Contacts of the helix formed by residues 324 - 336 (chain B) in PDB entry 1FO4
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 324 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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315B ALA 3.9 21.3 - - - +
316B VAL* 3.9 19.7 + - - +
319B LEU* 4.0 11.2 - - + +
320B PRO 3.8 9.9 - - - +
321B THR* 3.3 13.8 + - - -
323B LYS* 1.3 84.7 - - - +
325B GLU* 1.3 64.3 + - - +
326B VAL 3.3 2.7 - - - -
327B PHE* 3.9 23.6 - - + -
328B ARG* 2.9 47.4 + - - -
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Residues in contact with GLU 325 (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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321B THR* 3.9 8.9 - - - +
322B GLN* 4.2 9.1 - - - +
324B THR* 1.3 77.2 - - - +
326B VAL* 1.3 62.5 + - - +
328B ARG* 2.8 28.6 + - - +
329B GLY 3.2 15.2 + - - -
412B SER* 2.9 23.3 + - - +
416B GLU* 3.5 16.4 - - + +
417B PHE* 3.4 12.8 - - - -
418B PHE* 2.8 44.1 + - + +
526B LYS* 2.7 37.3 + - - +
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Residues in contact with VAL 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323B LYS 5.3 0.2 + - - -
324B THR* 3.3 0.4 - - - +
325B GLU* 1.3 72.3 - - - +
327B PHE* 1.3 67.2 + - - +
329B GLY* 2.9 11.8 + - - -
330B VAL* 3.0 16.7 + - + +
364B VAL* 4.6 6.5 - - + -
368B SER* 3.7 35.0 - - - +
370B THR* 5.2 0.2 - - - +
409B ILE* 3.8 22.4 - - + -
410B PRO* 3.5 25.1 - - + +
411B TYR 5.0 0.2 - - - -
412B SER* 4.4 14.0 + - - +
416B GLU* 5.9 1.8 - - - +
418B PHE* 4.0 19.0 - - + -
439B ARG* 5.4 4.9 - - - -
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Residues in contact with PHE 327 (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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297B ILE* 3.8 22.7 - - + -
312B LEU* 3.8 24.9 - - + -
315B ALA* 4.0 15.5 - - + -
316B VAL* 4.1 11.7 - - + -
323B LYS 4.5 0.9 - - - -
324B THR* 3.4 27.7 + - + +
326B VAL* 1.3 74.1 - - - +
328B ARG* 1.3 57.3 + - - +
330B VAL* 3.0 5.6 + - - +
331B LEU* 2.8 33.9 + - - +
409B ILE* 3.3 47.1 - - + -
410B PRO 3.6 9.6 - - - -
411B TYR* 3.6 41.7 - + - -
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Residues in contact with ARG 328 (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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316B VAL* 3.6 30.9 - - + +
321B THR* 3.0 35.3 + - - +
324B THR* 2.9 28.0 + - - +
325B GLU* 2.8 39.4 + - - +
327B PHE* 1.3 75.5 - - - +
329B GLY* 1.3 58.6 + - - +
331B LEU* 3.3 11.6 + - + +
332B GLU* 2.9 31.5 + - - +
526B LYS* 5.0 7.3 - - - +
548B LEU* 5.8 4.6 - - + +
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Residues in contact with GLY 329 (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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325B GLU 3.2 5.0 + - - -
326B VAL 2.9 9.1 + - - -
328B ARG* 1.3 79.2 - - - +
330B VAL* 1.3 61.8 + - - +
332B GLU* 3.3 3.5 + - - +
333B GLN* 3.3 19.2 + - - +
364B VAL* 4.6 3.6 - - - -
418B PHE* 4.1 13.5 - - - -
419B SER* 5.6 0.4 - - - -
420B ALA* 3.4 32.2 - - - +
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Residues in contact with VAL 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308B VAL* 4.7 3.4 - - + -
312B LEU* 3.6 20.9 - - + -
326B VAL* 3.0 17.4 + - + +
327B PHE 3.4 6.3 - - - +
329B GLY* 1.3 75.0 - - - +
331B LEU* 1.3 58.3 + - - +
