Contacts of the helix formed by residues 82 - 95 (chain 1) in PDB entry 1ZUD
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 PRO 82 (chain 1).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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611 ASP 3.7 2.7 - - - +
621 ASP* 3.3 16.1 - - - +
801 ASP 4.4 1.8 - - - +
811 ARG* 1.3 87.1 - - + +
831 LYS* 1.3 66.6 - - - +
841 SER 3.3 0.2 - - - -
851 GLN* 3.2 29.9 + - + +
861 VAL* 3.1 21.2 + - - +
1041 GLN* 3.6 43.3 - - + +
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Residues in contact with LYS 83 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361 LEU* 3.6 19.6 + - + +
371 GLY* 4.7 2.0 - - - -
591 ASP* 4.0 24.0 + - + +
611 ASP* 2.9 34.4 + - + +
621 ASP 3.4 20.2 - - - -
631 VAL* 3.8 16.4 - - + +
641 HIS* 5.5 0.2 - - - -
671 ASN* 3.1 27.0 + - - +
711 GLN* 2.8 30.9 + - - +
741 PHE* 3.7 12.3 - - + -
811 ARG 3.4 1.2 + - - -
821 PRO* 1.3 70.6 - - - +
841 SER* 1.3 61.9 + - - +
861 VAL* 3.9 1.2 - - - +
871 SER* 2.8 30.5 + - - -
1041 GLN* 6.0 0.2 - - - +
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Residues in contact with SER 84 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361 LEU* 3.5 15.6 - - - +
571 LEU* 3.8 15.3 - - - +
591 ASP* 3.9 8.8 + - - +
821 PRO* 4.8 0.2 - - - +
831 LYS* 1.3 77.7 - - - +
851 GLN* 1.3 60.5 + - - +
871 SER* 3.7 1.4 - - - -
881 GLN* 3.0 29.5 + - - +
1021 ALA* 3.4 13.7 - - - +
1031 LEU 3.8 18.2 - - - -
1041 GLN* 3.5 30.2 + - - +
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Residues in contact with GLN 85 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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811 ARG* 3.1 27.5 + - - +
821 PRO* 3.2 34.4 + - + +
841 SER* 1.3 81.2 + - - +
861 VAL* 1.3 66.5 + - - +
881 GLN* 3.4 14.9 + - - +
891 GLN* 3.0 23.5 + - + +
1021 ALA* 4.7 2.0 - - - -
1041 GLN* 4.4 8.1 + - - +
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Residues in contact with VAL 86 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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631 VAL* 4.3 6.1 - - + -
741 PHE* 3.7 20.0 - - + -
781 ASP* 3.3 37.5 - - + +
811 ARG* 3.5 42.2 - - + +
821 PRO* 3.1 16.8 + - + +
831 LYS 3.9 3.6 - - - +
851 GLN* 1.3 76.6 - - - +
871 SER* 1.3 54.4 + - - +
891 GLN* 3.2 7.8 + - - +
901 ARG* 2.7 48.6 + - - +
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Residues in contact with SER 87 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361 LEU* 3.5 23.3 - - - +
571 LEU* 4.3 9.9 - - - -
731 LEU* 3.6 23.4 - - - +
741 PHE* 3.4 17.1 - - - -
831 LYS 2.8 22.9 + - - -
841 SER 3.7 4.0 - - - -
861 VAL* 1.3 78.0 - - - +
881 GLN* 1.3 58.3 + - - +
901 ARG* 4.3 0.2 - - - -
911 LEU* 2.8 38.9 + - - +
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Residues in contact with GLN 88 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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571 LEU* 4.2 11.2 - - + +
841 SER 3.0 17.6 + - - +
851 GLN* 3.6 11.2 - - - +
861 VAL 3.3 0.2 - - - -
871 SER* 1.3 78.6 - - - +
891 GLN* 1.3 53.9 + - - +
911 LEU* 4.8 1.6 - - - -
921 THR* 2.7 40.4 + - - +
1001 LEU* 3.0 37.0 + - + +
1011 THR* 4.1 1.0 - - - +
1021 ALA* 3.5 26.7 - - + +
