Contacts of the helix formed by residues 742 - 757 (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 LEU 742 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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395D VAL* 4.6 25.4 - - + -
436D CYS* 6.1 3.4 - - + -
438D PHE* 5.7 13.2 - - + -
473D ASP* 5.9 3.6 - - + +
474D ILE* 6.1 5.4 - - + -
736D THR* 5.8 3.4 - - + -
740D SER* 3.6 10.6 + - - +
741D SER* 1.3 88.5 + - - +
743D GLY* 1.3 63.9 + - - +
744D ASN 3.1 1.0 + - - -
745D ALA* 3.2 10.0 + - + +
746D VAL* 3.0 36.1 + - + +
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Residues in contact with GLY 743 (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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490D ASP* 6.4 0.2 - - - -
492D SER* 5.0 3.5 - - - -
736D THR* 4.4 24.8 + - - +
740D SER* 4.3 8.1 + - - -
741D SER 3.2 3.0 - - - -
742D LEU* 1.3 77.1 - - - +
744D ASN* 1.3 56.1 + - - +
746D VAL* 3.7 6.7 - - - +
747D ASN* 2.9 30.8 + - - +
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Residues in contact with ASN 744 (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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740D SER 5.4 0.6 + - - -
741D SER 3.6 10.1 + - - +
742D LEU 3.1 0.8 + - - -
743D GLY* 1.3 75.9 - - - +
745D ALA* 1.3 63.8 + - - +
747D ASN* 3.1 11.9 + - - +
748D LEU* 2.9 37.5 + - - +
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Residues in contact with ALA 745 (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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436D CYS* 4.2 13.0 - - - -
741D SER 4.6 1.0 + - - +
742D LEU* 3.2 12.4 + - + +
744D ASN* 1.3 79.1 - - - +
746D VAL* 1.3 64.1 + - + +
748D LEU* 3.0 19.9 + - + +
749D ALA* 2.9 23.2 + - - +
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Residues in contact with VAL 746 (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* 3.9 22.2 - - + -
436D CYS* 4.1 20.9 - - + -
438D PHE* 5.4 4.7 - - + -
474D ILE* 4.7 12.6 - - + -
492D SER* 5.4 2.5 - - - -
734D ILE* 4.5 23.6 - - + -
736D THR* 5.8 2.5 - - + -
742D LEU* 3.0 35.9 + - + +
743D GLY* 3.7 6.7 - - - +
745D ALA* 1.3 75.5 - - - +
747D ASN* 1.3 64.0 + - - +
749D ALA* 3.1 3.7 + - - +
750D VAL* 2.9 36.0 + - + +
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Residues in contact with ASN 747 (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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486A GLU* 5.5 1.8 + - - -
492D SER* 3.9 17.3 - - - +
493D LYS* 3.5 60.0 + - - +
743D GLY 2.9 14.7 + - - +
744D ASN* 3.1 13.8 + - - +
746D VAL* 1.3 75.3 - - - +
748D LEU* 1.3 65.0 + - + +
750D VAL* 3.2 5.7 + - - +
751D LEU* 2.9 32.8 + - - +
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Residues in contact with LEU 748 (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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483A LEU* 3.7 23.7 - - + +
486A GLU* 5.1 11.7 - - + +
487A GLU* 5.7 5.4 - - + -
744D ASN* 2.9 31.0 + - - +
745D ALA* 3.0 24.0 + - + +
747D ASN* 1.3 77.5 - - + +
749D ALA* 1.3 62.5 + - - +
751D LEU* 3.1 12.2 + - + +
752D LYS* 2.9 21.6 + - - +
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Residues in contact with ALA 749 (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* 4.6 9.2 - - + -
435D HIS* 3.8 31.4 - - + -
436D CYS* 4.3 11.2 - - - -
745D ALA 2.9 12.0 + - - +
746D VAL 3.7 6.1 - - - +
748D LEU* 1.3 75.6 - - - +
750D VAL* 1.3 63.7 + - - +
752D LYS* 3.2 13.1 + - + +
753D LEU* 2.9 28.8 + - - +
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Residues in contact with VAL 750 (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* 5.7 4.0 - - + -
