Contacts of the helix formed by residues 403 - 423 (chain A) in PDB entry 3F4V
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 ASP 403 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391A GLN* 3.4 20.0 - - + +
400A TYR 3.5 2.9 - - - +
401A LEU 3.0 0.2 + - - -
402A ARG* 1.3 71.1 - - - +
404A THR* 1.3 64.8 + - - +
405A THR 3.2 3.4 - - - +
406A ARG* 2.8 44.0 + - + +
407A VAL* 3.0 8.5 + - - +
464A LYS* 3.5 12.0 - - - +
465A ALA* 3.1 10.8 + - - +
466A SER* 2.6 48.8 + - - -
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Residues in contact with THR 404 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402A ARG* 2.9 13.6 + - + +
403A ASP* 1.3 75.8 - - - +
405A THR* 1.3 70.1 + - - +
407A VAL* 3.3 12.2 + - - +
408A HIS* 3.0 23.4 + - - +
465A ALA* 5.2 1.1 - - - +
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Residues in contact with THR 405 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361A ILE* 4.0 17.0 - - + -
389A MET* 3.8 24.7 - - + -
403A ASP 3.2 1.2 - - - -
404A THR* 1.3 83.6 - - - +
406A ARG* 1.3 58.0 + - - +
408A HIS* 3.4 9.8 + - + +
409A PHE* 2.9 25.8 + - - +
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Residues in contact with ARG 406 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389A MET* 2.9 44.4 + - + +
390A ASP* 3.8 0.4 - - - +
391A GLN* 3.0 34.4 + - - +
403A ASP* 2.8 54.5 + - + +
405A THR* 1.3 77.1 - - - +
407A VAL* 1.3 67.7 + - - +
409A PHE* 3.2 0.5 + - - +
410A TYR* 2.9 50.0 + - + -
448A LYS 2.8 29.1 + - - -
449A PHE 3.9 5.0 + - - -
450A GLY 3.3 21.3 + - - -
451A ILE* 4.2 3.4 - - - -
464A LYS* 3.5 1.6 - - - +
466A SER* 3.4 11.7 - - - -
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Residues in contact with VAL 407 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A TRP* 4.0 14.4 - - + -
403A ASP 3.0 13.3 + - - +
404A THR* 3.5 13.0 - - - +
406A ARG* 1.3 75.5 - - - +
408A HIS* 1.3 63.1 + - - +
410A TYR* 3.3 4.1 + - - +
411A ARG* 3.0 37.8 + - - +
465A ALA* 4.0 14.6 - - + +
466A SER* 3.7 32.1 - - - +
469A TRP* 3.5 29.9 - - + -
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Residues in contact with HIS 408 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404A THR* 3.0 13.6 + - - +
405A THR* 3.6 12.9 - - + +
407A VAL* 1.3 76.9 - - - +
409A PHE* 1.3 58.3 - - - +
411A ARG* 3.7 30.2 - - - +
412A SER* 2.9 45.0 + - - -
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Residues in contact with PHE 409 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A TYR 4.3 3.6 - - - -
359A LEU* 4.3 9.9 - - + -
361A ILE* 3.9 18.8 - - + -
387A ASN* 3.6 25.4 - - - -
388A GLY* 3.3 35.4 - - - -
389A MET* 3.6 35.0 - - + -
405A THR 2.9 14.8 + - - +
406A ARG* 3.3 9.2 - - - +
408A HIS* 1.3 76.3 - - - +
410A TYR* 1.3 70.3 + + - +
412A SER* 3.8 1.7 - - - -
413A TYR* 2.9 76.7 + + - +
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Residues in contact with TYR 410 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387A ASN* 2.9 26.6 + - - -
388A GLY* 3.2 9.4 - - - -
389A MET 4.6 0.3 + - - -
406A ARG* 2.9 53.8 + - + +
407A VAL* 4.0 2.5 - - - +
409A PHE* 1.3 78.5 - + - +
