Contacts of the helix formed by residues 441 - 456 (chain A) in PDB entry 5DP0
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 GLN 441 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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393A TRP* 3.9 1.6 - - - -
439A ASN* 3.1 22.4 - - - +
440A LEU* 1.3 76.9 - - - +
442A GLY* 1.3 62.6 + - - +
443A GLU* 3.9 14.6 + - + +
444A GLU* 2.9 31.2 + - + +
445A PHE* 2.9 25.6 + - - +
503A ARG* 5.3 0.2 - - - +
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Residues in contact with GLY 442 (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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320A LEU* 4.5 9.0 - - - -
393A TRP* 3.5 28.0 - - - -
441A GLN* 1.3 74.0 - - - +
443A GLU* 1.3 65.3 + - - +
445A PHE* 3.3 4.5 + - - +
446A VAL* 3.1 29.6 + - - +
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Residues in contact with GLU 443 (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* 3.6 26.5 - - + +
320A LEU* 4.2 15.9 - - + +
441A GLN* 3.9 13.9 + - + +
442A GLY* 1.3 80.5 + - - +
444A GLU* 1.3 63.1 + - + +
446A VAL* 3.2 23.0 - - - +
447A CYS* 3.4 14.4 - - - -
489A LEU* 3.6 31.5 - - + +
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Residues in contact with GLU 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 LEU* 3.6 15.5 - - + +
441A GLN* 2.9 42.8 + - + +
443A GLU* 1.3 77.4 - - + +
445A PHE* 1.3 62.6 + - - +
447A CYS* 3.2 5.5 + - - +
448A LEU* 3.0 24.3 + - - +
486A LEU* 4.0 20.8 - - + +
489A LEU* 4.6 14.1 - - + -
490A MET* 3.8 17.2 - - + +
503A ARG* 2.8 42.8 + - - -
507A LEU* 3.9 4.2 - - + +
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Residues in contact with PHE 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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323A GLU* 3.6 20.9 - - - -
389A ILE* 3.4 43.1 - - + -
390A GLY* 4.2 7.6 - - - -
393A TRP* 3.5 55.9 - + + -
435A PHE* 5.1 0.4 - + - -
440A LEU* 4.1 14.1 - - + +
441A GLN 2.9 12.8 + - - +
442A GLY* 3.5 8.7 - - - +
443A GLU 3.3 0.2 - - - -
444A GLU* 1.3 76.5 - - - +
446A VAL* 1.3 71.6 + - + +
448A LEU* 3.1 6.2 + - + +
449A LYS* 3.0 46.9 + - + +
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Residues in contact with VAL 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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316A VAL* 4.8 3.1 - - + +
319A LEU* 3.8 35.3 - - + +
320A LEU* 4.1 16.8 - - + -
323A GLU* 3.6 41.3 - - + +
360A TRP* 5.3 3.4 + - - +
442A GLY 3.1 11.4 + - - +
443A GLU* 3.2 22.0 - - - +
445A PHE* 1.3 82.4 - - + +
447A CYS* 1.3 61.5 + - - +
449A LYS* 3.9 7.9 - - - +
450A SER* 3.3 23.6 + - - -
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Residues in contact with CYS 447 (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* 5.3 2.2 - - - -
319A LEU* 4.3 12.8 - - - -
443A GLU 3.4 14.4 - - - -
444A GLU 3.2 9.1 + - - +
445A PHE 3.1 0.4 - - - -
446A VAL* 1.3 80.9 - - - +
448A LEU* 1.3 65.3 + - - +
450A SER* 2.8 22.2 + - - -
451A ILE* 2.9 17.5 + - - +
482A ILE* 3.9 17.5 - - + -
485A THR* 4.2 26.0 - - - -
486A LEU* 3.6 24.5 - - + -
489A LEU* 4.3 4.3 - - - -
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Residues in contact with LEU 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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389A ILE* 4.0 12.6 - - + -
435A PHE* 4.5 18.4 - - + -
440A LEU* 4.2 26.7 - - + -
444A GLU 3.0 15.5 + - - +
445A PHE* 3.1 8.5 + - - +
447A CYS* 1.3 74.3 - - - +
449A LYS* 1.3 57.5 + - - +
451A ILE* 3.2 10.4 + - + +
452A ILE* 2.9 33.2 + - - +
486A LEU* 4.9 6.1 - - + -
507A LEU* 4.2 33.4 - - + +
508A LEU* 4.3 15.9 - - + -
511A LEU* 3.8 26.0 - - + +
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Residues in contact with LYS 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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323A GLU* 2.5 34.7 + - - -
324A PRO* 3.6 20.6 - - - +
360A TRP* 3.8 24.2 - - + +
386A ILE* 4.0 29.2 - - + +
389A ILE* 4.0 19.5 - - + +
