Contacts of the helix formed by residues 439 - 458 (chain A) in PDB entry 3F7F
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 439 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404A VAL* 4.5 3.7 - - - +
433A ILE 4.0 4.0 - - - +
434A MET* 3.9 5.8 - - + +
435A ALA* 3.0 33.8 + - - +
436A HIS* 3.3 33.4 + - - +
437A ASN 3.5 1.6 + - - -
438A GLU* 1.3 70.3 - - - +
440A GLU* 1.3 56.9 + - - +
441A GLU* 3.1 27.9 - - - +
442A TYR* 2.8 40.7 + - + +
443A LEU* 3.4 4.0 + - - +
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Residues in contact with GLU 440 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404A VAL* 5.1 11.4 - - + -
438A GLU* 2.6 24.4 + - + +
439A ASP* 1.3 70.4 - - - +
441A GLU* 1.3 62.7 + - - +
443A LEU* 3.3 11.4 + - + +
444A ALA* 3.0 25.5 + - - +
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Residues in contact with GLU 441 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439A ASP* 3.1 14.4 - - - +
440A GLU* 1.3 77.8 - - - +
442A TYR* 1.3 60.7 + - - +
444A ALA* 3.5 14.3 - - - +
445A ASN* 3.3 18.8 + - - +
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Residues in contact with TYR 442 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408A PHE* 4.3 11.7 - + - -
424A GLN* 3.6 19.0 + - - +
427A LEU* 3.2 42.5 - - + +
432A ILE* 4.0 23.7 + - + -
433A ILE* 4.9 1.2 - - - -
434A MET* 3.2 64.2 + - + +
439A ASP* 2.8 29.4 + - - +
441A GLU* 1.3 72.3 - - - +
443A LEU* 1.3 57.9 + - - +
444A ALA 2.9 1.1 - - - -
445A ASN* 2.3 42.9 + - - +
446A LEU* 3.2 7.2 + - + -
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Residues in contact with LEU 443 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403A ASP 5.4 0.2 - - - +
404A VAL* 3.6 38.6 - - + +
407A GLY* 4.1 19.5 - - - +
408A PHE* 4.6 7.0 - - + +
411A LEU* 4.3 11.7 - - + -
434A MET* 5.8 0.4 - - + -
439A ASP 3.4 4.8 + - - +
440A GLU* 3.3 13.8 + - + +
442A TYR* 1.3 83.6 - - + +
444A ALA* 1.3 65.3 + - - +
445A ASN 3.1 0.9 + - - -
446A LEU* 3.1 13.1 + - - +
447A GLU* 3.1 44.8 + - + +
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Residues in contact with ALA 444 (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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440A GLU 3.0 13.2 + - - +
441A GLU* 3.5 15.3 - - - +
442A TYR 2.7 4.4 + - - -
443A LEU* 1.3 82.7 - - - +
445A ASN* 1.3 60.5 + - - +
447A GLU* 3.5 17.2 - - - +
448A THR* 3.7 9.4 + - - -
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Residues in contact with ASN 445 (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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427A LEU* 4.0 17.3 - - + -
432A ILE* 3.8 31.0 - - + +
441A GLU* 3.3 21.6 + - - +
442A TYR* 2.3 29.2 + - - +
444A ALA* 1.3 67.2 - - - +
446A LEU* 1.3 64.6 + - - +
447A GLU 3.1 1.8 - - - -
448A THR* 2.9 18.2 + - - -
449A ILE* 3.0 18.0 + - + +
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Residues in contact with LEU 446 (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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408A PHE* 3.4 39.9 - - + -
411A LEU* 4.5 7.6 - - + -
420A PHE* 4.0 14.6 - - + -
423A ALA* 4.0 14.4 - - + -
424A GLN* 4.3 9.9 - - + +
427A LEU* 3.7 29.1 - - + +
442A TYR* 3.2 10.1 + - + -
443A LEU* 3.1 15.0 + - - +
445A ASN* 1.3 76.9 - - - +
447A GLU* 1.3 64.6 + - - +
449A ILE* 3.2 2.9 + - + +
450A LEU* 2.8 51.4 + - + +
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Residues in contact with GLU 447 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391A SER* 5.3 2.4 + - - -
411A LEU* 3.8 23.9 - - + +
414A ARG* 5.3 5.5 + - - -
415A TYR* 4.5 4.2 + - - -
443A LEU* 3.3 34.2 - - + +
444A ALA* 3.5 12.8 - - - +
446A LEU* 1.3 78.1 - - - +
448A THR* 1.3 59.8 + - - +
450A LEU* 3.7 8.3 - - - +
451A ARG* 3.0 30.5 + - - +
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Residues in contact with THR 448 (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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444A ALA 3.7 10.4 + - - -
445A ASN* 2.9 9.9 + - - -
447A GLU* 1.3 76.1 - - - +
449A ILE* 1.3 66.5 + - + +
451A ARG* 3.4 30.0 + - - +
452A ASP* 2.9 46.6 + - - +
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Residues in contact with ILE 449 (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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423A ALA* 3.4 36.6 - - + +
