Contacts of the helix formed by residues 277 - 281 (chain X) 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 X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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281U ARG* 2.9 39.3 + - - -
285U LEU* 3.8 13.0 - - - -
295U ALA* 3.5 16.4 - - - +
275X ILE 3.6 0.6 + - - -
276X PRO* 1.3 77.3 - - - +
278X ALA* 1.3 72.7 + - - +
279X VAL 3.5 0.7 + - - -
280X GLY* 3.4 9.1 + - - -
281X TYR* 3.2 17.3 + - - -
282X GLN 4.5 2.2 - - - -
283X PRO* 4.3 11.1 - - - +
268Y VAL* 5.8 3.6 - - - +
272Y THR* 5.5 2.1 + - - +
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Residues in contact with ALA 278 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281U ARG* 4.2 12.3 - - - +
294U GLU* 3.9 28.0 - - + +
295U ALA* 3.8 2.6 - - - +
277X SER* 1.3 78.4 + - - +
279X VAL* 1.3 71.5 + - + +
280X GLY 2.8 12.3 + - - -
281X TYR* 3.6 9.2 + - - +
320X PRO* 4.1 15.1 - - + +
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Residues in contact with VAL 279 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291T PRO 4.6 0.7 - - - -
292T GLY* 3.0 25.6 - - - -
293T ARG* 3.6 40.2 + - + +
277X SER 3.5 1.6 + - - -
278X ALA* 1.3 76.4 - - + +
280X GLY* 1.3 56.9 + - - +
281X TYR* 3.6 9.4 + - + -
319X ASP* 4.5 7.2 - - - +
320X PRO* 4.0 22.9 - - + -
265Y ASN* 5.3 15.5 - - - +
268Y VAL* 5.9 6.0 - - - +
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Residues in contact with GLY 280 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290T PRO* 5.5 3.4 - - - +
291T PRO 3.9 17.5 + - - -
292T GLY* 4.2 2.2 - - - -
266X SER* 5.0 5.9 - - - +
276X PRO* 4.1 15.2 - - - +
277X SER 3.4 8.6 + - - -
278X ALA 2.8 3.6 + - - -
279X VAL* 1.3 79.7 - - - +
281X TYR* 1.3 69.7 + - - +
268Y VAL* 5.9 1.4 - - - +
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Residues in contact with TYR 281 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293T ARG* 5.1 4.4 - - + -
339T TYR* 5.8 1.4 + - - -
259X PHE* 3.4 27.5 - + - -
262X THR* 4.4 9.4 - - + -
263X GLN* 4.9 4.5 - - + -
266X SER* 4.0 25.4 - - - -
269X SER* 5.5 0.2 - - - -
276X PRO* 4.1 2.1 - - - +
277X SER* 3.2 19.9 + - - -
278X ALA 3.6 7.4 + - - +
279X VAL* 3.6 11.1 - - + -
280X GLY* 1.3 84.2 - - - +
282X GLN* 1.3 70.5 + - - +
285X LEU* 3.7 22.7 - - + -
313X PRO* 3.5 5.0 - - - +
319X ASP* 2.9 41.3 + - - -
320X PRO* 4.0 21.8 - - + -
321X ALA* 3.9 10.8 - - + -
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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