Contacts of the helix formed by residues 752 - 764 (chain C) in PDB entry 1DQ8
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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102C COA 3.6 30.3 + - + +
562C LEU* 4.1 8.7 - - + +
565C SER* 4.6 2.8 + - - -
566C THR* 5.4 0.2 + - - -
750C ASN* 3.9 0.9 - - - -
751C ALA* 1.3 77.8 - - - +
753C ALA* 1.3 66.2 + - - +
754C ALA* 3.1 4.9 - - - +
755C ASN* 2.9 50.6 + - + +
756C ILE* 3.7 6.4 + - + +
849C GLY* 2.9 41.4 - - - -
850C GLU* 2.8 17.9 + - - -
853C LEU* 3.6 19.3 - - + +
202D MAH 4.1 7.9 - - + -
691D LYS* 5.3 3.6 - - + -
692D LYS* 5.0 2.5 - - - -
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Residues in contact with ALA 753 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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750C ASN* 3.0 23.0 + - + +
752C HIS* 1.3 74.7 - - - +
754C ALA* 1.3 57.7 + - - +
756C ILE* 3.1 7.3 + - - +
757C VAL* 2.9 31.2 + - - +
775C SER* 3.8 19.1 - - - +
777C CYS* 4.0 7.0 - - + -
797C MET* 4.7 2.0 - - + -
846C VAL* 3.6 34.5 - - + -
850C GLU* 3.5 2.2 + - - -
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Residues in contact with ALA 754 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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750C ASN* 4.5 1.0 + - - -
752C HIS 3.1 0.4 - - - -
753C ALA* 1.3 78.9 - - - +
755C ASN* 1.3 55.5 + - - +
757C VAL* 4.4 0.2 - - - -
758C THR* 2.7 37.9 + - - +
775C SER* 3.1 26.9 + - - +
691D LYS* 3.5 31.1 + - + +
769D ALA* 3.7 12.1 - - + +
772D VAL* 4.0 13.0 - - + -
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Residues in contact with ASN 755 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102C COA 3.7 4.0 - - - +
559C GLU* 3.0 12.7 + - - +
562C LEU* 3.7 17.5 - - + +
752C HIS* 2.9 41.5 + - + +
754C ALA* 1.3 79.9 - - - +
756C ILE* 1.3 61.9 + - - +
758C THR* 4.0 2.1 - - - -
759C ALA* 3.3 24.1 + - - +
202D MAH 2.8 25.9 + - - -
691D LYS* 2.8 31.0 + - - +
767D ASP* 4.2 0.5 - - - +
769D ALA* 3.3 9.0 - - - +
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Residues in contact with ILE 756 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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555C MET* 3.5 14.8 - - + -
562C LEU* 3.9 10.5 - - + -
566C THR* 3.0 33.7 - - + +
752C HIS* 4.3 11.7 - - + +
753C ALA* 3.1 6.8 + - - +
755C ASN* 1.3 74.0 - - - +
757C VAL* 1.3 66.7 + - - +
759C ALA* 3.3 1.7 + - - +
760C ILE* 3.1 32.1 + - + +
842C VAL 4.4 0.2 - - - +
845C THR* 3.4 30.1 - - + +
846C VAL* 3.7 32.5 - - + +
849C GLY* 4.3 12.3 - - - -
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Residues in contact with VAL 757 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
753C ALA 2.9 18.6 + - - +
754C ALA 4.0 0.7 - - - +
756C ILE* 1.3 78.6 - - - +
758C THR* 1.3 57.8 + - - +
760C ILE* 3.8 1.0 - - - -
761C TYR* 2.8 64.4 + - + -
771C ASN* 4.0 21.5 - - + -
774C SER* 4.0 12.6 - - - +
775C SER* 3.9 13.9 - - - +
797C MET* 3.8 29.4 - - + -
842C VAL* 4.0 15.7 - - + -
846C VAL* 4.1 2.5 - - + -
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Residues in contact with THR 758 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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754C ALA 2.7 22.6 + - - -
755C ASN 4.0 3.4 - - - -
757C VAL* 1.3 77.9 - - - +
759C ALA* 1.3 56.6 + - - +
761C TYR* 3.4 5.6 + - - +
762C ILE* 2.9 45.5 + - + +
