Contacts of the helix formed by residues 80 - 96 (chain A) in PDB entry 1ZHH
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 80 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78A VAL 3.9 1.0 + - - +
79A SER* 1.3 71.9 + - - +
81A TYR* 1.3 65.2 + - - +
82A TRP 3.3 2.5 - - - -
83A VAL* 3.3 22.5 + - + +
84A ARG* 3.0 59.7 + - + +
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Residues in contact with TYR 81 (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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79A SER* 2.9 16.9 + - - +
80A ASP* 1.3 80.2 + - - +
82A TRP* 1.3 106.6 + + + +
84A ARG* 3.4 6.7 + - - +
85A ASN* 3.1 26.4 + - + +
159A ASN* 6.4 0.2 - - + -
177A GLY* 5.7 1.4 - - - -
178A PHE* 3.5 28.8 - + - -
310A ARG* 4.7 19.9 - - - -
312A ASN* 3.5 33.7 + - + +
315A THR* 4.6 6.3 + - - +
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Residues in contact with TRP 82 (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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73A TYR* 3.5 40.5 + + + -
74A PRO* 3.7 31.7 - - + +
77A GLN* 4.5 18.5 + - + -
79A SER 5.1 0.6 + - - -
80A ASP 3.3 0.4 - - - -
81A TYR* 1.3 107.8 - + + +
83A VAL* 1.3 64.7 + - + +
85A ASN* 3.4 13.6 - - + +
86A ILE* 3.1 24.8 + - - +
134A THR* 3.8 28.7 - - + -
158A GLN* 3.8 36.3 - - + -
159A ASN* 4.5 19.1 - - + -
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Residues in contact with VAL 83 (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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79A SER 5.6 1.1 - - - +
80A ASP* 3.3 23.9 + - + +
82A TRP* 1.3 78.5 - - + +
84A ARG* 1.3 63.7 + - + +
86A ILE* 3.2 11.9 - - + +
87A ALA* 3.1 23.6 + - + +
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Residues in contact with ARG 84 (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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80A ASP* 3.0 49.0 + - + +
81A TYR* 3.6 5.4 - - - +
83A VAL* 1.3 78.1 - - + +
85A ASN* 1.3 58.5 + - - +
87A ALA* 3.3 4.0 + - - +
88A SER* 2.9 31.5 + - - -
312A ASN* 4.7 9.4 - - + +
313A ASP* 4.5 4.3 - - - +
360A PHE* 3.5 43.0 - - - -
363A SER* 3.0 41.8 + - - +
364A ASP* 3.0 29.3 + - - -
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Residues in contact with ASN 85 (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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73A TYR* 2.8 27.5 + - - -
81A TYR* 3.1 17.3 + - + +
82A TRP* 3.4 20.5 - - + +
83A VAL 3.3 0.4 - - - -
84A ARG* 1.3 75.8 - - - +
86A ILE* 1.3 57.1 + - - +
88A SER* 3.2 7.0 + - - -
89A PHE* 3.0 27.2 + - - +
158A GLN* 2.8 40.4 - - - +
312A ASN 6.0 1.6 - - - -
313A ASP* 5.8 1.3 - - - +
315A THR* 3.7 15.1 + - - -
316A GLY* 3.7 12.1 + - - +
319A MET* 3.9 5.2 - - - +
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Residues in contact with ILE 86 (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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71A VAL* 3.9 19.7 - - + -
73A TYR* 3.2 25.5 + - + +
82A TRP 3.1 12.1 + - - +
83A VAL* 3.2 18.4 - - + +
85A ASN* 1.3 73.6 - - - +
87A ALA* 1.3 64.2 + - + +
89A PHE* 4.0 17.3 - - + -
90A GLU* 2.9 47.7 + - + +
102A LEU* 3.7 23.6 - - + -
104A GLN* 4.2 19.3 - - - +
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Residues in contact with ALA 87 (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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83A VAL* 3.1 20.0 + - + +
84A ARG* 3.5 7.0 - - - +
86A ILE* 1.3 79.1 - - + +
88A SER* 1.3 56.5 + - - +
90A GLU* 4.1 4.6 - - - +
91A LYS* 3.1 31.2 + - - +
362A TYR 4.9 2.3 - - - +
363A SER* 4.2 21.1 - - - +
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Residues in contact with SER 88 (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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84A ARG 2.9 16.6 + - - -
85A ASN* 3.6 5.6 - - - -
87A ALA* 1.3 74.2 - - - +
89A PHE* 1.3 65.2 + - - +
92A ARG* 3.2 21.8 + - - +
313A ASP* 2.9 48.6 + - - +
316A GLY* 4.3 2.5 - - - -
