Contacts of the helix formed by residues 346 - 364 (chain A) in PDB entry 3FO5
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 GLU 346 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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347A ARG* 1.3 71.2 + - - +
348A ARG* 3.2 3.1 - - - -
349A TYR* 3.2 23.6 + - + +
350A ARG* 3.1 27.7 + - + +
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Residues in contact with ARG 347 (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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346A GLU* 1.3 80.6 - - - +
348A ARG* 1.3 58.2 + - - +
350A ARG* 3.3 26.3 + - - +
351A GLU* 2.9 26.9 + - - +
380B ASP* 4.8 6.3 - - - -
382B SER* 4.7 10.5 - - - +
383B ASN* 3.1 34.4 + - - +
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Residues in contact with ARG 348 (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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346A GLU 5.0 0.4 - - - -
347A ARG* 1.3 79.0 - - - +
349A TYR* 1.3 72.1 + - + +
351A GLU* 3.2 9.4 + - + +
352A ALA* 3.0 26.5 + - - +
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Residues in contact with TYR 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346A GLU* 3.2 25.2 + - + +
348A ARG* 1.3 88.6 - - + +
350A ARG* 1.3 56.9 + - - +
352A ALA* 3.4 8.5 + - + +
353A SER* 3.1 29.8 + - - -
596A TCE 4.9 13.5 - - + +
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Residues in contact with ARG 350 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346A GLU* 3.1 13.8 + - + +
347A ARG* 3.4 40.4 - - - +
349A TYR* 1.3 73.7 - - - +
351A GLU* 1.3 60.2 + - - +
353A SER* 3.4 8.2 + - - -
354A ALA* 3.0 28.4 + - - +
565A LEU* 4.1 5.5 - - + +
383B ASN* 2.9 30.3 + - - +
386B TYR* 3.3 53.8 - - + +
387B LEU* 5.7 1.2 - - - +
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Residues in contact with GLU 351 (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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347A ARG 2.9 12.5 + - - +
348A ARG* 3.2 12.1 + - + +
350A ARG* 1.3 73.1 - - - +
352A ALA* 1.3 65.6 - - - +
354A ALA* 3.3 4.4 + - - +
355A ARG* 3.0 41.6 + - - +
381B PRO 4.3 1.0 - - - +
382B SER 3.4 19.7 - - - +
383B ASN* 3.2 17.8 + - - -
384B GLN* 3.1 11.6 + - - +
385B VAL* 2.9 39.0 + - + +
386B TYR* 3.1 17.0 + - - +
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Residues in contact with ALA 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A ARG 3.0 12.8 + - - +
349A TYR* 3.5 13.2 - - + +
350A ARG 3.3 0.2 - - - -
351A GLU* 1.3 73.0 - - - +
353A SER* 1.3 66.1 + - - +
355A ARG* 3.2 17.9 + - - +
356A LYS* 3.0 22.7 + - - +
596A TCE 4.1 25.1 - - + +
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Residues in contact with SER 353 (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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349A TYR 3.1 12.2 + - - -
350A ARG* 3.5 7.2 - - - -
352A ALA* 1.3 78.2 - - - +
354A ALA* 1.3 61.7 + - - +
356A LYS* 3.1 5.2 + - - +
357A LYS* 3.0 20.1 + - - +
563A ALA* 3.1 24.4 + - - +
564A GLY* 4.0 10.1 + - - -
565A LEU* 3.5 23.8 - - - -
596A TCE 3.4 20.8 + - - -
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Residues in contact with ALA 354 (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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350A ARG 3.0 14.5 + - - +
351A GLU 3.5 6.3 - - - +
352A ALA 3.3 0.2 - - - -
353A SER* 1.3 74.7 - - - +
355A ARG* 1.3 62.0 + - - +
357A LYS* 3.4 3.6 + - - +
358A ILE* 3.2 25.5 + - - +
565A LEU* 3.9 14.3 - - + +
385B VAL* 3.4 25.1 - - + +
386B TYR* 3.7 21.8 - - + +
389B TYR* 4.6 8.4 - - + +
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Residues in contact with ARG 355 (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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351A GLU* 3.0 34.9 + - - +
352A ALA* 3.2 18.4 + - - +
354A ALA* 1.3 70.8 - - - +
356A LYS* 1.3 60.0 + - - +
358A ILE* 3.3 8.5 + - + +
359A ARG* 2.9 29.0 + - - +
385B VAL* 3.8 22.9 - - + -
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Residues in contact with LYS 356 (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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352A ALA 3.0 11.7 + - - +
