Contacts of the helix formed by residues 82 - 97 (chain D) in PDB entry 1ZME
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 82 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83C LEU* 3.6 21.1 - - + +
78D GLN* 2.8 47.9 + - - +
79D LEU* 4.0 2.9 - - - +
81D LYS* 1.3 80.0 + - - +
83D LEU* 1.3 65.9 + - - +
84D ASN 3.0 1.3 - - - -
85D ASP* 3.0 16.2 + - - +
86D LYS* 2.9 34.6 + - + +
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Residues in contact with LEU 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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79C LEU* 3.9 21.3 - - + -
82C ASP* 3.7 28.3 - - + +
83C LEU* 3.6 26.8 - - + +
86C LYS* 4.2 15.3 - - + +
79D LEU 3.0 16.7 + - - +
80D GLN* 3.9 5.6 - - - +
82D ASP* 1.3 75.3 - - - +
84D ASN* 1.3 59.5 + - - +
86D LYS* 3.4 0.6 + - - -
87D THR* 2.9 46.1 + - - +
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Residues in contact with ASN 84 (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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80D GLN* 3.2 20.6 + - - +
81D LYS* 3.5 14.0 - - - +
82D ASP 3.0 0.4 - - - -
83D LEU* 1.3 83.0 - - - +
85D ASP* 1.3 63.8 + - - +
87D THR* 3.8 5.2 - - - -
88D GLU* 3.2 23.7 + - - +
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Residues in contact with ASP 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* 3.1 32.2 + - - +
82D ASP* 3.0 21.0 + - - +
84D ASN* 1.3 78.7 - - - +
86D LYS* 1.3 63.0 + - + +
88D GLU* 3.1 17.6 + - - +
89D GLU* 2.9 28.1 + - - +
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Residues in contact with LYS 86 (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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83C LEU* 3.5 18.6 - - + -
86C LYS* 3.7 20.6 - - + -
87C THR* 3.6 27.6 - - - +
90C ASN* 3.3 19.5 + - + +
82D ASP* 2.9 26.4 + - - +
83D LEU 4.0 1.8 - - - +
85D ASP* 1.3 76.7 - - - +
87D THR* 1.3 56.5 + - - +
89D GLU* 4.3 12.6 + - - +
90D ASN* 2.7 37.0 + - - +
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Residues in contact with THR 87 (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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86C LYS* 3.8 24.2 - - - +
83D LEU* 2.9 41.2 + - - +
84D ASN* 3.8 6.7 - - - +
86D LYS* 1.3 75.2 - - - +
88D GLU* 1.3 59.0 + - - +
90D ASN* 3.4 1.2 - - - +
91D ASN* 3.0 43.2 + - - +
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Residues in contact with GLU 88 (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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84D ASN 3.2 10.3 + - - +
85D ASP* 3.1 21.8 - - - +
87D THR* 1.3 81.1 - - - +
89D GLU* 1.3 63.2 + - - +
91D ASN* 3.2 7.5 + - - +
92D ARG* 3.1 23.2 + - + +
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Residues in contact with GLU 89 (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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90C ASN* 3.3 23.9 + - - +
94C LYS* 3.8 30.7 + - - +
85D ASP 2.9 13.0 + - - +
86D LYS* 3.8 18.4 + - - +
88D GLU* 1.3 76.0 - - - +
90D ASN* 1.3 52.7 + - - +
92D ARG* 3.2 29.7 + - - +
93D LEU* 2.7 45.7 + - + +
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Residues in contact with ASN 90 (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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86C LYS* 3.4 27.6 - - + +
89C GLU* 2.9 32.3 + - - +
90C ASN* 2.8 25.2 + - - +
93C LEU* 4.0 3.0 - - - +
86D LYS 2.7 21.7 + - - +
87D THR 3.4 6.1 - - - +
89D GLU* 1.3 73.6 - - - +
91D ASN* 1.3 61.4 + - - +
93D LEU* 3.8 3.0 - - - +
94D LYS* 3.0 64.2 + - - +
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Residues in contact with ASN 91 (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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86C LYS* 5.6 1.2 - - - +
87D THR* 3.0 34.1 + - - +
88D GLU* 3.7 6.0 - - - +
90D ASN* 1.3 87.3 + - - +
92D ARG* 1.3 61.4 + - - +
94D LYS* 3.8 12.4 - - - +
95D ALA* 3.2 23.7 + - - +
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Residues in contact with ARG 92 (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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94C LYS* 5.3 4.0 - - - +
88D GLU* 3.1 13.5 + - + +
89D GLU* 3.5 28.8 + - - +
91D ASN* 1.3 74.5 - - - +
93D LEU* 1.3 94.7 + - - +
95D ALA* 3.4 7.1 + - - +
96D LEU* 3.1 32.8 + - + +
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Residues in contact with LEU 93 (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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90C ASN* 3.4 34.5 - - + +
93C LEU* 3.8 23.1 - - + -
94C LYS* 3.6 18.4 - - + +
97C LEU* 4.1 19.6 - - + +
89D GLU* 2.7 32.7 + - - +
90D ASN 3.8 0.2 - - - +
92D ARG* 1.3 108.2 - - - +
94D LYS* 1.3 62.2 + - - +
96D LEU* 3.0 9.9 + - + +
97D LEU* 2.9 22.5 + - - +
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Residues in contact with LYS 94 (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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86C LYS* 5.4 2.8 - - - +
89C GLU* 3.5 29.9 + - - -
93C LEU* 3.6 20.9 - - + -
90D ASN* 3.0 48.2 + - - +
91D ASN* 3.8 13.5 - - - +
93D LEU* 1.3 76.0 - - - +
95D ALA* 1.3 57.1 + - - +
97D LEU* 3.4 3.9 + - - +
98D LEU* 3.0 27.3 + - - +
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Residues in contact with ALA 95 (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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91D ASN 3.2 15.0 + - - +
92D ARG* 3.7 7.2 - - - +
93D LEU 3.2 0.4 - - - -
94D LYS* 1.3 75.7 - - - +
96D LEU* 1.3 64.1 + - - +
98D LEU* 3.8 21.0 + - + +
99D GLU* 3.8 13.7 - - - +
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Residues in contact with LEU 96 (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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97C LEU* 4.0 26.0 - - + +
92D ARG* 3.1 24.2 + - + +
93D LEU* 3.0 14.1 + - + +
95D ALA* 1.3 75.5 - - - +
97D LEU* 1.3 66.2 + - - +
98D LEU 3.1 1.3 - - - -
99D GLU* 3.1 46.4 + - - +
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Residues in contact with LEU 97 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93C LEU* 3.3 28.3 - - + +
96C LEU* 3.4 39.9 - - + +
97C LEU* 3.6 24.6 - - + +
93D LEU 2.9 11.6 + - - +
94D LYS 3.8 7.2 - - - +
96D LEU* 1.3 76.5 - - - +
98D LEU* 1.3 62.3 - - - +
99D GLU 3.2 6.9 + - - +
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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