Contacts of the helix formed by residues 324 - 336 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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315A ALA 3.8 9.0 - - - +
316A VAL* 3.8 35.6 + - - +
319A LEU* 3.9 12.1 - - + +
320A PRO 3.8 9.8 - - - +
321A THR* 3.1 13.1 + - - -
323A LYS* 1.3 82.8 - - - +
325A GLU* 1.3 63.1 + - - +
326A VAL 3.3 2.5 - - - -
327A PHE* 3.2 20.8 + - + -
328A ARG* 2.7 49.9 + - - -
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Residues in contact with GLU 325 (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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321A THR* 4.1 10.4 - - - +
322A GLN* 4.3 6.8 - - - +
324A THR* 1.3 76.2 - - - +
326A VAL* 1.3 61.2 + - + +
328A ARG* 2.6 31.8 + - - +
329A GLY 3.2 15.2 + - - -
412A SER* 2.9 28.1 - - - +
416A GLU 3.6 11.0 - - - +
417A PHE* 3.4 10.7 - - - -
418A PHE* 2.9 42.5 + - + +
526A LYS* 2.7 38.0 + - - +
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Residues in contact with VAL 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A THR 3.3 0.2 - - - -
325A GLU* 1.3 76.3 - - + +
327A PHE* 1.3 66.7 + - - +
329A GLY* 3.0 12.1 + - - -
330A VAL* 3.0 15.8 + - + +
364A VAL* 4.8 1.3 - - + -
365A PHE* 6.4 0.2 - - + -
368A SER* 3.7 31.4 - - - +
409A ILE* 3.9 20.2 - - + -
410A PRO* 3.7 22.9 - - + +
412A SER* 4.3 10.8 - - - -
416A GLU* 5.9 4.7 - - + +
418A PHE* 4.0 31.9 - - + -
439A ARG* 5.6 3.4 - - - -
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Residues in contact with PHE 327 (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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297A ILE* 3.7 26.0 - - + -
312A LEU* 3.8 23.7 - - + +
315A ALA* 4.1 15.5 - - + -
316A VAL* 3.9 10.3 - - + -
319A LEU* 4.5 0.2 - - + -
323A LYS 4.4 2.2 - - - -
324A THR* 3.2 29.5 + - + +
326A VAL* 1.3 75.2 - - - +
328A ARG* 1.3 58.3 + - - +
330A VAL* 3.2 4.6 + - - +
331A LEU* 2.9 34.0 + - - +
409A ILE* 3.4 34.8 - - + -
410A PRO 3.4 18.6 - - - -
411A TYR* 3.5 42.4 - + - -
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Residues in contact with ARG 328 (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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316A VAL* 3.5 30.3 - - + -
321A THR* 3.0 36.0 + - - +
324A THR* 2.7 31.1 + - - +
325A GLU* 2.6 45.8 + - - +
327A PHE* 1.3 77.4 - - - +
329A GLY* 1.3 56.4 + - - +
331A LEU* 3.2 11.2 + - + +
332A GLU* 2.9 30.7 + - - +
418A PHE 6.0 0.2 - - - +
526A LYS* 5.2 5.3 - - - +
548A LEU* 6.3 2.2 - - + -
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Residues in contact with GLY 329 (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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325A GLU 3.2 4.8 + - - -
326A VAL 3.0 8.2 + - - -
328A ARG* 1.3 79.4 - - - +
330A VAL* 1.3 62.1 + - - +
332A GLU* 3.3 3.6 + - - -
333A GLN* 3.2 18.2 + - - +
364A VAL* 4.7 3.4 - - - -
418A PHE* 4.1 13.4 + - - -
419A SER* 5.0 0.9 - - - -
420A ALA* 3.3 33.8 - - - +
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Residues in contact with VAL 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A VAL* 4.7 3.1 - - + -
312A LEU* 3.6 21.5 - - + -
326A VAL* 3.0 14.1 + - + +
327A PHE 3.5 6.5 - - - +
329A GLY* 1.3 75.4 - - - +
331A LEU* 1.3 59.4 + - - +
333A GLN* 3.2 7.5 + - - +
334A LEU* 2.9 43.7 + - + +
361A LEU* 4.4 11.9 - - + -
