Contacts of the helix formed by residues 423 - 437 (chain D) in PDB entry 5VOT
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 GLY 423 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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404D PRO 3.4 7.9 - - - -
405D TYR 3.1 11.7 - - - -
406D VAL* 4.1 0.2 - - - -
407D MET* 4.4 1.1 - - - -
422D GLU* 1.3 77.9 - - - +
424D TYR* 1.3 66.4 - - - +
425D CYS 3.4 0.2 - - - -
426D VAL* 3.3 11.5 + - - +
427D ASP* 3.3 9.4 + - - +
766D TRP* 3.3 32.8 + - - -
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Residues in contact with TYR 424 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404D PRO 2.7 21.1 + - - +
405D TYR* 2.8 16.8 + + - -
423D GLY* 1.3 70.2 - - - -
425D CYS* 1.3 66.2 + - - +
427D ASP* 3.0 8.6 + - + +
428D LEU* 2.9 26.3 + - + -
495D PHE* 4.5 16.8 - + - -
496D MET* 3.7 27.9 - - + +
759D LEU* 3.3 34.5 + - + +
762D LEU* 3.4 34.8 - - + -
763D LYS 3.6 2.2 - - - -
766D TRP* 3.5 31.4 - + + +
767D TRP* 3.5 23.3 - + + -
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Residues in contact with CYS 425 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405D TYR* 2.8 48.7 + - - +
406D VAL* 3.8 13.0 - - + -
424D TYR* 1.3 78.6 - - - +
426D VAL* 1.3 57.6 + - - +
428D LEU* 3.3 15.6 + - - +
429D ALA* 2.9 28.4 + - - +
476D ILE* 4.0 16.5 - - + +
477D ALA* 3.9 11.2 - - - -
478D PRO* 3.6 16.4 - - - -
495D PHE* 6.1 3.4 - - - -
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Residues in contact with VAL 426 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406D VAL* 4.4 11.2 - - + -
418D ASN 5.1 2.9 - - - +
421D TYR* 4.2 16.8 - - + +
422D GLU* 3.4 39.5 - - - +
423D GLY* 3.4 10.8 - - - +
424D TYR 3.1 0.8 - - - -
425D CYS* 1.3 74.2 - - - +
427D ASP* 1.3 65.6 + - - +
429D ALA* 3.1 8.7 + - - +
430D ALA* 2.9 27.6 + - + +
440D TYR* 5.5 2.1 + - - +
442D LEU* 4.8 15.5 - - + -
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Residues in contact with ASP 427 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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423D GLY 3.3 5.2 + - - +
424D TYR* 3.0 8.1 + - - +
426D VAL* 1.3 81.8 - - - +
428D LEU* 1.3 62.4 + - - +
430D ALA* 3.3 9.0 + - - +
431D GLU* 2.9 31.6 + - + +
762D LEU* 4.3 26.7 - - + +
765D LYS* 3.8 12.5 + - - -
766D TRP* 2.9 32.2 + - - +
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Residues in contact with LEU 428 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424D TYR* 2.9 21.0 + - + +
425D CYS* 3.3 18.4 - - - +
427D ASP* 1.3 76.5 - - - +
429D ALA* 1.3 57.3 + - - +
431D GLU* 3.1 5.2 + - - +
432D ILE* 2.9 53.9 + - + +
476D ILE* 3.6 23.6 - - + -
477D ALA 5.6 0.4 - - - +
495D PHE* 4.6 24.2 - - + -
734D ILE* 3.7 17.7 - - + -
750D VAL* 5.7 3.8 - - + -
753D LEU* 5.1 3.6 - - + -
759D LEU* 4.5 23.1 - - + -
762D LEU* 5.4 2.1 - - - +
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Residues in contact with ALA 429 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397D VAL* 5.2 2.9 - - + -
425D CYS 2.9 17.1 + - - +
426D VAL* 3.1 10.3 + - + +
428D LEU* 1.3 72.9 - - - +
430D ALA* 1.3 58.5 + - - +
432D ILE* 4.1 1.1 - - - +
433D ALA* 2.9 33.1 + - - +
438D PHE* 5.4 0.3 - - - -
440D TYR* 4.7 19.9 - - + -
442D LEU* 4.9 10.1 - - + -
476D ILE* 4.2 28.2 - - + +