768C ALA* 4.9 4.3 - - + -
771C ASN* 2.7 30.3 + - - +
768D ALA* 3.7 30.5 - - + -
769D ALA* 3.5 13.6 - - + +
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Residues in contact with ALA 759 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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555C MET* 3.8 24.5 - - + -
556C ALA* 3.0 30.8 + - - +
557C THR* 3.1 26.7 - - + +
562C LEU* 4.3 0.9 - - + -
755C ASN 3.3 16.8 + - - +
756C ILE 3.3 3.3 + - - +
758C THR* 1.3 76.2 - - - +
760C ILE* 1.3 61.6 + - - +
762C ILE 3.6 0.2 + - - -
763C ALA* 3.1 17.2 + - - +
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Residues in contact with ILE 760 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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553C VAL* 3.6 31.6 - - + -
554C PRO 3.9 11.0 - - - +
555C MET* 4.3 6.5 - - + -
756C ILE* 3.1 35.4 + - + +
757C VAL 3.9 2.5 - - - +
759C ALA* 1.3 73.0 - - - +
761C TYR* 1.3 64.3 + - + +
763C ALA* 3.2 0.7 + - - -
764C CYS* 2.8 45.3 + - + +
766C GLN* 5.9 0.2 - - + -
802C ILE* 5.7 0.7 - - + -
821C LEU* 5.3 2.0 - - + -
838C LEU* 4.7 9.4 - - + -
841C ILE* 4.7 2.2 - - + +
842C VAL* 4.1 33.4 - - + +
845C THR* 3.9 11.0 - - + +
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Residues in contact with TYR 761 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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757C VAL* 2.8 46.6 + - + +
758C THR* 3.7 6.7 - - - +
760C ILE* 1.3 81.9 - - + +
762C ILE* 1.3 62.2 + - - +
765C GLY* 3.2 5.0 + - - -
766C GLN* 2.9 52.5 + - + +
767C ASP 3.5 21.1 - - - -
768C ALA* 4.4 12.1 - - - -
770C GLN* 4.5 4.5 - - + -
771C ASN* 5.0 2.0 - - + -
774C SER* 3.0 25.7 + - - -
800C ILE* 3.6 9.9 - - - +
801C GLU 2.9 34.3 + - - -
802C ILE* 3.8 21.1 - - + -
842C VAL* 4.3 10.7 - - + +
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Residues in contact with ILE 762 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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536C ILE* 4.4 13.5 - - + -
556C ALA* 3.7 28.9 - - + +
758C THR* 2.9 37.1 + - + +
761C TYR* 1.3 76.5 - - - +
763C ALA* 1.3 63.5 + - - +
764C CYS 3.5 0.2 + - - -
765C GLY* 3.7 6.4 + - - -
766C GLN 5.4 1.1 - - - -
768C ALA* 4.0 17.3 - - + -
814C GLN* 4.6 0.5 + - - -
534D MET* 3.6 12.7 - - + +
536D ILE* 4.0 29.5 - - + +
762D ILE* 3.9 27.8 - - + -
768D ALA* 4.2 5.6 - - + -
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Residues in contact with ALA 763 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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538C VAL* 4.9 2.0 - - + -
554C PRO* 3.7 24.7 - - + +
555C MET 4.2 0.7 - - - +
556C ALA* 3.7 17.2 - - + +
759C ALA 3.1 18.6 + - - +
760C ILE 3.2 4.0 + - - +
762C ILE* 1.3 78.5 - - - +
764C CYS* 1.3 58.0 + - - +
814C GLN* 3.6 5.9 - - - -
817C CYS* 3.2 21.7 - - - +
534D MET* 3.2 27.2 - - + +
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Residues in contact with CYS 764 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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554C PRO* 4.0 24.9 - - - -
760C ILE* 2.8 34.1 + - + +
763C ALA* 1.3 75.6 - - - +
765C GLY* 1.3 58.8 + - - +
766C GLN* 3.0 27.8 + - + +
809C THR* 3.4 8.5 - - - +
814C GLN* 3.8 10.8 - - - -
817C CYS* 4.1 7.4 - - - -
818C LEU* 3.6 28.3 - - + +
821C LEU* 4.2 11.2 - - - -
838C 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