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Residues in contact with GLN 89 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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781 ASP* 4.1 1.0 + - - -
811 ARG* 3.4 31.8 - - - +
851 GLN* 3.0 16.8 + - + +
861 VAL* 3.5 5.8 + - - +
881 GLN* 1.3 75.4 + - - +
901 ARG* 1.3 106.3 + - - +
921 THR* 3.3 8.1 + - - -
931 GLN* 2.7 50.7 + - + +
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Residues in contact with ARG 90 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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451 LEU* 6.0 0.2 - - - +
731 LEU* 3.6 40.7 + - + +
751 THR* 3.8 23.1 + - - +
771 GLU* 4.1 10.5 + - - +
781 ASP* 3.3 25.5 + - - -
811 ARG* 5.2 0.4 - - - +
861 VAL* 2.7 45.6 + - + +
891 GLN* 1.3 109.1 + - - +
911 LEU* 1.3 63.4 + - - +
931 GLN* 3.1 32.2 + - - +
941 LEU* 3.2 11.1 + - - +
753 THR* 5.0 2.1 - - - +
903 ARG* 5.7 4.9 - - - +
933 GLN* 3.9 12.9 + - - -
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Residues in contact with LEU 91 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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441 ALA* 3.8 24.7 - - + +
451 LEU* 3.7 36.6 - - + +
481 ALA* 4.0 10.4 - - + +
551 LEU* 4.5 1.8 - - + -
571 LEU* 3.6 27.6 - - + -
731 LEU* 3.9 22.9 - - + -
871 SER* 2.8 26.6 + - - +
901 ARG* 1.3 73.0 - - - +
921 THR* 1.3 57.2 + - - +
941 LEU* 3.2 7.1 + - + +
951 ASN* 2.9 29.6 + - - +
1001 LEU* 3.6 22.6 - - + +
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Residues in contact with THR 92 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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881 GLN* 2.7 26.2 + - - +
891 GLN* 3.4 8.3 - - - -
901 ARG 3.2 0.2 - - - -
911 LEU* 1.3 77.7 - - - +
931 GLN* 1.3 62.4 + - + +
951 ASN 3.9 3.6 - - - -
961 PRO* 3.1 40.4 - - + +
1001 LEU* 3.4 17.3 - - - +
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Residues in contact with GLN 93 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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891 GLN* 2.7 43.5 + - - +
901 ARG* 3.1 25.4 + - - +
921 THR* 1.3 79.5 - - + +
941 LEU* 1.3 59.8 + - - +
753 THR* 3.7 17.5 - - + +
763 THR* 2.9 30.5 + - - -
773 GLU* 3.1 34.1 + - - +
903 ARG* 4.4 8.0 + - - -
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Residues in contact with LEU 94 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81 ARG* 3.0 17.7 + - - -
451 LEU* 3.5 47.1 - - + +
481 ALA* 4.3 6.5 - - + -
491 GLY* 4.1 13.9 - - - +
901 ARG 3.2 7.8 + - - +
911 LEU* 3.2 11.1 + - + +
931 GLN* 1.3 80.4 - - - +
951 ASN* 1.3 60.4 + - + +
961 PRO* 4.1 0.4 - - - -
683 LEU* 3.5 32.3 - - + +
713 GLN 5.0 3.4 - - - +
723 ILE* 5.2 7.2 - - + +
743 PHE 3.3 22.7 - - - +
753 THR* 4.1 7.1 - - + +
763 THR* 3.4 9.9 + - - -
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Residues in contact with ASN 95 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81 ARG* 3.6 21.3 + - - +
91 TYR* 2.9 24.5 + - - -
481 ALA* 2.8 32.3 + - + +
491 GLY 4.7 0.2 + - - -
911 LEU 2.9 16.1 + - - +
921 THR* 3.2 7.2 - - - +
941 LEU* 1.3 80.6 - - + +
961 PRO* 1.3 61.9 - - - +
971 ASP* 2.9 25.6 + - - +
981 ILE* 3.6 29.5 + - + +
1001 LEU* 4.3 2.4 - - - +
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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