* 4.5 0.9 - - - -
304T GLY* 4.3 10.3 + - - -
306T ASP* 3.7 12.8 + - - +
308T TYR 5.0 1.6 + - - -
310T ARG* 3.7 31.6 - - + +
312T HIS* 4.1 7.4 + - - -
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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