Contacts of the helix formed by residues 338 - 349 (chain B) in PDB entry 5F2R
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 THR 338 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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223B PHE* 3.4 22.3 - - - -
225B LEU* 4.2 27.4 - - + -
230B PHE* 3.2 34.4 - - + -
253B LEU* 4.0 18.2 - - + -
258B PHE* 5.6 1.1 - - + -
334B LEU 3.8 9.2 - - - +
335B PHE* 2.7 24.3 + - - +
337B SER* 1.3 77.4 + - - +
339B MET* 1.3 69.1 + - - +
340B LYS 3.3 0.6 + - - -
341B PRO* 3.5 1.9 - - - +
342B VAL* 3.5 8.5 - - - +
371B ILE* 5.0 2.5 - - + +
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Residues in contact with MET 339 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223B PHE* 4.2 9.9 - - + -
335B PHE 4.4 2.9 - - - +
336B ARG* 3.0 19.5 + - + +
338B THR* 1.3 96.8 + - - +
340B LYS* 1.3 65.2 + - - +
341B PRO 3.5 0.2 - - - -
342B VAL* 3.2 8.4 + - - +
343B GLN* 3.1 22.7 + - - +
371B ILE* 5.0 2.2 - - + +
374B LEU* 3.6 38.4 - - + +
375B VAL* 3.7 16.6 - - + +
378B PHE* 3.8 44.4 - - + -
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Residues in contact with LYS 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336B ARG 4.4 0.8 + - - +
337B SER* 3.3 9.7 + - - +
338B THR 3.3 0.2 - - - -
339B MET* 1.3 78.8 - - - +
341B PRO* 1.3 71.8 - - + +
343B GLN* 3.3 9.4 + - + +
344B LYS* 3.0 21.4 + - + +
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Residues in contact with PRO 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230B PHE* 3.8 17.0 - - + -
232B VAL* 4.1 3.8 - - + -
248B ASN* 3.8 6.0 - - - +
249B GLY* 3.6 42.6 - - - +
250B ASP* 5.3 2.7 - - + -
337B SER 3.3 15.0 - - - +
338B THR 3.5 6.5 - - - +
340B LYS* 1.3 92.3 - - + +
342B VAL* 1.3 56.2 + - - +
344B LYS* 3.6 8.4 - - + +
345B VAL* 3.0 32.1 + - - +
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Residues in contact with VAL 342 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221B LEU* 3.7 23.6 - - + -
223B PHE* 3.8 27.4 - - + -
232B VAL* 4.0 18.8 - - + -
338B THR 3.5 17.9 - - - +
339B MET* 3.2 12.5 + - - +
341B PRO* 1.3 74.9 - - - +
343B GLN* 1.3 64.8 + - - +
345B VAL* 3.2 4.7 + - - +
346B LEU* 3.0 23.3 + - + +
378B PHE* 3.4 28.0 - - + -
379B PHE* 3.9 8.5 - - + -
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Residues in contact with GLN 343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339B MET 3.1 9.3 + - - +
340B LYS* 3.7 11.2 - - + +
342B VAL* 1.3 78.5 - - - +
344B LYS* 1.3 58.2 + - - +
346B LEU* 3.3 14.9 + - - +
347B GLU* 3.0 55.2 + - - +
351B LEU 5.5 0.8 + - - -
353B LYS* 4.3 9.4 - - - +
378B PHE* 3.7 25.0 - - + -
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Residues in contact with LYS 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248B ASN* 3.6 22.7 - - - +
340B LYS 3.0 16.2 + - - +
341B PRO* 3.6 9.6 - - + +
342B VAL 3.2 0.2 - - - -
343B GLN* 1.3 78.1 - - - +
345B VAL* 1.3 56.0 + - - +
347B GLU* 3.4 16.8 + - - +
348B ASP* 2.9 63.1 + - - +
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Residues in contact with VAL 345 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221B LEU* 4.6 11.7 - - + -
232B VAL* 3.8 20.6 - - + +
234B LEU* 3.5 36.6 - - + +
246B ALA* 4.3 6.3 - - + -
247B THR* 4.2 4.3 - - - +
248B ASN* 3.5 28.5 - - + +
341B PRO 3.0 19.7 + - - +
342B VAL 3.2 8.0 + - - +
344B LYS* 1.3 75.3 - - - +
346B LEU* 1.3 58.2 + - - +
348B ASP* 3.4 6.9 + - - +
349B SER* 2.7 38.1 + - - +
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Residues in contact with LEU 346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221B LEU* 4.3 11.7 - - + -
234B LEU* 4.7 4.7 - - + -
342B VAL* 3.0 19.3 + - + +
343B GLN* 3.4 16.6 - - - +
345B VAL* 1.3 77.4 - - - +
347B GLU* 1.3 61.7 + - - +
349B SER* 3.2 3.5 + - - -
350B ASP 3.0 4.7 + - - -
351B LEU* 2.9 47.0 + - + +
352B LYS* 4.6 0.9 - - - +
353B LYS* 4.0 36.8 - - + +
356B ILE* 3.7 32.8 - - + -
378B PHE* 4.2 17.3 - - + -
379B PHE* 4.7 2.9 - - + -
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Residues in contact with GLU 347 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343B GLN* 3.0 47.1 + - - +
344B LYS* 3.6 21.7 - - + +
346B LEU* 1.3 77.2 - - - +
348B ASP* 1.3 64.6 + - - +
350B ASP* 3.1 21.9 + - - +
351B LEU 4.7 1.8 - - - +
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Residues in contact with ASP 348 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246B ALA* 4.7 11.2 - - + -
247B THR 5.6 1.2 - - - +
248B ASN* 4.6 6.1 + - - -
344B LYS* 2.9 52.0 + - - +
345B VAL* 3.8 6.8 - - - +
347B GLU* 1.3 76.8 - - - +
349B SER* 1.3 58.3 + - - +
350B ASP* 3.2 8.6 + - - +
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Residues in contact with SER 349 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234B LEU* 3.0 35.7 - - - +
245B VAL* 3.8 13.0 - - - +
246B ALA* 3.3 17.7 - - - +
345B VAL 2.7 22.5 + - - -
346B LEU 3.2 3.3 + - - -
348B ASP* 1.3 75.4 - - - +
350B ASP* 1.3 69.2 + - - +
351B LEU* 3.4 13.4 + - - +
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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