317A ILE* 3.4 13.5 + - - +
362A TYR* 3.5 17.7 - - - +
363A SER 4.8 0.4 - - - +
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Residues in contact with PHE 89 (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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69A ILE* 3.9 14.8 - - + -
85A ASN 3.0 16.5 + - - +
86A ILE* 3.6 23.3 - - + +
88A SER* 1.3 76.1 + - - +
90A GLU* 1.3 66.3 + - + +
92A ARG* 3.2 4.9 + - - +
93A LEU* 3.0 45.4 + - + +
102A LEU* 4.4 5.8 - - + -
132A ILE* 3.6 26.9 - - + -
316A GLY* 3.4 27.1 - - - +
319A MET* 3.7 21.5 - - + -
320A ALA* 3.6 26.7 - - + -
323A ILE* 3.6 20.2 - - + -
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Residues in contact with GLU 90 (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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86A ILE* 2.9 37.0 + - + +
87A ALA* 4.2 4.7 - - - +
89A PHE* 1.3 77.6 - - + +
91A LYS* 1.3 60.9 + - - +
93A LEU* 3.3 8.8 + - - +
94A TYR* 3.0 24.4 + - - +
100A TYR* 2.5 39.8 + - + +
102A LEU* 3.7 25.8 - - + +
104A GLN* 4.7 4.5 + - - -
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Residues in contact with LYS 91 (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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87A ALA 3.1 19.0 + - - +
90A GLU* 1.3 76.2 - - - +
92A ARG* 1.3 58.0 + - - +
94A TYR* 3.4 9.1 + - + +
95A LYS* 3.0 49.7 + - + +
361A ARG 4.8 1.8 + - - +
362A TYR* 2.8 58.3 + - + +
364A ASP 4.2 2.0 + - - -
365A ASN 3.0 22.4 + - - -
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Residues in contact with ARG 92 (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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51A ALA 2.9 28.1 + - - -
52A VAL 3.8 4.0 + - - -
54A ALA 3.0 18.9 + - - -
55A GLN 4.1 0.6 + - - -
56A PRO* 3.9 24.1 - - - +
88A SER 3.2 18.5 + - - +
89A PHE 3.2 0.4 + - - +
91A LYS* 1.3 73.6 - - - +
93A LEU* 1.3 59.8 + - - +
95A LYS* 3.3 2.5 + - - +
96A LEU* 2.9 41.8 + - + +
317A ILE* 3.4 35.9 - - + +
320A ALA* 3.7 22.9 - - + -
321A GLU* 2.9 22.2 + - - -
361A ARG* 5.4 1.4 - - - +
362A TYR* 3.0 38.5 + - + -
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Residues in contact with LEU 93 (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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69A ILE* 3.8 12.3 - - + -
89A PHE* 3.0 47.7 + - + +
90A GLU* 3.3 7.4 + - - +
92A ARG* 1.3 73.8 - - - +
94A TYR* 1.3 63.0 + - - +
96A LEU* 3.1 6.6 + - - +
97A ASN 3.1 4.9 + - - -
98A ILE* 3.1 55.8 + - + +
100A TYR* 3.7 37.2 - - + -
320A ALA* 3.8 23.8 - - + +
323A ILE* 4.8 8.1 - - + -
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Residues in contact with TYR 94 (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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90A GLU 3.0 13.7 + - - +
91A LYS* 3.5 12.1 - - + +
93A LEU* 1.3 76.7 - - - +
95A LYS* 1.3 73.5 + - + +
97A ASN* 3.0 25.8 + - - +
98A ILE 5.0 3.1 - - - +
100A TYR* 4.7 5.5 - - + +
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Residues in contact with LYS 95 (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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56A PRO* 3.9 27.0 - - + +
58A PRO* 4.1 12.8 - - - +
91A LYS* 3.0 42.3 + - - +
92A ARG* 3.9 4.9 - - - +
94A TYR* 1.3 88.8 - - + +
96A LEU* 1.3 59.2 + - - +
97A ASN* 3.3 4.8 + - - +
362A TYR* 3.3 30.1 - - + +
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Residues in contact with LEU 96 (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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56A PRO* 3.9 7.9 - - + -
57A VAL 3.5 35.0 - - - +
58A PRO* 4.0 3.4 - - - -
59A LEU* 2.8 29.4 + - - +
92A ARG* 2.9 36.1 + - + +
93A LEU 3.6 4.0 - - - +
94A TYR 3.1 0.4 - - - -
95A LYS* 1.3 76.2 - - - +
97A ASN* 1.3 67.2 + - - +
98A ILE* 3.9 13.0 - - + -
320A ALA* 3.8 25.1 - - + +
321A GLU* 3.6 31.6 - - - +
324A LYS* 3.8 11.9 - - + +
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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