426A ILE* 4.3 22.7 - - + -
427A LEU* 4.5 15.7 - - + -
432A ILE* 6.2 1.8 - - + -
445A ASN* 3.0 16.9 + - + +
446A LEU* 3.9 6.7 - - - +
448A THR* 1.3 78.9 - - + +
450A LEU* 1.3 56.9 + - - +
452A ASP* 2.8 13.0 + - + +
453A VAL* 2.6 43.5 + - + +
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Residues in contact with LEU 450 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411A LEU* 3.7 37.5 - - + -
415A TYR* 3.7 30.3 - - + -
419A ILE* 4.1 11.5 - - + +
420A PHE* 3.6 32.1 - - + -
423A ALA* 3.5 22.7 - - + -
446A LEU* 2.8 43.7 + - + +
447A GLU* 3.7 2.7 - - - +
449A ILE* 1.3 70.8 - - - +
451A ARG* 1.3 65.4 + - - +
453A VAL* 3.8 0.7 - - - +
454A LYS* 2.8 26.9 + - - +
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Residues in contact with ARG 451 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392A GLU* 5.2 15.9 - - + +
414A ARG* 6.0 1.8 - - - +
415A TYR* 3.8 16.5 + - - +
447A GLU 3.0 19.1 + - - +
448A THR* 3.5 34.2 + - - +
450A LEU* 1.3 77.1 - - - +
452A ASP* 1.3 76.5 + - - +
454A LYS* 3.5 3.8 + - - +
455A THR* 3.0 34.9 + - - +
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Residues in contact with ASP 452 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448A THR* 2.9 33.5 + - - +
449A ILE* 2.8 21.3 + - + +
451A ARG* 1.3 87.1 + - - +
453A VAL* 1.3 55.2 + - + +
455A THR* 3.1 10.2 + - - +
456A ALA* 2.7 37.1 + - - +
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Residues in contact with VAL 453 (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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419A ILE* 3.9 17.5 - - + -
422A ARG* 3.7 16.2 - - + +
423A ALA* 4.2 5.2 - - - -
426A ILE* 4.1 20.2 - - + -
449A ILE* 2.6 42.2 + - + +
450A LEU* 3.8 3.4 - - - +
452A ASP* 1.3 70.6 - - + +
454A LYS* 1.3 53.7 + - - +
456A ALA* 3.0 6.7 + - - -
457A PHE* 2.7 68.0 + - + -
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Residues in contact with LYS 454 (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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6A ARG* 4.9 1.4 - - - +
8A ASP* 3.1 28.4 + - - -
385A SER* 4.8 0.4 + - - -
388A ASP* 3.0 36.3 + - - +
415A TYR* 4.1 20.0 - - + -
419A ILE* 3.8 27.8 - - + +
450A LEU 2.8 18.5 + - - +
451A ARG* 3.5 4.9 - - - +
453A VAL* 1.3 77.8 - - - +
455A THR* 1.3 55.4 + - - +
457A PHE* 3.0 1.5 + - - +
458A ASN* 2.7 59.4 + - - +
480A ASN* 5.7 0.2 - - - +
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Residues in contact with THR 455 (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 THR* 3.1 42.4 - - + +
384A LYS* 5.6 7.1 - - - -
451A ARG* 3.0 21.5 + - - +
452A ASP* 3.1 13.9 + - - +
454A LYS* 1.3 78.6 - - - +
456A ALA* 1.3 65.8 + - - +
458A ASN* 3.4 8.3 + - - +
459A GLU 3.4 12.0 + - - -
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Residues in contact with ALA 456 (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 THR* 4.5 11.7 - - + -
422A ARG* 6.1 2.5 - - - +
452A ASP 2.7 17.4 + - - +
453A VAL* 3.4 11.4 - - - +
455A THR* 1.3 68.3 - - - +
457A PHE* 1.3 72.5 + - + +
458A ASN 2.9 1.3 - - - -
459A GLU* 2.8 23.3 + - - +
476A PHE* 4.3 5.5 - - - +
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Residues in contact with PHE 457 (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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418A GLN* 3.4 34.5 - - + -
419A ILE* 3.5 27.8 - - + -
422A ARG* 3.9 35.4 - - + -
453A VAL* 2.7 40.8 + - + +
454A LYS* 3.5 5.6 - - - +
456A ALA* 1.3 75.6 - - + +
458A ASN* 1.3 65.2 + - - +
459A GLU 3.5 0.3 + - - -
475A CYS* 3.2 11.4 - - - +
477A GLN* 3.1 64.8 + - + +
480A ASN* 3.7 9.6 - - - +
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Residues in contact with ASN 458 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A ARG* 3.0 32.9 + - - +
8A ASP* 3.6 16.3 - - - +
359A THR 5.0 3.3 - - - +
361A SER* 6.1 0.5 - - - -
454A LYS* 2.7 57.0 + - - +
455A THR* 3.6 9.2 - - - +
456A ALA 2.9 0.8 + - - -
457A PHE* 1.3 79.5 - - - +
459A GLU* 1.3 66.5 + - - -
460A ALA* 3.1 4.3 + - - +
473A VAL* 6.1 0.2 - - - +
475A CYS* 3.9 15.9 - - - -
480A ASN* 4.3 10.5 + - - +
481A HIS 5.0 1.0 - - - +
482A SER* 3.7 5.5 + - - -
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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
------------------------------------------------------------
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