Contacts of the strand formed by residues 248 - 252 (chain g) in PDB entry 5FLX
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 LEU 248 (chain g).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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199g THR* 5.0 0.4 - - + -
208g ALA* 4.4 10.5 - - + -
216g ALA* 5.0 14.6 - - + -
218g LEU* 4.0 26.9 - - + -
230g LEU* 5.3 4.7 - - + -
239g LEU* 4.8 11.4 - - + -
240g CYS 3.3 24.2 - - - +
241g PHE* 3.7 29.6 - - + -
246g TYR 3.6 3.3 + - - +
247g TRP* 1.3 72.3 - - - +
249g CYS* 1.3 68.3 + - - +
250g ALA* 3.6 2.0 + - + -
258g ILE* 3.5 2.8 - - - -
259g TRP* 2.7 54.5 + - + +
260g ASP 5.9 0.4 - - - -
261g LEU* 6.3 1.3 - - + -
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Residues in contact with CYS 249 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239g LEU* 3.4 17.3 - - - +
240g CYS 3.5 19.7 + - - +
247g TRP 4.0 2.0 + - - -
248g LEU* 1.3 72.2 - - - +
250g ALA* 1.3 61.6 + - - +
256g ILE* 3.8 21.8 - - - -
257g LYS 3.7 3.4 - - - -
258g ILE* 4.4 9.4 - - + -
289g LEU* 3.6 28.0 - - + +
291g TRP* 3.5 38.4 - - + +
298g LEU* 4.5 13.5 - - - -
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Residues in contact with ALA 250 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216g ALA* 5.8 2.0 - - + -
236g ILE* 4.7 14.4 - - + -
239g LEU* 3.7 17.5 - - + -
248g LEU* 3.6 2.0 + - + +
249g CYS* 1.3 75.6 - - - +
251g ALA* 1.3 59.6 + - - +
252g THR* 3.8 3.5 + - + -
256g ILE* 3.5 4.3 - - - +
257g LYS* 2.6 48.1 + - + +
259g TRP* 4.1 22.4 - - + +
289g LEU* 4.1 3.6 - - - -
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Residues in contact with ALA 251 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236g ILE* 3.1 28.3 - - - +
237g ASN* 3.4 3.6 + - - -
238g ALA* 3.3 22.1 + - + +
250g ALA* 1.3 71.2 - - - +
252g THR* 1.3 60.5 + - - +
255g SER 4.5 1.1 - - - -
256g ILE* 4.6 4.5 - - + +
286g CYS* 3.6 35.2 - - + +
288g SER 5.2 0.4 - - - +
289g LEU* 3.6 22.5 - - + +
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Residues in contact with THR 252 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232g GLY* 5.5 3.6 - - - +
234g ASP* 4.0 13.0 - - + +
235g ILE 3.3 7.9 - - - +
236g ILE* 4.1 18.8 - - + -
237g ASN* 5.5 1.3 - - - -
250g ALA* 3.8 6.5 + - + +
251g ALA* 1.3 80.0 - - - +
253g GLY* 1.3 66.5 + - - +
254g PRO* 4.3 0.4 - - - +
255g SER* 2.2 44.5 + - - +
257g LYS* 3.1 45.5 + - + +
284g PRO 4.3 0.3 - - - +
286g CYS* 4.1 15.2 + - - +
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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