333B GLN* 3.3 7.7 + - - +
334B LEU* 2.9 44.2 + - + +
348B LEU* 6.3 0.4 - - + -
361B LEU* 4.5 13.5 - - + -
364B VAL* 3.8 21.7 - - + +
365B PHE* 4.4 9.6 - - + -
409B ILE* 4.2 31.2 - - + -
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Residues in contact with LEU 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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309B GLU* 3.7 31.8 - - + +
312B LEU* 3.6 28.7 - - + +
313B LEU* 3.9 24.7 - - + -
316B VAL* 3.5 33.0 - - + -
327B PHE 2.8 18.4 + - - +
328B ARG* 3.6 11.0 - - + +
329B GLY 3.2 0.2 - - - -
330B VAL* 1.3 73.6 - - - +
332B GLU* 1.3 64.9 + - - +
334B LEU* 3.9 6.0 - - + +
335B ARG* 3.1 22.7 + - - +
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Residues in contact with GLU 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 ARG 2.9 16.2 + - - +
329B GLY* 3.6 7.6 - - - +
330B VAL 3.3 0.2 - - - -
331B LEU* 1.3 75.1 - - - +
333B GLN* 1.3 59.3 + - - +
335B ARG* 2.8 62.0 + - - +
336B TRP* 3.3 33.6 + - - -
420B ALA* 4.2 20.6 - - + +
421B PHE* 5.4 2.4 - - - -
422B LYS 5.6 1.6 + - - -
548B LEU* 3.3 41.8 - - + +
549B PHE 5.6 1.0 + - - -
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Residues in contact with GLN 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 GLY 3.3 12.1 + - - +
330B VAL 3.3 6.7 + - - +
331B LEU 3.2 0.2 - - - -
332B GLU* 1.3 73.2 - - - +
334B LEU* 1.3 63.9 + - - +
335B ARG 3.0 4.5 - - - -
336B TRP* 2.9 17.8 + - - +
337B PHE* 3.1 12.9 + - - +
360B ASP* 3.5 38.1 + - + +
361B LEU* 4.1 11.2 - - + -
364B VAL* 4.0 9.4 - - + -
420B ALA* 4.0 3.8 - - + -
421B PHE 3.3 22.7 + - - +
422B LYS* 3.4 23.3 - - - +
435B THR* 3.1 19.9 + - - -
436B CYS 3.4 15.8 + - - -
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Residues in contact with LEU 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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305B LEU* 4.0 34.8 - - + +
308B VAL* 4.5 5.6 - - + -
309B GLU* 3.7 50.7 - - + +
330B VAL* 2.9 38.6 + - + +
331B LEU* 3.4 7.4 + - + +
333B GLN* 1.3 75.4 - - - +
335B ARG* 1.3 56.2 + - - +
337B PHE* 3.3 16.3 + - + -
343B LYS* 2.7 35.1 + - + +
361B LEU* 4.2 20.2 - - + -
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Residues in contact with ARG 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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137B GLU* 5.7 3.4 + - - -
144B GLN* 3.1 29.6 + - - +
309B GLU* 4.4 4.2 + - - -
331B LEU 3.1 12.5 + - - +
332B GLU* 2.8 48.1 + - - +
334B LEU* 1.3 78.3 - - - +
336B TRP* 1.3 88.8 + - + +
337B PHE 3.4 0.6 + - - -
338B ALA 5.4 0.3 - - - +
343B LYS* 4.5 2.9 - - - +
548B LEU* 4.4 4.6 - - - +
549B PHE* 2.6 54.9 + - - +
550B GLN* 4.1 2.8 - - - +
551B LYS* 4.8 2.6 - - - +
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Residues in contact with TRP 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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144B GLN* 5.4 4.0 - - - -
332B GLU* 3.3 43.6 + - - -
333B GLN* 2.9 6.8 + - - +
335B ARG* 1.3 121.5 - - + +
337B PHE* 1.3 60.3 + - - +
338B ALA 3.7 5.0 + - - -
422B LYS* 2.8 55.6 + - + -
427B ARG* 3.3 62.6 - - + +
428B GLU* 4.6 13.7 - - + -
429B ASP 5.0 2.9 - - - +
430B ASP 4.4 5.2 + - - +
549B PHE* 3.7 22.8 - + + +
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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