Contacts of the helix formed by residues 752 - 764 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100A COA 3.6 32.5 - - + +
200A MAH 4.2 7.6 - - + -
562A LEU* 3.9 6.1 - - + -
565A SER* 4.7 2.5 - - - -
566A THR* 5.4 0.4 - - - -
750A ASN* 3.9 1.6 - - - -
751A ALA* 1.3 75.9 - - + +
753A ALA* 1.3 66.4 + - - +
754A ALA 3.1 3.4 - - - +
755A ASN* 2.9 44.0 + - - +
756A ILE* 3.6 19.5 - - + +
849A GLY* 3.0 30.8 + - - -
850A GLU* 2.8 23.8 + - - -
853A LEU* 3.5 21.5 - - + +
691B LYS* 5.4 4.9 - - + -
692B LYS* 4.9 2.5 - - - -
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Residues in contact with ALA 753 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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750A ASN* 3.0 23.4 + - + +
752A HIS* 1.3 74.0 - - - +
754A ALA* 1.3 64.4 + - - +
756A ILE* 3.0 7.6 + - - +
757A VAL* 2.9 23.8 + - - +
775A SER* 3.5 22.0 - - - +
777A CYS* 4.0 6.5 - - + -
797A MET* 4.5 2.5 - - + -
846A VAL* 3.8 33.4 - - + +
850A GLU* 3.6 2.4 + - - -
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Residues in contact with ALA 754 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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750A ASN* 4.6 1.0 + - - -
752A HIS 3.1 0.4 - - - -
753A ALA* 1.3 78.6 - - - +
755A ASN* 1.3 61.6 + - - +
758A THR* 2.7 30.9 + - - -
771A ASN* 3.4 15.7 - - - +
775A SER* 3.0 25.5 + - - +
691B LYS* 3.5 29.8 + - + +
769B ALA* 3.9 8.1 - - + +
772B VAL* 3.8 5.8 - - + -
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Residues in contact with ASN 755 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A COA 3.7 5.7 - - - +
200A MAH 3.0 26.9 + - - +
559A GLU* 3.2 12.6 + - - +
562A LEU* 3.7 22.8 - - + +
752A HIS* 2.9 36.3 + - - +
754A ALA* 1.3 77.3 - - - +
756A ILE* 1.3 61.7 + - - +
758A THR* 4.0 1.6 - - - -
759A ALA* 3.1 25.5 + - - +
691B LYS* 2.8 26.0 + - - +
767B ASP* 4.3 0.3 - - - +
769B ALA* 3.3 13.5 - - - +
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Residues in contact with ILE 756 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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555A MET* 5.5 3.4 - - - -
562A LEU* 4.1 8.5 - - + -
566A THR* 3.9 15.3 - - + +
752A HIS* 3.6 44.4 - - + +
753A ALA 3.0 7.1 + - - +
755A ASN* 1.3 77.9 - - - +
757A VAL* 1.3 65.7 + - - +
759A ALA* 3.3 4.9 + - - +
760A ILE* 3.1 32.6 + - + +
842A VAL 4.3 0.4 - - - +
845A THR* 3.6 29.4 - - + +
846A VAL* 3.6 35.2 - - + +
849A GLY* 4.0 9.4 - - - -
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Residues in contact with VAL 757 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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753A ALA 2.9 16.7 + - - +
756A ILE* 1.3 75.7 - - - +
758A THR* 1.3 59.3 + - - +
760A ILE* 3.5 1.2 + - - -
761A TYR* 2.9 69.8 + - + -
771A ASN* 3.5 23.1 - - - +
774A SER* 4.0 15.9 - - - +
775A SER* 4.3 4.7 - - - -
797A MET* 3.7 28.7 - - + -
842A VAL* 3.9 17.3 - - + -
846A VAL* 4.1 2.5 - - + -
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Residues in contact with THR 758 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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754A ALA 2.7 22.3 + - - -
755A ASN 4.0 2.2 - - - -
757A VAL* 1.3 78.5 - - - +
759A ALA* 1.3 63.8 + - - +
761A TYR* 3.3 5.6 + - - +
762A ILE* 3.0 37.5 + - + +
768A ALA* 5.0 6.5 - - + +
