Contacts of the helix formed by residues 752 - 764 (chain D) in PDB entry 1DQA
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 HIS 752 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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204C MAH 4.1 7.0 - - + -
691C LYS* 5.3 5.2 - - + -
692C LYS* 4.9 2.9 - - - -
104D COA 3.5 36.8 - - + +
562D LEU* 4.1 13.5 - - + -
565D SER* 4.8 2.2 - - - -
750D ASN* 4.0 0.9 - - - -
751D ALA* 1.3 77.4 - - - +
753D ALA* 1.3 65.4 + - - +
754D ALA 3.1 3.1 - - - +
755D ASN* 3.0 44.9 + - + +
756D ILE* 3.7 6.0 + - + +
846D VAL 5.7 0.2 - - - -
849D GLY* 3.1 34.1 + - - -
850D GLU* 2.7 21.3 + - - -
853D LEU* 3.4 19.7 - - + +
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Residues in contact with ALA 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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750D ASN* 3.1 22.4 + - + +
752D HIS* 1.3 75.8 - - - +
754D ALA* 1.3 62.6 + - - +
756D ILE* 3.2 5.8 + - - +
757D VAL* 3.0 27.1 + - - +
775D SER 3.6 20.6 - - - +
777D CYS* 3.9 6.1 - - + -
797D MET* 4.5 2.5 - - + -
846D VAL* 3.6 33.8 - - + +
850D GLU* 3.5 2.4 + - - -
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Residues in contact with ALA 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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691C LYS* 3.5 33.8 + - + +
769C ALA* 3.8 4.2 - - - +
772C VAL* 3.9 4.5 - - + -
750D ASN* 4.6 1.0 + - - -
752D HIS 3.1 0.6 - - - -
753D ALA* 1.3 79.3 - - - +
755D ASN* 1.3 56.6 - - - +
758D THR* 2.7 36.7 + - - -
771D ASN* 3.3 14.8 - - - +
775D SER* 3.0 27.8 + - - +
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Residues in contact with ASN 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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204C MAH 2.9 28.1 + - - +
691C LYS* 2.7 26.3 + - - +
767C ASP* 4.3 0.3 - - - +
769C ALA* 3.3 14.6 - - - +
104D COA 3.7 3.6 - - - +
559D GLU* 3.3 12.2 + - - +
562D LEU* 3.6 20.4 - - + +
752D HIS* 3.0 40.8 + - - +
754D ALA* 1.3 79.2 - - - +
756D ILE* 1.3 61.6 + - - +
758D THR* 4.1 1.4 - - - -
759D ALA* 3.2 24.6 + - - +
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Residues in contact with ILE 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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555D MET* 3.5 13.9 - - + -
562D LEU* 3.9 8.5 - - + -
566D THR* 3.0 35.2 - - + +
752D HIS* 4.4 11.0 - - + +
753D ALA* 3.2 7.2 + - - +
755D ASN* 1.3 74.4 - - + +
757D VAL* 1.3 67.8 + - - +
759D ALA* 3.3 2.1 + - - +
760D ILE* 3.0 35.7 + - + +
845D THR* 3.6 26.7 - - + +
846D VAL* 3.6 33.4 - - + +
849D GLY* 4.2 11.4 - - - -
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Residues in contact with VAL 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 ALA 3.0 22.2 + - - +
756D ILE* 1.3 79.0 - - - +
758D THR* 1.3 58.1 + - - +
760D ILE* 3.9 1.1 - - - -
761D TYR* 2.9 69.2 + - + -
771D ASN* 3.5 20.6 - - + +
774D SER* 4.0 17.7 - - - +
775D SER* 4.2 2.9 - - - +
797D MET* 3.8 28.5 - - + -
800D ILE* 6.1 0.4 - - + -
842D VAL* 4.0 12.1 - - + -
846D VAL* 4.0 6.1 - - + -
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Residues in contact with THR 758 (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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768C ALA* 3.7 31.2 - - + +
769C ALA* 3.5 14.5 - - + +
556D ALA 5.8 0.2 - - - +
754D ALA 2.7 24.2 + - - -
755D ASN 4.1 2.9 - - - -
757D VAL* 1.3 78.2 - - - +
759D ALA* 1.3 57.1 + - - +
761D TYR* 3.4 5.3 + - - +
