Contacts of the helix formed by residues 72 - 85 (chain D) in PDB entry 1ZR4
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 ASP 72 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71D ARG* 1.3 85.0 + - + +
73D THR* 1.3 58.8 + - - +
74D ALA* 2.8 39.3 + - - +
75D ASP* 3.4 14.2 + - - +
76D MET* 3.0 29.2 + - - +
112D SER* 6.0 0.2 - - - -
116D GLN* 3.3 19.2 + - - +
81E LYS* 3.2 24.3 + - - -
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Residues in contact with THR 73 (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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72D ASP* 1.3 73.1 + - - +
74D ALA* 1.3 61.1 - - - +
76D MET* 3.3 9.6 - - - +
77D ILE* 3.1 38.3 + - + +
109D THR 4.4 7.2 - - - +
112D SER* 3.2 41.2 + - - +
113D ALA* 3.5 6.6 + - + +
116D GLN* 2.6 30.4 + - - -
77E ILE* 4.2 13.7 - - + -
109E THR* 4.8 6.1 - - + -
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Residues in contact with ALA 74 (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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72D ASP* 2.8 17.3 + - - +
73D THR* 1.3 69.7 - - - +
75D ASP* 1.3 66.8 + - - +
77D ILE* 3.1 8.5 + - - +
78D GLN* 2.9 26.1 + - + +
116D GLN* 5.4 0.2 - - - +
74E ALA* 5.5 4.8 - - - +
77E ILE* 4.0 26.9 - - + +
78E GLN* 5.0 12.6 - - + +
81E LYS* 4.8 16.4 - - + +
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Residues in contact with ASP 75 (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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45D ARG* 2.7 42.4 + - - -
70D GLY* 4.1 1.5 - - - -
71D ARG* 4.0 20.0 + - - -
72D ASP* 3.4 19.7 + - - +
74D ALA* 1.3 75.2 - - - +
76D MET* 1.3 57.9 + - - +
78D GLN* 2.8 29.8 + - - +
79D LEU* 2.9 29.9 + - - +
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Residues in contact with MET 76 (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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66D LEU* 3.8 29.8 - - - -
69D LEU* 3.7 35.7 - - + -
70D GLY* 3.8 22.4 - - - +
72D ASP 3.0 11.1 + - - +
73D THR* 3.3 16.2 - - - +
75D ASP* 1.3 81.3 - - - +
77D ILE* 1.3 63.4 + - + +
79D LEU* 3.7 4.6 + - + +
80D ILE* 3.4 35.1 + - + +
92D PHE* 4.4 4.0 - - + -
108D VAL* 4.4 9.0 - - - -
112D SER* 4.9 11.9 - - - +
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Residues in contact with ILE 77 (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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73D THR* 3.1 21.3 + - + +
74D ALA* 3.1 7.6 + - - +
76D MET* 1.3 76.2 - - + +
78D GLN* 1.3 62.3 + - - +
80D ILE* 3.2 11.2 + - + +
81D LYS* 2.8 33.3 + - + +
108D VAL* 6.4 1.3 - - + -
109D THR* 4.0 28.9 - - + +
112D SER* 5.9 0.2 - - - +
72E ASP* 5.5 0.2 - - - +
73E THR* 4.1 9.9 - - + -
74E ALA* 3.7 26.5 - - + +
77E ILE* 3.8 26.0 - - + -
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Residues in contact with GLN 78 (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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74D ALA 2.9 13.8 + - - +
75D ASP* 2.8 15.7 + - - +
77D ILE* 1.3 72.9 - - - +
79D LEU* 1.3 67.8 + - + +
81D LYS* 2.9 33.5 + - - +
82D GLU* 2.8 51.1 + - + +
74E ALA* 4.0 19.5 - - + +
78E GLN* 6.5 1.1 - - + -
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Residues in contact with LEU 79 (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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45D ARG* 4.2 6.7 - - - +
48D LEU* 4.0 16.8 - - + -
52D ARG* 3.3 36.6 - - - +
69D LEU* 3.3 50.3 - - + +
75D ASP* 2.9 37.1 + - - +
76D MET* 3.8 8.7 - - - +
78D GLN* 1.3 72.5 - - + +
80D ILE* 1.3 63.1 + - - +
82D GLU* 3.2 8.1 + - + +
83D PHE* 3.1 38.0 + - + -
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Residues in contact with ILE 80 (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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76D MET* 3.4 38.5 + - + +
77D ILE* 3.2 12.5 + - + +
78D GLN 3.1 0.6 - - - -
79D LEU* 1.3 79.9 - - - +
81D LYS* 1.3 52.6 + - - +
83D PHE* 3.4 6.7 + - - +
84D ASP* 2.7 34.5 + - + +
90D ILE* 4.0 14.8 - - + -
92D PHE* 4.8 2.2 - - + -
99D THR* 3.8 30.1 - - + -
105D LYS* 4.2 34.3 - - + -
108D VAL* 4.2 15.7 - - + -
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Residues in contact with LYS 81 (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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77D ILE* 2.8 20.9 + - + +
78D GLN* 3.3 33.8 + - - +
80D ILE* 1.3 74.4 - - - +
82D GLU* 1.3 63.9 + - - +
84D ASP* 3.2 15.5 + - + +
85D ALA* 3.2 15.4 + - - +
72E ASP* 4.6 22.7 + - - +
74E ALA* 5.3 3.1 - - + -
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Residues in contact with GLU 82 (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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52D ARG* 3.7 24.4 + - - +
78D GLN* 2.8 56.9 + - - +
79D LEU* 3.4 10.1 - - - +
81D LYS* 1.3 76.1 - - - +
83D PHE* 1.3 68.6 + - + +
85D ALA* 3.4 10.5 + - - +
86D GLN* 3.5 13.3 + - - +
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Residues in contact with PHE 83 (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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48D LEU* 5.0 10.1 - - + -
51D LEU* 5.5 0.9 - - + -
52D ARG* 3.6 39.9 - - + -
55D VAL* 4.5 4.0 - - + -
61D ILE* 3.4 30.7 - - + -
69D LEU* 5.0 8.3 - - + -
79D LEU* 3.1 26.0 + - + -
80D ILE* 3.6 7.4 - - - +
82D GLU* 1.3 80.6 - - + +
84D ASP* 1.3 64.2 + - - +
86D GLN* 2.9 29.4 + - - -
87D GLY 3.2 9.7 + - - -
88D VAL* 3.2 35.6 + - + +
90D ILE* 3.4 29.6 - - + -
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Residues in contact with ASP 84 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80D ILE* 2.7 22.1 + - + +
81D LYS* 3.2 10.7 + - + +
83D PHE* 1.3 73.5 - - - +
85D ALA* 1.3 59.5 + - - +
86D GLN 3.0 4.5 + - - -
87D GLY* 3.3 10.9 + - - -
88D VAL 3.9 9.4 + - - +
89D SER* 5.9 0.5 - - - -
99D THR 4.2 4.9 - - - +
105D LYS* 3.0 39.0 + - - -
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Residues in contact with ALA 85 (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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81D LYS* 3.2 12.5 + - + +
82D GLU* 3.4 4.9 + - - +
84D ASP* 1.3 77.3 + - - +
86D GLN* 1.3 55.6 + - - +
87D GLY 3.5 0.6 + - - -
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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