411A ARG* 1.3 60.4 + - - +
413A TYR* 4.8 0.7 - - - -
414A LEU* 2.8 37.4 + - + +
430A TYR* 3.1 28.5 - - - -
432A ALA* 3.5 20.2 - - + +
433A TRP 3.2 17.2 + - - -
449A PHE 4.9 0.3 + - - -
451A ILE* 3.9 13.3 - - + +
466A SER* 4.5 4.9 - - - -
469A TRP* 3.9 22.2 - + + -
470A PHE* 3.6 18.4 - + + -
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Residues in contact with ARG 411 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ASN 5.1 0.9 - - - -
6A TRP* 2.8 43.6 + - - +
7A LEU 4.0 12.6 - - - +
8A GLY* 4.0 18.4 - - - +
10A LEU* 3.7 3.1 - - + +
407A VAL* 3.0 31.5 + - - +
408A HIS* 3.7 37.7 - - - +
410A TYR* 1.3 75.4 - - - +
412A SER* 1.3 55.5 + - - +
415A THR* 2.7 43.8 + - - +
469A TRP* 3.7 18.4 - - + -
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Residues in contact with SER 412 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363A PRO* 3.5 26.7 - - - -
408A HIS* 2.9 42.5 + - - -
409A PHE* 3.9 2.7 - - - -
411A ARG* 1.3 75.0 + - - +
413A TYR* 1.3 65.9 + - - +
415A THR* 3.3 7.2 + - - -
416A GLN* 3.1 27.0 + - - +
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Residues in contact with TYR 413 (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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314A GLN* 3.6 19.3 - - - -
315A TYR 2.7 29.0 + - - -
316A THR* 4.2 0.3 - - - -
360A TYR 3.6 3.8 + - - -
361A ILE* 4.1 2.2 - - + -
362A VAL 2.9 36.1 + - - -
363A PRO* 3.6 27.6 - - + -
366A MET* 3.7 17.7 - - + +
387A ASN* 3.3 37.0 - - - +
409A PHE* 2.9 56.3 + + - +
410A TYR* 4.3 1.8 - - - +
412A SER* 1.3 73.4 - - - +
414A LEU* 1.3 58.0 + - - +
416A GLN* 3.2 5.5 + - - +
417A LEU* 2.9 27.5 + - - +
430A TYR* 5.8 0.7 - - - -
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Residues in contact with LEU 414 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A LEU* 3.8 15.0 - - + -
15A PHE* 3.9 21.0 - - + -
21A PHE* 4.1 5.8 - - + -
410A TYR 2.8 21.5 + - - +
413A TYR* 1.3 74.0 - - - +
415A THR* 1.3 59.9 + - - +
417A LEU* 3.7 10.0 - - + +
418A LYS* 2.9 30.3 + - - +
430A TYR* 3.7 47.1 - - + +
469A TRP* 3.8 26.7 - - + -
470A PHE* 4.0 18.6 - - + -
473A MET* 4.1 8.7 - - + -
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Residues in contact with THR 415 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A GLY 4.8 5.4 + - - +
10A LEU* 3.9 17.5 - - + +
411A ARG* 2.7 28.1 + - - +
412A SER* 3.3 8.0 + - - -
414A LEU* 1.3 77.2 - - - +
416A GLN* 1.3 63.8 + - - +
418A LYS* 3.4 9.5 + - + +
419A LYS* 3.0 26.8 + - + +
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Residues in contact with GLN 416 (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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363A PRO* 3.4 34.3 - - + +
364A TRP* 3.6 17.5 - - - +
366A MET* 4.4 2.2 - - + -
367A TYR* 3.3 36.9 - - - +
412A SER 3.1 13.4 + - - +
413A TYR 3.6 6.1 - - - +
414A LEU 3.2 0.2 - - - -
415A THR* 1.3 82.8 - - - +
417A LEU* 1.3 65.7 + - - +
419A LYS* 3.3 22.6 + - - +
420A ALA* 3.1 18.2 + - - +
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Residues in contact with LEU 417 (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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15A PHE* 4.7 1.8 - - + -