762D ILE* 3.0 40.1 + - + +
768D ALA* 4.9 7.4 - - + +
771D ASN* 3.0 28.4 + - + +
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Residues in contact with ALA 759 (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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555D MET* 3.8 29.8 - - + -
556D ALA 2.9 40.5 + - - +
557D THR* 4.3 1.1 - - - -
562D LEU* 4.1 10.8 - - + -
755D ASN 3.2 18.3 + - - +
756D ILE 3.9 2.9 - - - +
758D THR* 1.3 77.4 - - - +
760D ILE* 1.3 62.5 + - - +
763D ALA* 3.2 12.5 + - - +
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Residues in contact with ILE 760 (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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553D VAL* 3.9 22.4 - - + -
554D PRO 3.9 11.7 - - - +
555D MET* 4.5 5.8 - - + -
756D ILE* 3.0 40.5 + - + +
757D VAL* 4.0 2.5 - - - +
759D ALA* 1.3 73.2 - - - +
761D TYR* 1.3 66.3 + - + +
763D ALA 3.3 0.9 + - - -
764D CYS* 2.8 46.3 + - + +
766D GLN* 5.8 0.2 - - + -
802D ILE* 5.6 0.7 - - + -
821D LEU* 5.2 2.2 - - + -
838D LEU* 4.7 9.4 - - + -
841D ILE* 5.1 1.8 - - + -
842D VAL* 4.1 32.8 - - + +
845D THR* 3.8 18.4 - - - +
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Residues in contact with TYR 761 (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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757D VAL* 2.9 48.1 + - + +
758D THR* 3.6 6.1 - - - +
760D ILE* 1.3 81.8 - - + +
762D ILE* 1.3 62.1 + - - +
764D CYS 3.4 0.5 + - - -
765D GLY* 3.2 4.7 + - - -
766D GLN* 2.9 53.3 + - + +
767D ASP 3.6 20.0 - - - -
768D ALA* 4.4 11.9 - - - -
770D GLN* 4.7 4.3 - - + -
771D ASN* 4.8 3.1 - - + -
774D SER* 3.1 24.0 + - - -
800D ILE* 3.5 15.6 - - - +
801D GLU 2.9 28.0 + - - -
802D ILE* 3.6 22.4 - - + +
842D VAL* 4.4 10.5 - - + +
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Residues in contact with ILE 762 (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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534C MET* 3.6 12.0 - - + +
536C ILE* 3.9 27.6 - - + +
762C ILE* 3.8 29.8 - - + -
768C ALA* 4.1 4.7 - - + -
536D ILE* 4.2 15.9 - - + -
556D ALA* 3.6 28.5 - - + +
758D THR* 3.0 37.4 + - + +
759D ALA 4.2 0.2 - - - +
761D TYR* 1.3 76.4 - - - +
763D ALA* 1.3 62.1 + - - +
764D CYS 3.4 0.3 + - - -
765D GLY* 3.7 6.1 + - - -
766D GLN 5.4 1.1 - - - -
768D ALA* 3.9 19.3 - - + -
814D GLN* 4.5 1.2 + - - -
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Residues in contact with ALA 763 (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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534C MET* 3.3 20.0 - - - +
538D VAL* 4.8 2.7 - - + -
554D PRO* 3.8 19.7 - - + +
555D MET 4.2 0.7 - - - +
556D ALA* 3.7 21.4 - - + +
759D ALA 3.2 19.3 + - - +
760D ILE 3.8 3.6 - - - +
762D ILE* 1.3 78.5 - - - +
764D CYS* 1.3 58.2 + - - +
814D GLN* 3.6 6.6 - - - +
817D CYS* 3.3 26.3 - - - +
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Residues in contact with CYS 764 (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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554D PRO* 4.0 24.7 - - - -
760D ILE* 2.8 32.4 + - + +
762D ILE 3.3 0.2 - - - -
763D ALA* 1.3 79.6 - - - +
765D GLY* 1.3 57.3 + - - +
766D GLN* 3.0 27.5 + - + +
809D THR* 3.7 8.3 - - - +
814D GLN* 3.7 10.5 - - - +
817D CYS* 4.1 7.2 - - - -
818D LEU* 3.6 29.2 - - + +
821D LEU* 4.2 10.5 - - - -
838D LEU* 4.9 2.9 - - + -
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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