Contacts of the helix formed by residues 752 - 764 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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691A LYS* 5.4 3.8 - - + -
692A LYS* 4.8 2.9 - - - -
102B COA 3.4 34.3 - - + +
202B MAH 4.1 7.0 - - + -
562B LEU* 4.1 6.1 - - + -
565B SER* 4.8 2.5 - - - -
566B THR* 5.5 0.2 - - - -
750B ASN* 4.0 1.3 - - - -
751B ALA* 1.3 76.5 - - - +
753B ALA* 1.3 65.8 + - - +
754B ALA* 3.1 4.7 - - - +
755B ASN* 3.0 43.7 + - - +
756B ILE* 3.7 20.0 - - + +
849B GLY* 2.9 31.8 + - - -
850B GLU* 2.8 21.5 + - - -
853B LEU* 3.5 19.1 - - + +
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Residues in contact with ALA 753 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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750B ASN* 3.0 18.4 + - + +
752B HIS* 1.3 74.7 - - - +
754B ALA* 1.3 63.0 + - - +
756B ILE* 3.1 6.4 + - - +
757B VAL* 2.9 25.2 + - - +
775B SER* 3.6 23.6 - - - +
777B CYS* 3.9 10.1 - - + -
797B MET* 4.7 1.6 - - + -
846B VAL* 3.7 33.8 - - + +
850B GLU* 3.6 3.2 + - - +
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Residues in contact with ALA 754 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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691A LYS* 3.5 30.4 + - + +
769A ALA* 4.0 8.1 - - + +
772A VAL* 3.9 4.0 - - + -
750B ASN* 4.6 0.8 + - - -
752B HIS 3.0 0.6 + - - -
753B ALA* 1.3 80.4 - - - +
755B ASN* 1.3 55.0 + - - +
757B VAL* 4.4 0.2 - - - -
758B THR* 2.7 36.6 + - - -
771B ASN* 3.6 15.3 - - - +
775B SER* 3.0 27.1 + - - +
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Residues in contact with ASN 755 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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691A LYS* 2.8 25.6 + - - +
767A ASP* 4.3 0.2 - - - +
769A ALA* 3.3 14.5 - - - +
102B COA 3.7 3.6 - - - +
202B MAH 3.0 27.1 + - - +
559B GLU* 3.1 13.0 + - - +
562B LEU* 3.6 23.7 - - + +
752B HIS* 3.0 37.1 + - - +
754B ALA* 1.3 78.0 - - - +
756B ILE* 1.3 63.4 + - + +
758B THR* 3.9 1.6 - - - -
759B ALA* 3.1 25.1 + - - +
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Residues in contact with ILE 756 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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555B MET* 5.4 3.6 - - - -
562B LEU* 4.1 7.9 - - + -
566B THR* 3.9 15.0 - - + +
752B HIS* 3.7 42.6 - - + +
753B ALA 3.1 5.3 + - - +
755B ASN* 1.3 75.2 - - + +
757B VAL* 1.3 68.1 + - - +
758B THR 3.3 0.2 + - - -
759B ALA* 3.3 4.8 + - - +
760B ILE* 3.0 35.4 + - + +
842B VAL* 4.2 0.4 - - + +
845B THR* 3.7 31.2 - - + +
846B VAL* 3.6 34.3 - - + +
849B GLY* 4.0 10.3 - - - -
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Residues in contact with VAL 757 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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753B ALA 2.9 19.8 + - - +
756B ILE* 1.3 76.5 - - - +
758B THR* 1.3 58.2 + - - +
760B ILE* 3.9 1.3 - - - -
761B TYR* 2.9 69.7 + - + -
771B ASN* 3.6 20.9 - - - +
774B SER* 4.0 12.6 - - - +
775B SER* 3.8 9.6 - - - +
797B MET* 3.8 28.9 - - + -
842B VAL* 4.0 15.0 - - + -
846B VAL* 4.1 2.2 - - + -
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Residues in contact with THR 758 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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768A ALA* 3.7 30.7 - - + +
769A ALA* 3.4 14.6 - - + +
556B ALA 5.7 0.2 - - - +
754B ALA 2.7 24.7 + - - -
755B ASN 3.9 2.7 - - - -
757B VAL* 1.3 78.0 - - - +
759B ALA* 1.3 57.4 + - - +
761B TYR* 3.3 6.0 + - - +