19A PHE* 4.3 13.7 - - + -
366A MET* 3.9 12.4 - - + +
367A TYR 5.4 0.2 - - - +
370A VAL* 3.9 28.7 - - + -
384A ILE* 4.0 15.0 - - + -
413A TYR 2.9 16.0 + - - +
414A LEU* 3.7 13.7 - - + +
416A GLN* 1.3 74.1 - - - +
418A LYS* 1.3 63.7 + - - +
420A ALA* 3.0 7.0 + - - +
421A ILE* 2.9 32.5 + - + +
427A VAL* 4.1 18.8 - - + -
430A TYR* 3.6 38.4 - - + -
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Residues in contact with LYS 418 (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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9A GLY 5.6 1.1 - - - -
10A LEU* 4.0 14.1 - - + -
14A ALA* 2.8 51.9 + - + +
15A PHE* 4.1 15.4 - - + -
414A LEU 2.9 17.5 + - - +
415A THR* 3.5 9.0 - - + +
416A GLN 3.3 0.2 - - - -
417A LEU* 1.3 77.9 - - - +
419A LYS* 1.3 55.9 + - - +
421A ILE* 3.2 4.9 + - - +
422A ASP* 2.8 65.5 + - - +
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Residues in contact with LYS 419 (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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367A TYR* 3.7 30.8 - - + -
415A THR 3.0 14.4 + - - +
416A GLN* 3.4 29.5 + - - +
418A LYS* 1.3 77.2 - - - +
420A ALA* 1.3 62.1 + - - +
422A ASP* 3.4 7.1 + - - +
423A GLU* 3.1 46.7 + - + +
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Residues in contact with ALA 420 (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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367A TYR* 3.7 25.3 - - + -
370A VAL* 3.6 33.2 - - + -
371A ASN* 4.5 5.6 - - - +
374A LYS* 5.0 1.0 - - - +
416A GLN 3.1 5.8 + - - +
417A LEU* 3.0 10.5 + - - +
419A LYS* 1.3 80.5 - - - +
421A ILE* 1.3 62.2 + - - +
423A GLU* 3.2 12.1 + - - +
424A GLY 3.3 0.7 + - - -
425A ALA* 3.1 21.3 + - + +
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Residues in contact with ILE 421 (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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15A PHE* 4.0 14.1 - - + -
16A PRO* 3.6 30.1 - - + -
19A PHE* 3.7 31.4 - - + -
417A LEU* 2.9 33.8 + - + +
418A LYS* 3.7 7.6 - - - +
420A ALA* 1.3 75.7 - - - +
422A ASP* 1.3 63.8 + - - +
424A GLY* 2.9 21.0 + - - -
425A ALA 3.7 13.7 + - - +
427A VAL* 3.9 25.1 - - + +
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Residues in contact with ASP 422 (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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14A ALA 4.5 2.6 - - - +
16A PRO* 6.1 0.2 - - - +
418A LYS* 2.8 57.1 + - - +
419A LYS* 3.8 6.9 - - - +
421A ILE* 1.3 82.1 - - - +
423A GLU* 1.3 60.3 + - + +
424A GLY 3.2 1.0 + - - -
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Residues in contact with GLU 423 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367A TYR* 2.5 38.7 + - - -
371A ASN* 4.3 6.1 - - - +
374A LYS* 3.6 20.9 + - + -
419A LYS* 3.1 29.9 + - - +
420A ALA* 3.6 10.3 - - - +
421A ILE 3.1 1.2 - - - -
422A ASP* 1.3 78.5 - - + +
424A GLY* 1.3 57.5 + - - +
425A ALA 3.7 0.2 - - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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