Contacts of the helix formed by residues 277 - 281 (chain O) in PDB entry 3FKS
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 SER 277 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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281L ARG* 3.3 30.0 + - - +
285L LEU* 3.9 10.2 - - - +
295L ALA* 3.6 10.9 - - - +
275O ILE 3.5 0.8 + - - -
276O PRO* 1.3 77.7 - - - +
278O ALA* 1.3 71.7 + - - +
279O VAL 3.5 2.6 + - - -
280O GLY 3.7 5.0 + - - -
281O TYR* 2.9 25.5 + - - +
282O GLN 3.9 4.0 + - - -
283O PRO* 3.8 23.1 + - - +
268P VAL* 6.0 1.2 - - - +
272P THR* 5.6 1.2 + - - -
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Residues in contact with ALA 278 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281L ARG* 3.7 26.5 - - - +
294L GLU* 4.4 10.5 - - + +
295L ALA* 3.9 4.6 - - - +
277O SER* 1.3 79.3 + - - +
279O VAL* 1.3 77.3 + - + +
280O GLY 3.3 0.5 + - - -
281O TYR* 3.3 17.8 + - - +
320O PRO* 3.6 15.6 - - + +
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Residues in contact with VAL 279 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291K PRO 4.6 0.4 - - - -
292K GLY* 4.0 14.0 - - - -
293K ARG* 3.5 44.5 + - + +
277O SER 3.5 1.6 + - - -
278O ALA* 1.3 79.3 - - + +
280O GLY* 1.3 59.9 + - - +
281O TYR* 3.2 19.5 + - + -
319O ASP* 4.6 0.4 - - - +
320O PRO* 4.0 16.4 - - + -
265P ASN* 5.3 11.2 - - - +
268P VAL* 6.2 2.6 - - - +
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Residues in contact with GLY 280 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290K PRO* 5.6 4.0 - - - +
291K PRO 3.9 19.2 + - - -
292K GLY* 4.4 4.3 - - - -
298K GLY* 6.0 1.4 - - - -
266O SER* 4.2 11.8 - - - +
269O SER* 6.1 0.3 - - - -
276O PRO* 4.5 14.9 - - - +
277O SER 3.7 7.9 + - - -
278O ALA 3.2 1.6 - - - -
279O VAL* 1.3 77.0 - - - +
281O TYR* 1.3 63.9 + - - +
268P VAL* 5.8 2.6 - - - +
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Residues in contact with TYR 281 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293K ARG* 5.6 3.5 - - + -
259O PHE* 3.6 23.0 - + - -
262O THR* 4.3 10.8 - - + -
263O GLN* 5.2 2.0 - - - -
266O SER* 4.3 12.3 - - - -
269O SER* 5.6 0.2 - - - -
276O PRO* 4.0 2.3 - - - +
277O SER* 2.9 28.5 + - - -
278O ALA 3.3 21.3 + - - +
279O VAL* 3.2 16.7 - - + -
280O GLY* 1.3 80.7 - - - +
282O GLN* 1.3 71.5 + - - +
283O PRO* 4.0 0.3 - - - +
285O LEU* 3.4 28.0 - - + -
313O PRO* 4.0 2.9 - - - +
319O ASP* 2.7 41.6 + - - -
320O PRO* 3.7 13.9 - - + -
321O ALA* 4.0 13.7 - - + -
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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