432D ILE* 3.8 21.8 - - + -
492D SER* 4.7 9.0 - - - +
493D LYS 4.5 11.9 - - - +
495D PHE* 4.3 25.6 - - + -
734D ILE* 4.8 9.9 - - + -
746D VAL* 2.9 29.2 + - + +
747D ASN* 3.4 13.0 - - - +
749D ALA* 1.3 75.3 - - - +
751D LEU* 1.3 67.9 + - + +
753D LEU* 3.1 8.7 + - - +
754D ASN* 2.9 22.5 + - + +
759D LEU* 4.6 6.4 - - + +
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Residues in contact with LEU 751 (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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481A ILE* 5.4 8.7 - - + +
482A THR* 5.8 0.9 - - - -
483A LEU* 3.6 25.8 - - + +
486A GLU* 3.5 35.9 - - + -
493D LYS* 4.3 17.7 - - + -
747D ASN* 2.9 39.1 + - - +
748D LEU* 3.4 10.3 - - + +
750D VAL* 1.3 78.4 - - + +
752D LYS* 1.3 64.0 + - - +
754D ASN* 3.1 15.7 + - - +
755D GLU* 2.9 26.9 + - + +
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Residues in contact with LYS 752 (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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483A LEU* 3.8 26.6 - - + +
435D HIS* 4.5 21.2 + - + +
748D LEU 2.9 12.9 + - - +
749D ALA* 3.4 14.4 - - - +
751D LEU* 1.3 74.1 - - - +
753D LEU* 1.3 50.3 + - - +
755D GLU* 3.2 6.2 + - - +
756D GLN* 2.7 67.2 + - + +
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Residues in contact with LEU 753 (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* 5.1 2.0 - - + -
431D GLU* 3.8 33.0 - - + +
432D ILE* 4.0 19.1 - - + -
435D HIS* 3.4 25.8 - - + +
749D ALA 2.9 18.6 + - - +
750D VAL* 3.5 7.9 - - - +
752D LYS* 1.3 74.6 - - + +
754D ASN* 1.3 53.5 + - - +
756D GLN* 2.9 25.2 + - + +
757D GLY* 2.6 34.1 + - - -
758D LEU* 3.8 13.7 + - + -
759D LEU* 4.0 30.7 - - + +
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Residues in contact with ASN 754 (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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658A PHE* 6.0 0.3 - - - -
728A ASP* 5.6 5.4 - - - +
729A SER* 3.5 29.5 + - - +
730A LYS* 5.3 3.4 - - - +
494D PRO 5.2 6.3 + - - -
495D PHE* 5.1 13.0 + - + +
750D VAL* 2.9 16.2 + - + +
751D LEU* 3.1 19.9 + - + +
753D LEU* 1.3 76.3 - - - +
755D GLU* 1.3 62.9 + - + +
757D GLY* 3.2 13.3 + - - -
759D LEU* 4.0 14.9 - - + +
760D ASP* 5.3 4.5 - - - +
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Residues in contact with GLU 755 (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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482A THR* 3.2 16.6 - - + -
483A LEU* 2.6 51.2 + - - +
484A VAL* 4.1 8.5 + - - +
658A PHE* 4.7 19.3 - - + -
661A ARG* 6.1 1.0 - - - +
730A LYS* 6.1 3.4 - - - +
751D LEU 2.9 12.4 + - - +
752D LYS* 3.7 6.7 - - - +
754D ASN* 1.3 77.1 - - + +
756D GLN* 1.3 61.8 + - + +
757D GLY* 3.3 1.6 + - - -
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Residues in contact with GLN 756 (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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435D HIS* 4.5 7.8 - - - -
752D LYS* 2.7 55.8 + - + +
753D LEU* 3.2 29.7 - - + +
755D GLU* 1.3 73.3 - - + +
757D GLY* 1.3 55.6 + - - +
758D LEU* 2.9 19.2 + - + +
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Residues in contact with GLY 757 (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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753D LEU 2.6 13.3 + - - -
754D ASN* 3.2 9.6 + - - -
755D GLU 3.1 4.9 - - - -
756D GLN* 1.3 71.1 - - - +
758D LEU* 1.3 57.7 + - - +
759D LEU* 3.0 3.8 - - - -
760D ASP* 2.8 43.0 + - - +
761D LYS* 3.6 2.8 + - - +
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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