Contacts of the helix formed by residues 330 - 346 (chain B) in PDB entry 1FLL
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 VAL 330 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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326B GLN 2.9 23.1 - - - +
327B MET* 3.2 19.1 - - + +
328B LEU 2.5 8.3 + - - -
329B SER* 1.3 77.3 - - - +
331B HIS* 1.3 64.6 + - + +
332B ASP 3.8 0.4 - - - -
333B ILE* 3.9 10.0 - - - +
334B ARG* 2.9 35.4 + - + +
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Residues in contact with HIS 331 (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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327B MET* 2.8 42.3 + - - +
328B LEU* 2.9 11.1 + - + +
330B VAL* 1.3 91.2 - - + +
332B ASP* 1.3 61.7 + - - +
333B ILE 2.8 1.8 - - - -
334B ARG* 3.4 10.4 - - + +
335B LEU* 2.5 54.0 + - + +
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Residues in contact with ASP 332 (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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328B LEU* 4.0 11.4 + - - +
329B SER* 4.8 6.7 - - - -
330B VAL 4.4 0.2 - - - +
331B HIS* 1.3 77.0 - - - +
333B ILE* 1.3 56.3 + - + +
335B LEU* 4.5 5.2 - - - +
336B ALA* 2.6 34.5 + - - +
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Residues in contact with ILE 333 (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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329B SER* 3.0 35.7 - - - +
330B VAL* 3.9 9.6 - - + +
331B HIS 2.8 0.2 - - - -
332B ASP* 1.3 80.2 - - + +
334B ARG* 1.3 58.1 + - + +
336B ALA* 2.8 6.4 + - + +
337B ASP* 2.7 52.8 + - - +
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Residues in contact with ARG 334 (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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330B VAL* 2.9 31.8 + - + +
331B HIS* 3.1 12.7 + - + +
333B ILE* 1.3 79.7 - - + +
335B LEU* 1.3 52.9 + - + +
337B ASP* 4.3 8.2 + - - +
338B MET* 2.7 65.8 + - - +
341B ARG* 6.0 1.2 - - - +
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Residues in contact with LEU 335 (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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331B HIS* 2.5 41.4 + - + +
332B ASP* 4.5 4.9 - - - +
334B ARG* 1.3 71.7 - - + +
336B ALA* 1.3 67.2 + - - +
338B MET* 3.4 14.8 - - + +
339B ASP* 2.9 24.8 + - - +
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Residues in contact with ALA 336 (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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332B ASP 2.6 25.3 + - - +
333B ILE* 2.8 14.1 + - + +
335B LEU* 1.3 81.3 - - - +
337B ASP* 1.3 66.1 + - - +
339B ASP* 3.4 4.1 + - - +
340B LEU* 3.3 14.5 + - - +
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Residues in contact with ASP 337 (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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333B ILE* 2.7 39.9 + - - +
334B ARG* 4.3 9.6 + - - +
336B ALA* 1.3 79.8 - - - +
338B MET* 1.3 57.4 + - - +
340B LEU* 2.7 38.8 + - + +
341B ARG* 2.9 8.5 + - - +
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Residues in contact with MET 338 (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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334B ARG* 2.7 54.1 + - - +
335B LEU* 3.2 21.8 - - + +
337B ASP* 1.3 76.5 - - - +
339B ASP* 1.3 63.8 + - - +
341B ARG* 3.3 32.8 + - - +
342B PHE* 3.6 18.7 + - + -
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Residues in contact with ASP 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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335B LEU 2.9 18.2 + - - +
336B ALA* 3.9 3.8 - - - +
338B MET* 1.3 73.4 - - + +
340B LEU* 1.3 65.3 + - - +
342B PHE* 3.0 34.0 + - - +
343B GLN* 3.6 6.6 + - - +
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Residues in contact with LEU 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 ALA 3.3 7.5 + - - +
337B ASP* 2.7 28.6 + - + +
339B ASP* 1.3 74.7 - - - +
341B ARG* 1.3 56.9 + - - +
342B PHE 3.4 0.3 + - - -
343B GLN* 3.7 12.6 + - + +
344B VAL* 3.0 39.8 + - + +
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Residues in contact with ARG 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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334B ARG* 6.0 1.2 - - - +
337B ASP 2.9 8.2 + - - +
338B MET* 3.4 27.6 - - - +
339B ASP 3.2 0.2 - - - -
340B LEU* 1.3 75.3 - - - +
342B PHE* 1.3 70.6 + - - +
344B VAL* 3.2 12.3 + - + +
345B LEU* 3.0 19.8 + - + +
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Residues in contact with PHE 342 (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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338B MET* 3.6 22.1 + - + -
339B ASP* 3.0 24.5 + - - +
341B ARG* 1.3 77.5 - - - +
343B GLN* 1.3 52.4 + - - +
345B LEU* 2.4 41.8 + - + +
346B GLU* 2.6 37.2 + - + +
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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 ASP* 3.6 6.4 + - - +
340B LEU* 4.0 15.2 - - + +
341B ARG 3.5 0.2 - - - -
342B PHE* 1.3 79.1 - - - +
344B VAL* 1.3 49.3 + - + +
346B GLU* 3.4 21.8 + - + +
347B THR* 2.5 53.1 + - + +
359B ARG* 6.1 0.8 - - - +
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Residues in contact with VAL 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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340B LEU* 3.0 35.7 - - + +
341B ARG* 3.3 11.9 - - + +
342B PHE 2.8 2.2 + - - -
343B GLN* 1.3 71.6 - - + +
345B LEU* 1.3 57.7 + - - +
347B THR* 2.7 21.4 + - - +
348B ALA* 3.0 18.4 + - + +
379B GLN* 4.4 19.9 - - + +
380B PRO* 4.6 10.1 - - + +
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Residues in contact with LEU 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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341B ARG* 3.0 13.7 + - + +
342B PHE* 2.4 29.6 + - + +
344B VAL* 1.3 69.4 - - - +
346B GLU* 1.3 57.2 - - + -
347B THR 3.0 5.9 + - - -
348B ALA* 3.7 14.5 + - + +
350B TYR* 3.7 23.3 - - + +
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Residues in contact with GLU 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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342B PHE* 2.6 43.8 + - + +
343B GLN* 3.5 27.2 + - + +
344B VAL 3.2 0.2 - - - -
345B LEU* 1.3 73.6 - - + +
347B THR* 1.3 60.4 + - + +
348B ALA 5.3 0.4 - - - -
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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