Contacts of the helix formed by residues 765 - 776 (chain D) in PDB entry 5ON2
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 THR 765 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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640D ASP* 3.4 38.4 - - + +
644D LEU* 4.0 16.6 - - + -
670D LEU* 4.1 13.9 - - + +
761D LEU* 2.8 24.0 + - + +
762D ASN 3.5 2.9 - - - -
764D PHE* 1.3 80.7 - - + +
766D PRO* 1.3 64.1 - - - +
767D HIS 3.4 2.5 - - - -
768D ILE* 3.4 21.0 - - - +
769D CYS* 3.1 27.5 + - - +
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Residues in contact with PRO 766 (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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18D TRP* 3.9 11.1 - - + -
64D ARG* 3.4 39.0 - - - +
116D GLY 4.2 0.2 - - - +
640D ASP* 3.6 7.9 - - - +
643D ARG* 3.4 30.3 - - - +
762D ASN* 3.2 23.5 - - - +
764D PHE 3.6 8.1 - - - +
765D THR* 1.3 85.4 - - - +
767D HIS* 1.3 64.6 + - - +
769D CYS 4.1 1.1 - - - -
770D PHE* 3.2 28.4 + - - +
782D ILE* 4.9 0.2 - - - +
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Residues in contact with HIS 767 (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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10D ILE* 4.7 3.1 - - + -
11D GLU* 3.7 46.6 + - + -
14D VAL* 4.1 14.0 - - + +
15D GLN* 3.4 24.5 + - + +
18D TRP* 3.8 16.7 - + - -
115D LEU 3.6 26.2 - - - -
116D GLY* 3.7 10.5 - - - -
639D ALA* 4.3 7.2 - - + -
640D ASP* 2.8 27.0 + - - +
765D THR 3.4 0.4 - - - -
766D PRO* 1.3 85.5 - - + +
768D ILE* 1.3 63.7 - - - +
770D PHE* 3.5 3.6 + - - +
771D THR* 2.9 27.5 + - - -
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Residues in contact with ILE 768 (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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5D TYR* 3.6 40.4 + - + +
10D ILE* 5.2 2.2 - - - +
640D ASP* 2.9 24.2 + - - +
670D LEU* 3.9 39.9 - - + +
673D VAL* 5.4 2.0 - - + -
674D TRP* 4.0 13.2 - - + -
765D THR* 3.4 25.4 - - - +
767D HIS* 1.3 72.6 - - - +
769D CYS* 1.3 64.7 + - - +
771D THR* 3.4 6.5 + - - -
772D LEU* 2.9 50.1 + - + +
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Residues in contact with CYS 769 (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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758D VAL* 3.2 42.8 - - + +
761D LEU* 3.4 24.9 - - - -
762D ASN* 3.5 10.5 - - - +
765D THR* 3.1 26.3 + - - +
766D PRO 4.5 0.2 - - - +
767D HIS 3.3 0.6 - - - -
768D ILE* 1.3 81.9 - - - +
770D PHE* 1.3 57.6 + - - +
772D LEU* 4.3 4.0 - - - +
773D TRP* 2.8 35.9 + - - +
782D ILE* 3.6 10.3 - - + +
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Residues in contact with PHE 770 (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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14D VAL* 3.7 33.4 - - + -
17D HIS* 3.8 35.4 - + + -
18D TRP* 4.4 4.5 - - + -
766D PRO 3.2 19.9 + - - +
767D HIS 3.7 3.8 - - - +
769D CYS* 1.3 78.0 - - - +
771D THR* 1.3 63.2 + - - +
773D TRP* 3.7 3.4 + - - +
774D GLN* 3.5 42.5 + - + +
781D ASP* 3.6 32.8 - - + -
782D ILE* 3.7 26.8 - - + +
783D ASP* 4.1 14.8 - - - -
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Residues in contact with THR 771 (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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10D ILE* 3.1 26.5 - - + +
14D VAL* 4.2 6.1 - - - +
674D TRP* 4.1 26.5 - - + -
767D HIS 2.9 14.7 + - - -
768D ILE* 3.5 8.5 - - - -
769D CYS 3.2 0.4 - - - -
770D PHE* 1.3 80.2 - - - +
772D LEU* 1.3 63.6 + - - +
774D GLN* 3.3 18.5 + - - +
775D GLU* 3.3 24.2 + - + +
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Residues in contact with LEU 772 (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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1D MET* 4.9 7.0 - - - -
673D VAL* 3.9 28.0 - - + +
674D TRP* 3.8 30.3 - - + -
677D VAL* 3.6 32.1 - - + -
758D VAL* 4.2 20.2 - - + -
768D ILE* 2.9 40.6 + - + +
769D CYS* 3.4 6.2 + - - +
771D THR* 1.3 73.4 - - - +
773D TRP* 1.3 60.0 + - - +
775D GLU* 3.4 6.9 + - + +
776D LEU* 3.1 35.1 + - - +
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Residues in contact with TRP 773 (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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755D LEU* 3.5 34.8 - - + -
758D VAL* 4.3 8.5 - - + +
759D ARG* 3.5 45.8 - - + -
769D CYS 2.8 22.8 + - - +
770D PHE 3.8 6.1 - - - +
772D LEU* 1.3 73.8 - - - +
774D GLN* 1.3 60.8 + - + +
776D LEU* 3.5 8.1 + - + +
778D GLY* 3.0 48.5 + - - -
779D GLU* 3.6 12.6 + - + -
780D GLY 3.3 27.4 + - - -
781D ASP* 4.0 1.2 - - - -
782D ILE* 3.6 36.6 - - + +
785D ALA* 4.1 13.7 - - + -
786D PRO* 5.6 2.5 - - + -
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Residues in contact with GLN 774 (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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770D PHE* 3.5 38.9 - - + +
771D THR* 3.3 10.8 + - - +
773D TRP* 1.3 82.3 - - + +
775D GLU* 1.3 64.0 + - + +
777D LYS* 3.2 16.0 + - - +
778D GLY 4.9 3.4 - - - +
780D GLY 5.5 4.0 - - - +
781D ASP* 6.0 3.6 - - - +
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Residues in contact with GLU 775 (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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1D MET* 3.6 62.7 + - + +
677D VAL* 4.5 6.1 - - + -
681D THR* 3.3 18.6 - - - +
771D THR* 3.3 25.7 + - + +
772D LEU* 3.8 11.9 - - + +
773D TRP 3.4 0.2 - - - -
774D GLN* 1.3 79.2 - - - +
776D LEU* 1.3 59.1 + - - +
777D LYS* 3.3 8.9 + - - +
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Residues in contact with LEU 776 (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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677D VAL* 4.1 21.3 - - + -
680D HIS* 4.4 11.0 - - + -
681D THR* 4.4 4.9 - - + -
751D GLN* 3.1 41.1 + - - +
754D LEU* 3.8 42.0 - - + +
755D LEU* 4.2 16.7 - - + +
758D VAL* 3.9 16.6 - - + -
772D LEU 3.1 22.7 + - - +
773D TRP* 3.5 7.2 + - + +
774D GLN 3.3 0.6 - - - -
775D GLU* 1.3 75.8 - - - +
777D LYS* 1.3 70.6 + - - +
778D GLY* 3.3 1.3 + - - -
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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