762B ILE* 2.9 42.7 + - + +
768B ALA* 5.0 7.0 - - + +
771B ASN* 3.0 27.5 + - + +
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Residues in contact with ALA 759 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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555B MET* 3.8 24.2 - - + -
556B ALA 3.0 41.3 + - - +
557B THR* 4.3 0.9 - - - -
562B LEU* 4.0 16.6 - - + -
755B ASN 3.1 17.7 + - - +
756B ILE* 3.9 4.5 - - - +
758B THR* 1.3 76.7 - - - +
760B ILE* 1.3 62.9 + - - +
762B ILE 3.5 0.2 + - - -
763B ALA* 3.1 13.0 + - - +
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Residues in contact with ILE 760 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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553B VAL* 3.8 23.1 - - + -
554B PRO 3.9 17.9 - - - +
555B MET* 4.5 5.8 - - + -
756B ILE* 3.0 37.1 + - + +
757B VAL 4.0 2.0 - - - +
759B ALA* 1.3 74.2 - - - +
761B TYR* 1.3 60.9 + - + +
763B ALA* 3.2 2.4 + - - +
764B CYS* 2.8 44.9 + - + +
766B GLN* 5.8 0.4 - - + -
802B ILE* 5.8 0.4 - - + -
821B LEU* 5.3 1.8 - - + -
838B LEU* 4.7 9.6 - - + -
841B ILE* 4.8 2.0 - - + +
842B VAL* 4.0 33.7 - - + -
845B THR* 3.9 11.4 - - + +
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Residues in contact with TYR 761 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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757B VAL* 2.9 47.4 + - + +
758B THR* 3.6 6.3 - - - +
760B ILE* 1.3 82.0 - - + +
762B ILE* 1.3 62.3 + - - +
765B GLY* 3.3 4.3 + - - -
766B GLN* 3.0 50.0 + - + +
767B ASP 3.5 24.0 - - - -
768B ALA* 4.4 12.8 - - - -
770B GLN* 4.6 3.6 - - + -
771B ASN* 4.9 2.5 - - + -
774B SER* 3.0 24.2 + - - -
800B ILE* 3.5 15.6 - - - +
801B GLU 2.8 28.4 + - - -
802B ILE* 3.7 21.5 - - + -
842B VAL* 4.3 10.5 - - + -
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Residues in contact with ILE 762 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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534A MET* 3.6 13.2 - - + +
536A ILE* 4.0 26.3 - - + +
762A ILE* 4.1 23.3 - - + -
768A ALA* 4.2 7.4 - - + -
536B ILE* 4.2 17.5 - - + -
556B ALA* 3.6 30.5 - - + +
557B THR* 6.0 0.2 - - - -
758B THR* 2.9 39.7 + - + +
759B ALA 4.1 0.2 - - - +
761B TYR* 1.3 76.4 - - - +
763B ALA* 1.3 62.0 + - - +
765B GLY* 3.8 5.9 + - - -
766B GLN 5.5 0.9 - - - -
768B ALA* 4.1 17.7 - - + -
814B GLN* 4.5 0.9 + - - -
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Residues in contact with ALA 763 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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534A MET* 3.3 20.3 - - - +
538B VAL* 5.0 2.5 - - + -
554B PRO* 3.7 23.8 - - + +
555B MET 4.2 0.4 - - - +
556B ALA* 3.7 17.9 - - + +
759B ALA 3.1 18.2 + - - +
760B ILE 3.2 4.0 + - - +
762B ILE* 1.3 78.3 - - - +
764B CYS* 1.3 59.9 + - - +
765B GLY 3.5 0.2 - - - -
814B GLN* 3.7 4.7 - - - -
817B CYS* 3.3 27.2 - - - +
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Residues in contact with CYS 764 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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554B PRO* 4.0 24.0 - - - -
760B ILE* 2.8 31.4 + - + +
761B TYR 3.4 0.2 + - - -
762B ILE 3.3 0.2 - - - -
763B ALA* 1.3 80.8 - - - +
765B GLY* 1.3 58.2 + - - +
766B GLN* 2.9 26.6 + - + +
809B THR* 3.7 0.7 - - - +
814B GLN* 3.7 10.8 - - - -
817B CYS* 4.0 7.4 - - - -
818B LEU* 3.6 32.6 - - + +
821B LEU* 4.1 15.0 - - - -
838B LEU* 4.8 3.1 - - + -
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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