390A GLY* 5.3 2.0 - - - +
445A PHE* 3.0 38.3 + - + +
446A VAL* 3.9 7.6 - - - +
447A CYS 3.2 0.2 - - - -
448A LEU* 1.3 76.4 - - - +
450A SER* 1.3 63.6 + - - +
452A ILE* 3.2 12.8 + - - +
453A LEU* 3.0 20.1 + - - +
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Residues in contact with SER 450 (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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319A LEU* 4.2 12.7 - - - +
360A TRP* 4.1 6.4 - - - -
364A VAL* 4.0 23.1 - - - -
446A VAL 3.3 12.5 + - - -
447A CYS* 2.8 22.0 + - - -
449A LYS* 1.3 75.5 - - - +
451A ILE* 1.3 65.0 + - - +
453A LEU* 3.0 10.8 + - - +
454A LEU* 3.0 25.8 + - - +
482A ILE* 3.3 22.7 - - - +
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Residues in contact with ILE 451 (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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447A CYS 2.9 20.9 + - - +
448A LEU* 3.2 11.6 + - + +
450A SER* 1.3 76.2 + - - +
452A ILE* 1.3 57.3 + - - +
454A LEU* 3.2 1.2 + - - -
455A ASN* 2.8 35.7 + - + +
479A LEU* 4.0 15.3 - - + +
482A ILE* 3.6 29.4 - - + -
483A THR* 5.1 6.3 - - - +
486A LEU* 4.0 22.2 - - + -
508A LEU* 4.2 13.2 - - + -
511A LEU* 3.8 20.6 - - + -
509B LEU* 3.8 27.6 - - + -
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Residues in contact with ILE 452 (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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382A ALA* 3.9 3.6 - - + +
385A GLU* 3.7 28.7 - - + +
386A ILE* 4.1 13.5 - - + -
389A ILE* 3.7 39.7 - - + -
448A LEU 2.9 15.3 + - - +
449A LYS* 3.3 8.3 - - - +
450A SER 3.2 0.2 - - - -
451A ILE* 1.3 76.0 - - - +
453A LEU* 1.3 63.0 + - - +
455A ASN* 4.6 1.6 - - - +
456A SER* 3.1 41.5 + - - +
511A LEU* 3.9 23.3 - - + -
514A ILE* 4.2 20.9 - - + -
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Residues in contact with LEU 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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360A TRP* 3.9 16.8 - - + -
361A ALA* 4.2 4.9 - - + -
364A VAL* 3.8 34.5 - - + -
367A PHE* 3.7 35.9 - - + -
378A LEU* 3.4 28.8 - - + +
379A LEU* 3.7 30.5 - - + -
382A ALA* 4.3 7.0 - - - +
386A ILE* 4.2 9.2 - - + -
449A LYS 3.0 11.1 + - - +
450A SER 3.0 9.0 + - - +
452A ILE* 1.3 78.9 - - - +
454A LEU* 1.3 61.2 + - + +
456A SER 4.7 0.7 + - - -
457A GLY 5.0 0.3 + - - -
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Residues in contact with LEU 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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364A VAL* 4.7 10.8 - - + -
365A PRO 4.9 0.4 - - - +
366A GLY 5.3 1.1 - - - -
367A PHE* 4.2 25.1 - - + +
370A LEU* 4.6 6.5 - - + -
378A LEU* 3.8 27.3 - - + +
450A SER 3.0 14.0 + - - +
453A LEU* 1.3 81.3 - - + +
455A ASN* 1.3 61.4 + - - +
458A VAL* 3.5 8.0 - - - +
475A ILE* 3.4 31.2 - - + +
478A VAL* 3.7 33.4 - - + -
479A LEU* 3.9 17.7 - - + -
482A ILE* 4.1 18.6 - - + -
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Residues in contact with ASN 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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451A ILE* 2.8 20.5 + - + +
452A ILE* 4.6 1.5 - - - +
454A LEU* 1.3 77.6 - - - +
456A SER* 1.3 67.9 + - - +
457A GLY 3.0 5.2 + - - -
458A VAL* 3.0 21.1 + - - +
479A LEU* 4.3 15.6 - - + +
511A LEU* 5.8 2.0 - - - +
515A ARG* 4.1 2.4 - - - +
509B LEU* 3.5 47.9 + - + +
512B SER* 4.1 11.9 + - - -
513B HIS* 3.0 38.1 + - - -
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Residues in contact with SER 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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381A CYS* 4.2 8.1 - - - +
382A ALA* 4.0 13.5 - - - -
385A GLU* 3.0 35.0 + - - -
452A ILE* 3.1 23.4 + - - +
454A LEU 3.7 0.2 - - - -
455A ASN* 1.3 78.4 + - - +
457A GLY* 1.3 56.2 + - - +
461A PHE 2.8 16.7 - - - +
515A ARG* 3.2 33.7 + - - +
512B SER* 5.0 0.7 + - - -
513B HIS* 4.5 0.4 + - - -
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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