Contacts of the helix formed by residues 75 - 90 (chain D) in PDB entry 1Z1G
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 THR 75 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73D SER 5.7 0.9 - - - +
74D VAL* 1.3 84.6 - - - +
76D LEU* 1.3 64.9 + - - +
78D SER* 3.0 43.4 + - - +
79D TRP* 3.0 13.2 + - - +
113D ASP* 2.7 35.0 + - - +
114D ALA 2.9 17.2 + - - -
115D PRO* 3.8 2.2 - - - -
116D LEU* 4.1 0.7 - - - +
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Residues in contact with LEU 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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75D THR* 1.3 70.0 + - - +
77D HIS* 1.3 76.5 + - + +
79D TRP* 3.0 8.2 + - + +
80D LEU* 2.8 46.4 + - + +
107D ILE* 4.5 13.5 - - + -
108D ARG* 6.2 0.2 - - - -
111D LEU* 4.3 20.4 - - + -
112D PRO 3.9 18.4 - - - +
113D ASP* 3.9 0.7 - - - +
114D ALA 2.8 12.6 + - - +
116D LEU* 3.7 17.8 - - + +
119D ILE* 3.7 22.7 - - + -
147D LEU* 5.2 6.7 - - + -
151D PHE* 5.3 5.6 - - + -
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Residues in contact with HIS 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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76D LEU* 1.3 89.1 - - + +
78D SER* 1.3 53.7 + - - +
80D LEU* 3.2 6.4 + - - +
81D ASP* 2.8 38.5 + - - +
108D ARG* 2.9 70.0 + - + +
111D LEU 3.4 9.4 + - - -
113D ASP* 2.6 47.8 + - + +
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Residues in contact with SER 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 VAL* 5.4 2.7 - - - -
75D THR* 3.0 33.7 + - - +
77D HIS* 1.3 77.8 - - - +
79D TRP* 1.3 57.2 + - - +
81D ASP* 3.2 24.8 + - - +
82D ARG* 3.4 7.8 + - - +
113D ASP* 4.0 3.2 + - - -
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Residues in contact with TRP 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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74D VAL* 4.0 14.8 - - + -
75D THR 3.0 8.9 + - - +
76D LEU* 3.0 15.2 + - + +
78D SER* 1.3 74.6 - - - +
80D LEU* 1.3 61.6 + - + +
81D ASP 2.9 1.3 - - - -
82D ARG* 2.7 40.4 + - + +
83D TYR* 2.4 42.6 + + + +
86D ILE* 5.1 6.7 - - + -
116D LEU* 4.3 12.1 - - + -
150D ALA* 3.2 27.8 + - + +
151D PHE* 5.7 3.6 - + - -
153D GLU* 3.5 11.4 - - + -
154D ALA* 2.8 45.9 - - + +
157D GLU* 4.1 5.2 - - + -
159D HIS* 3.6 30.3 - + - -
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Residues in contact with LEU 80 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76D LEU* 2.8 36.9 + - + +
77D HIS* 3.5 7.4 - - + +
79D TRP* 1.3 78.4 - - + +
81D ASP* 1.3 55.2 + - - +
83D TYR* 3.1 12.2 - - + +
84D GLU* 2.8 39.4 + - - +
104D ILE* 2.9 44.2 - - + +
107D ILE* 4.2 22.2 - - + -
108D ARG* 3.8 25.8 - - + +
147D LEU* 5.2 2.9 - - + -
150D ALA* 5.0 15.9 - - + -
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Residues in contact with ASP 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 HIS* 2.8 26.3 + - - +
78D SER* 3.2 17.9 + - - +
80D LEU* 1.3 78.3 - - - +
82D ARG* 1.3 62.0 + - - +
84D GLU* 3.4 20.8 + - - +
85D LYS* 3.7 12.5 + - - +
108D ARG* 3.1 24.6 + - - -
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Residues in contact with ARG 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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78D SER 3.4 6.8 + - - +
79D TRP* 2.7 46.0 + - + +
81D ASP* 1.3 74.1 - - - +
83D TYR* 1.3 66.7 + - - +
84D GLU 3.1 2.0 - - - -
85D LYS* 3.1 30.7 + - + +
86D ILE* 3.1 49.6 + - - +
157D GLU* 2.6 31.3 + - - -