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Residues in contact with ALA 430 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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426D VAL* 2.9 14.5 + - + +
427D ASP* 3.6 13.9 - - - +
429D ALA* 1.3 76.2 - - - +
431D GLU* 1.3 59.1 + - + +
433D ALA* 3.9 2.8 - - - +
434D LYS* 2.9 30.2 + - - +
440D TYR* 4.6 13.3 + - - +
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Residues in contact with GLU 431 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427D ASP* 2.9 22.3 + - + +
428D LEU* 3.6 6.5 - - + +
430D ALA* 1.3 78.7 - - + +
432D ILE* 1.3 57.3 + - - +
434D LYS* 3.1 9.6 + - - +
435D HIS* 2.9 53.4 + - - -
753D LEU* 3.8 25.0 - - + +
758D LEU* 4.1 20.9 - - + +
759D LEU* 5.8 1.6 - - + -
762D LEU* 5.0 13.3 - - + +
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Residues in contact with ILE 432 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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428D LEU* 2.9 36.7 + - + +
429D ALA* 4.1 5.2 - - - +
431D GLU* 1.3 75.4 - - - +
433D ALA* 1.3 58.2 + - - +
435D HIS* 3.3 3.6 + - - +
436D CYS* 2.9 35.7 + - - +
438D PHE* 4.2 9.0 - - + -
474D ILE* 5.5 1.8 - - + -
476D ILE* 5.1 11.7 - - + -
734D ILE* 5.7 4.0 - - + -
746D VAL* 3.9 31.4 - - + -
749D ALA* 4.6 4.7 - - + -
750D VAL* 3.8 33.2 - - + +
753D LEU* 4.0 21.3 - - + -
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Residues in contact with ALA 433 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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429D ALA 2.9 19.1 + - - +
430D ALA* 4.1 2.5 - - - +
432D ILE* 1.3 76.6 - - - +
434D LYS* 1.3 54.4 + - - +
437D GLY* 2.7 32.6 + - - -
438D PHE* 3.5 32.8 + - + +
440D TYR* 3.7 31.6 - - + -
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Residues in contact with LYS 434 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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430D ALA 2.9 20.9 + - - +
431D GLU* 3.1 11.2 + - - +
433D ALA* 1.3 79.6 - - - +
435D HIS* 1.3 90.7 + - + +
437D GLY* 3.5 7.5 + - - -
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Residues in contact with HIS 435 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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431D GLU* 2.9 44.0 + - - +
432D ILE 4.1 1.6 - - - +
434D LYS* 1.3 100.3 + - + +
436D CYS* 1.3 60.6 + - - +
749D ALA* 3.8 25.1 - - + -
752D LYS* 4.5 21.3 + - + +
753D LEU* 3.4 34.3 - - + +
756D GLN* 4.5 9.9 - - - -
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Residues in contact with CYS 436 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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432D ILE* 2.9 20.9 + - - +
433D ALA 3.7 0.2 - - - -
435D HIS* 1.3 78.4 - - - +
437D GLY* 1.3 66.2 + - - +
438D PHE* 3.4 19.4 - - + +
742D LEU* 6.1 4.3 - - + -
745D ALA* 4.2 13.7 - - - -
746D VAL* 4.1 38.1 - - + -
749D ALA* 4.3 9.9 - - - -
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Residues in contact with GLY 437 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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433D ALA 2.7 18.0 + - - -
434D LYS* 3.5 6.7 + - - -
435D HIS 3.5 2.4 - - - -
436D CYS* 1.3 78.2 - - - +
438D PHE* 1.3 58.4 + - - +
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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