353A SER 3.1 9.2 + - - +
355A ARG* 1.3 75.7 - - - +
357A LYS* 1.3 63.7 + - - +
359A ARG* 3.3 32.2 + - - +
360A LEU* 3.0 28.7 + - + +
407A SER* 4.1 22.6 + - - -
417A THR* 5.1 1.0 + - - -
419A GLU* 4.9 4.3 + - - -
562A VAL* 3.8 30.2 + - - +
563A ALA* 3.9 12.1 - - + -
596A TCE 3.8 47.0 - - - +
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Residues in contact with LYS 357 (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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353A SER 3.0 6.9 + - - -
354A ALA 3.7 7.9 - - - +
356A LYS* 1.3 76.4 - - - +
358A ILE* 1.3 64.0 + - + +
360A LEU* 3.2 5.0 + - - +
361A ASP* 2.8 47.0 + - - +
556A ASN* 2.8 23.0 + - - +
559A THR* 3.4 16.6 - - - +
560A THR* 3.1 29.8 - - - +
563A ALA* 3.6 17.6 - - + +
565A LEU* 3.9 10.5 - - + -
389B TYR* 3.9 29.2 - - + -
392B VAL* 6.1 2.0 - - - +
396B LYS* 4.4 5.5 - - - +
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Residues in contact with ILE 358 (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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354A ALA 3.2 6.7 + - - +
355A ARG* 3.3 10.3 + - + +
357A LYS* 1.3 77.6 - - + +
359A ARG* 1.3 64.6 + - - +
361A ASP* 3.5 6.3 + - - +
362A ARG* 3.1 64.9 + - + +
385B VAL* 3.5 32.5 - - + -
495B ARG* 4.7 23.6 - - - +
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Residues in contact with ARG 359 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355A ARG 2.9 13.9 + - - +
356A LYS* 3.3 31.4 + - - +
358A ILE* 1.3 77.8 - - - +
360A LEU* 1.3 71.6 + - - +
362A ARG* 3.4 7.6 + - - +
363A LYS* 2.9 39.1 + - + +
419A GLU* 2.7 42.8 + - - -
596A TCE 5.8 1.4 + - - -
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Residues in contact with LEU 360 (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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356A LYS* 3.0 30.6 + - + +
357A LYS 3.8 2.7 - - - +
359A ARG* 1.3 87.7 - - - +
361A ASP* 1.3 63.5 - - - +
363A LYS* 3.1 4.9 + - + -
364A TYR* 3.0 42.5 + - + +
419A GLU* 3.6 39.7 - - + +
424A LEU* 4.1 12.1 - - + -
559A THR* 3.8 26.5 - - + +
562A VAL* 3.7 30.1 - - + -
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Residues in contact with ASP 361 (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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357A LYS* 2.8 50.2 + - - +
358A ILE* 3.9 5.6 - - - +
360A LEU* 1.3 76.6 - - - +
362A ARG* 1.3 62.2 + - + +
364A TYR 3.4 1.9 + - - -
365A ILE* 3.0 28.1 + - - +
555A LEU* 4.7 9.4 - - - +
556A ASN* 3.9 9.1 - - - +
559A THR* 2.6 30.1 + - - +
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Residues in contact with ARG 362 (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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358A ILE* 3.1 47.4 + - + +
359A ARG* 3.6 6.6 - - - +
361A ASP* 1.3 75.6 - - + +
363A LYS* 1.3 66.3 + - - +
364A TYR 3.3 0.3 + - - -
365A ILE* 3.4 28.9 + - + +
467B GLU* 5.8 1.8 + - - -
468B ASP* 5.6 3.4 + - - -
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Residues in contact with LYS 363 (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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359A ARG* 2.9 25.2 + - + +
360A LEU* 3.1 10.7 + - + +
362A ARG* 1.3 79.2 - - - +
364A TYR* 1.3 92.8 + - + +
365A ILE* 3.4 1.1 + - - +
366A VAL 5.1 1.4 + - - +
419A GLU* 3.1 34.5 + - - +
420A ASP 4.5 4.7 - - - -
421A ASP* 5.7 5.3 - - - +
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Residues in contact with TYR 364 (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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360A LEU* 3.0 31.8 + - + +
361A ASP 3.6 3.1 - - - -
363A LYS* 1.3 100.9 - - + +
365A ILE* 1.3 62.6 + - - +
366A VAL 3.1 14.0 + - - +
367A SER* 4.0 2.3 + - - -
419A GLU* 3.0 26.9 - - - +
420A ASP 2.6 29.7 + - - -
421A ASP 4.2 7.4 - - - -
422A LYS 4.4 5.2 - - - -
423A PHE* 3.4 32.3 - - - -
424A LEU* 3.8 26.2 - - + -
555A LEU* 3.3 36.8 - - + +
595A GOL 5.0 1.3 - - - +
498B CYS* 3.7 5.7 - - - -
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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