Contacts of the helix formed by residues 278 - 287 (chain A) in PDB entry 5F0L
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 278 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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238A TYR* 3.6 30.8 + - + -
239A LYS* 3.9 18.6 - - + -
243A LEU* 3.6 20.4 - - + +
274A PHE* 2.7 23.0 + - - +
275A HIS* 3.2 12.7 + - - -
277A GLN* 1.3 84.4 - - + +
279A LEU* 1.3 58.7 + - - +
280A ASN 3.6 0.9 - - - -
281A PRO* 3.7 11.0 - - + -
282A PHE* 3.1 30.0 + - - +
503A SO4 3.2 2.7 - - - -
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Residues in contact with LEU 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275A HIS 3.1 22.4 - - - +
276A LEU* 3.8 10.1 - - - +
278A THR* 1.3 74.3 - - - +
280A ASN* 1.3 56.8 + - - +
282A PHE* 3.4 3.1 + - - +
283A LEU* 3.0 39.7 + - + +
302A LEU* 4.2 12.3 - - + -
306A LEU* 3.9 24.9 - - + -
322A ILE* 4.2 3.4 - - + -
324A LEU* 3.5 29.2 - - + -
327A ILE* 4.0 23.3 - - + -
328A PHE* 4.0 15.5 - - + -
503A SO4 2.7 27.5 + - - +
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Residues in contact with ASN 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279A LEU* 1.3 74.9 - - - +
281A PRO* 1.4 72.4 - - + +
284A ARG* 3.1 45.6 + - - +
327A ILE* 3.6 27.8 - - - +
331A GLN* 3.0 27.6 + - - +
503A SO4 3.1 25.2 + - - +
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Residues in contact with PRO 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243A LEU* 4.7 12.3 - - + -
247A LEU* 4.2 10.9 - - + +
277A GLN 5.2 1.8 - - - +
278A THR* 3.7 23.6 - - + +
279A LEU 4.0 0.2 - - - +
280A ASN* 1.4 95.1 - - + +
282A PHE* 1.3 61.8 + - - +
284A ARG* 3.5 22.3 + - - +
285A ALA* 3.2 20.3 + - - +
503A SO4 4.2 5.8 - - - +
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Residues in contact with PHE 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238A TYR* 5.7 0.2 - - - -
243A LEU* 4.9 9.6 - - + +
247A LEU* 4.9 5.8 - - + +
263A MET* 3.6 32.9 - - + +
266A ILE* 3.8 32.5 - - + -
267A ILE* 3.5 30.7 - - + -
275A HIS* 5.6 5.6 - + - +
278A THR* 3.1 20.5 + - - +
279A LEU* 3.4 5.8 + - - +
281A PRO* 1.3 78.4 - - - +
283A LEU* 1.3 61.9 + - + +
285A ALA* 3.2 9.0 + - - +
286A CYS* 3.1 29.6 + - - -
298A ILE* 3.5 23.8 - - + -
302A LEU* 4.0 23.1 - - + -
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Residues in contact with LEU 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279A LEU* 3.0 26.2 + - + +
282A PHE* 1.3 87.4 - - + +
284A ARG* 1.3 63.6 + - - +
285A ALA 3.2 1.1 - - - -
286A CYS* 3.5 9.5 + - + +
287A ALA* 3.3 17.3 + - - +
299A ILE* 4.0 29.6 - - + -
302A LEU* 4.3 11.2 - - + -
327A ILE* 4.4 8.3 - - + -
328A PHE* 4.0 27.4 - - + -
331A GLN* 3.6 43.9 - - + +
332A VAL* 6.1 0.9 - - + +
335A VAL* 3.6 11.4 - - + +
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Residues in contact with ARG 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280A ASN* 3.1 50.9 + - - +
281A PRO* 3.7 20.8 + - - +
282A PHE 3.4 0.2 - - - -
283A LEU* 1.3 75.9 - - - +
285A ALA* 1.3 61.3 + - - +
286A CYS 3.4 0.2 - - - -
287A ALA* 3.6 8.6 + - - +
288A GLU* 3.6 21.8 + - - +
331A GLN* 4.2 13.9 + - - +
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Residues in contact with ALA 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247A LEU* 3.9 22.7 - - + -
251A VAL* 4.4 17.7 - - + +
263A MET* 3.8 14.1 - - + -
281A PRO 3.2 12.2 + - - +
282A PHE 3.2 10.7 + - - +
283A LEU 3.2 0.2 - - - -
284A ARG* 1.3 75.6 - - - +
286A CYS* 1.3 64.1 + - - +
288A GLU* 3.1 13.4 + - - +
289A LEU* 3.2 21.9 + - + +
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Residues in contact with CYS 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263A MET* 3.5 15.0 - - - -
282A PHE* 3.1 26.8 + - - -
283A LEU* 3.6 20.0 - - + +
284A ARG 3.4 0.2 - - - -
285A ALA* 1.3 74.8 - - - +
287A ALA* 1.3 62.0 + - - +
288A GLU 3.2 1.0 + - - -
289A LEU* 3.2 25.4 + - - +
295A VAL* 3.9 27.6 - - + +
298A ILE* 3.8 24.5 - - - -
299A ILE* 4.5 2.9 - - + -
335A VAL* 4.1 7.6 - - + -
339A ARG* 3.8 6.2 + - - -
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Residues in contact with ALA 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283A LEU 3.3 10.8 + - - +
284A ARG* 3.8 12.1 - - - +
285A ALA 3.3 0.6 - - - -
286A CYS* 1.3 78.1 - - - +
288A GLU* 1.3 59.2 + - + +
331A GLN* 5.9 0.9 - - - +
334A THR* 4.7 9.6 - - + +
335A VAL* 4.1 14.7 - - + +
338A SER* 3.4 30.3 - - - +
339A ARG* 3.2 14.7 + - - -
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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