771A ASN* 3.0 28.6 + - + +
768B ALA* 3.7 30.7 - - + +
769B ALA* 3.5 13.4 - - + +
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Residues in contact with ALA 759 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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555A MET* 3.7 24.2 - - + -
556A ALA 3.0 42.5 + - - +
557A THR* 4.4 1.3 - - - -
562A LEU* 4.2 15.0 - - + -
755A ASN 3.1 16.0 + - - +
756A ILE* 3.3 4.4 + - - +
758A THR* 1.3 80.1 - - - +
760A ILE* 1.3 61.3 + - - +
762A ILE 3.6 0.3 + - - -
763A ALA* 3.2 12.1 + - - +
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Residues in contact with ILE 760 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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553A VAL* 3.7 30.7 - - + -
554A PRO 3.8 11.4 - - - +
555A MET* 4.4 6.1 - - + -
756A ILE* 3.1 35.4 + - + +
757A VAL 4.0 2.2 - - - +
759A ALA* 1.3 72.8 - - - +
761A TYR* 1.3 62.4 + - + +
763A ALA* 3.2 0.3 + - - -
764A CYS* 2.8 46.7 + - + +
766A GLN* 6.0 0.2 - - + -
802A ILE* 5.9 0.4 - - + -
821A LEU* 5.1 2.2 - - + -
838A LEU* 4.6 9.6 - - + -
841A ILE* 5.1 1.6 - - + -
842A VAL* 4.0 34.3 - - + +
845A THR* 3.9 11.4 - - + +
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Residues in contact with TYR 761 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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757A VAL* 2.9 47.5 + - + +
758A THR* 3.6 6.5 - - - +
760A ILE* 1.3 81.7 - - + +
762A ILE* 1.3 62.5 + - - +
765A GLY 3.2 4.2 + - - -
766A GLN* 2.8 50.4 + - + +
767A ASP 3.5 22.9 - - - -
768A ALA* 4.4 12.6 - - - -
770A GLN* 4.5 3.6 - - + -
771A ASN* 4.9 2.5 - - + -
774A SER* 3.1 22.8 + - - -
800A ILE* 3.3 17.8 - - - +
801A GLU 2.9 28.2 + - - -
802A ILE* 3.6 21.9 - - + +
842A VAL* 4.2 11.2 - - + -
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Residues in contact with ILE 762 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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536A ILE* 4.4 18.2 - - + -
556A ALA* 3.5 29.8 - - + +
758A THR* 3.0 39.1 + - + +
761A TYR* 1.3 76.8 - - - +
763A ALA* 1.3 59.9 + - - +
765A GLY* 3.7 5.9 + - - -
766A GLN 5.3 1.3 - - - -
768A ALA* 4.0 17.9 - - + -
814A GLN* 4.3 1.9 + - - -
534B MET* 3.6 13.2 - - + +
536B ILE* 4.2 24.5 - - + +
762B ILE* 4.1 24.0 - - + -
768B ALA* 4.2 7.4 - - + -
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Residues in contact with ALA 763 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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538A VAL* 4.8 2.7 - - + -
554A PRO* 3.9 18.8 - - + +
555A MET 4.3 0.7 - - - +
556A ALA* 3.7 19.5 - - + +
759A ALA 3.2 18.4 + - - +
760A ILE 3.2 3.8 + - - +
762A ILE* 1.3 77.7 - - - +
764A CYS* 1.3 58.7 + - - +
765A GLY 3.6 0.2 + - - -
814A GLN* 3.6 5.5 - - - -
817A CYS* 3.2 30.3 - - + +
534B MET* 3.2 21.0 - - + +
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Residues in contact with CYS 764 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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554A PRO* 4.1 20.6 - - - -
760A ILE* 2.8 35.3 + - + +
763A ALA* 1.3 80.1 - - - +
765A GLY* 1.3 61.0 + - - +
766A GLN* 3.2 22.4 + - + +
809A THR* 3.4 1.0 - - - +
814A GLN* 3.8 10.8 - - - -
817A CYS* 4.2 5.8 - - - -
818A LEU* 3.4 34.5 - - + +
821A LEU* 4.1 14.1 - - - -
838A LEU* 4.7 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