159D HIS* 5.4 0.8 + - - -
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Residues in contact with TYR 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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79D TRP* 2.4 32.4 + + + +
80D LEU* 3.1 20.4 - - + +
82D ARG* 1.3 66.4 - - - +
84D GLU* 1.3 69.1 + - - +
86D ILE* 2.8 27.2 + - + +
87D LEU* 3.1 51.3 + - + +
100D TYR* 5.0 4.2 - + - -
104D ILE* 4.5 19.1 - - + -
107D ILE* 6.5 0.4 - - + -
146D THR* 4.0 18.5 - - + +
149D ASP* 2.7 35.5 + - - +
150D ALA* 3.1 42.2 + - + -
153D GLU* 5.4 7.0 - - + -
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Residues in contact with GLU 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 LEU 2.8 14.8 + - - +
81D ASP* 3.4 13.1 - - - +
83D TYR* 1.3 79.1 - - - +
85D LYS* 1.3 54.6 + - + +
87D LEU* 2.8 41.1 + - - +
88D ALA* 3.2 5.9 + - - +
97D LEU* 5.5 0.2 - - - +
101D MSE 3.7 35.6 - - + +
104D ILE* 3.4 29.4 - - + +
108D ARG* 3.0 30.1 + - - -
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Residues in contact with LYS 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 ASP 4.0 11.9 - - - +
82D ARG* 3.1 28.5 + - + +
84D GLU* 1.3 79.3 - - + +
86D ILE* 1.3 63.8 + - + +
87D LEU 3.3 0.3 + - - -
88D ALA* 3.3 17.0 + - - +
89D SER* 3.5 10.6 + - - -
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Residues in contact with ILE 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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79D TRP* 5.1 6.1 - - + -
82D ARG* 3.2 57.4 - - - +
83D TYR* 2.8 19.3 + - + +
85D LYS* 1.3 72.6 - - + +
87D LEU* 1.3 67.6 + - + +
89D SER* 3.3 11.3 + - - -
90D ARG* 3.2 20.8 + - - +
153D GLU* 4.8 25.4 - - + +
157D GLU* 4.8 2.2 - - - +
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Residues in contact with LEU 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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83D TYR* 3.1 54.3 - - + +
84D GLU* 2.8 31.6 + - + +
86D ILE* 1.3 79.1 - - + +
88D ALA* 1.3 60.2 + - - +
90D ARG* 2.9 37.4 + - - +
91D GLY 4.3 1.4 + - - -
92D ILE* 4.6 4.9 - - - +
97D LEU* 3.9 21.7 - - + +
100D TYR* 4.8 17.7 - - + -
101D MSE 5.0 3.4 - - - -
104D ILE* 4.2 12.6 - - + -
149D ASP* 4.6 4.0 - - - +
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Residues in contact with ALA 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 GLU 3.2 6.7 + - - +
85D LYS* 3.3 13.4 + - - +
87D LEU* 1.3 78.6 - - - +
89D SER* 1.3 57.0 + - - +
91D GLY* 4.2 6.3 + - - -
92D ILE* 6.0 0.6 - - - +
97D LEU* 4.3 21.7 - - + +
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Residues in contact with SER 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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85D LYS 3.5 8.1 + - - -
86D ILE* 3.3 17.4 + - - -
87D LEU 3.0 0.4 - - - -
88D ALA* 1.3 76.0 - - - +
90D ARG* 1.3 57.0 + - - +
91D GLY* 2.8 14.7 + - - -
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Residues in contact with ARG 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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169C ARG* 4.8 20.8 - - - +
86D ILE* 3.2 11.3 + - + +
87D LEU* 2.9 27.6 + - - +
89D SER* 1.3 76.3 - - - +
91D GLY* 1.3 62.8 + - - +
92D ILE* 4.5 12.4 - - + +
100D TYR* 5.9 3.2 - - - -
149D ASP* 4.3 21.7 + - - -
153D GLU* 3.1 26.8 + - - +
18I C 4.7 7.7 + - - -
19I A 3.7 34.6 + - - +
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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