364A VAL* 3.7 21.3 - - + +
365A PHE* 4.2 17.7 - - + -
409A ILE* 4.3 21.5 - - + -
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Residues in contact with LEU 331 (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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309A GLU* 3.7 40.4 - - + +
312A LEU* 3.7 18.2 - - + +
313A LEU* 3.8 28.9 - - + -
316A VAL* 3.6 32.5 - - + -
327A PHE 2.9 17.9 + - - +
328A ARG* 3.2 9.4 + - + +
330A VAL* 1.3 75.4 - - - +
332A GLU* 1.3 64.1 + - - +
334A LEU* 3.9 6.6 - - + +
335A ARG* 3.0 23.7 + - - +
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Residues in contact with GLU 332 (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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328A ARG 2.9 13.8 + - - +
329A GLY* 3.5 11.2 - - - +
330A VAL 3.2 0.2 - - - -
331A LEU* 1.3 75.8 - - - +
333A GLN* 1.3 61.3 + - - +
335A ARG* 2.7 60.5 + - - +
336A TRP* 3.3 35.3 + - - -
420A ALA 4.2 22.4 - - - +
421A PHE* 5.5 3.1 - - - -
422A LYS 5.7 0.9 + - - -
548A LEU* 3.5 36.8 - - + +
549A PHE 5.7 0.7 - - - -
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Residues in contact with GLN 333 (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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329A GLY 3.5 13.0 - - - +
330A VAL 3.2 6.6 + - - +
332A GLU* 1.3 76.7 - - - +
334A LEU* 1.3 65.7 + - - +
335A ARG 3.0 2.0 - - - -
336A TRP* 2.9 17.4 + - - +
337A PHE* 3.0 13.5 + - - +
360A ASP* 3.2 32.2 + - + +
361A LEU* 4.2 10.5 - - + -
364A VAL* 3.9 10.5 - - + +
420A ALA* 3.9 8.0 - - + +
421A PHE* 3.5 15.6 + - - -
422A LYS* 3.4 23.6 - - - +
435A THR* 2.9 27.2 + - - -
436A CYS 3.6 12.5 + - - -
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Residues in contact with LEU 334 (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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305A LEU* 3.9 29.2 - - + +
308A VAL* 4.4 6.1 - - + -
309A GLU* 3.6 50.0 - - + +
330A VAL* 2.9 36.9 + - + +
331A LEU* 3.9 8.7 - - + +
333A GLN* 1.3 75.4 - - - +
335A ARG* 1.3 61.3 + - - +
337A PHE* 3.1 32.1 + - + +
343A LYS* 2.9 27.7 + - + +
361A LEU* 4.5 11.9 - - + -
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Residues in contact with ARG 335 (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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137A GLU* 5.6 2.6 + - - -
144A GLN* 3.0 30.7 + - - +
309A GLU* 4.1 6.5 + - - -
331A LEU 3.0 13.6 + - - +
332A GLU* 2.7 49.1 + - - +
334A LEU* 1.3 77.6 - - - +
336A TRP* 1.3 82.4 + - + +
337A PHE 3.4 0.4 + - - -
343A LYS* 4.3 1.5 + - - +
548A LEU* 4.3 5.1 - - - +
549A PHE* 2.6 56.6 + - - +
550A GLN* 4.2 5.1 - - - +
551A LYS* 4.6 7.5 - - - +
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Residues in contact with TRP 336 (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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144A GLN* 5.0 4.7 - - - -
332A GLU* 3.3 38.8 + - - -
333A GLN* 2.9 9.3 + - - +
335A ARG* 1.3 122.0 - - + +
337A PHE* 1.3 55.8 + - - +
338A ALA 3.6 4.5 + - - -
422A LYS* 2.8 56.5 + - + -
427A ARG* 3.4 59.8 - - + +
428A GLU* 4.0 18.2 - - + -
429A ASP 4.6 6.0 + - - +
430A ASP 4.5 0.7 - - - +
549A PHE* 3.7 27.8 - + + +
551A LYS* 6.3 2.5 - - + -
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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