Contacts of the helix formed by residues 80 - 89 (chain B) in PDB entry 1Z6T
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 TYR 80 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19B ASP* 4.2 6.5 - - + -
20B ILE* 3.6 16.8 - - + -
21B LYS* 2.7 39.9 + - - +
25B ILE* 3.9 18.2 - - + -
75B LEU* 2.9 38.4 + - + +
76B LEU* 5.1 0.9 - - - -
78B GLU* 4.0 20.9 - - + -
79B GLY* 1.3 73.0 - - - +
81B LYS* 1.3 63.6 + - - +
82B ASP 3.3 2.7 - - - -
83B LEU* 4.0 28.7 - - + -
84B ALA* 3.1 23.9 + - - +
430B GLY* 3.5 30.0 + - - -
431B LYS* 4.0 4.0 - - + -
433B PHE* 4.8 2.3 - - - -
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Residues in contact with LYS 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76B LEU* 4.5 12.4 - - + +
79B GLY 3.0 9.8 + - - +
80B TYR* 1.3 74.9 - - - +
82B ASP* 1.3 80.3 + - - +
84B ALA* 3.7 2.8 + - - +
85B ALA* 3.1 23.9 + - - +
112B THR* 4.2 17.5 - - + -
116B GLU* 3.2 39.7 + - + +
554D LEU* 6.3 3.3 - - - +
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Residues in contact with ASP 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80B TYR 3.3 0.4 - - - -
81B LYS* 1.3 106.1 + - - +
83B LEU* 1.3 61.9 + - + +
85B ALA* 3.3 10.8 - - + +
86B LEU* 3.1 32.8 + - + +
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Residues in contact with LEU 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B HIS* 5.8 0.2 - - - +
15B ALA* 3.6 36.8 - - + +
16B LEU* 3.8 16.8 - - + +
19B ASP* 3.7 27.1 - - + +
20B ILE* 3.3 33.0 - - + -
75B LEU* 4.7 3.4 - - + -
80B TYR* 3.6 23.0 + - + +
81B LYS 3.5 0.2 - - - -
82B ASP* 1.3 78.3 - - + +
84B ALA* 1.3 62.7 + - - +
86B LEU* 3.3 15.7 + - + +
87B LEU* 3.3 23.2 + - - +
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Residues in contact with ALA 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B TYR* 3.2 31.7 - - + +
75B LEU* 4.2 10.8 - - + +
76B LEU* 3.5 29.4 - - + -
80B TYR 3.1 18.4 + - - +
81B LYS 3.9 0.4 - - - +
83B LEU* 1.3 73.0 - - - +
85B ALA* 1.3 55.6 + - - +
87B LEU* 2.9 4.9 + - - +
88B HIS 2.7 32.2 + - - -
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Residues in contact with ALA 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81B LYS 3.1 15.6 + - - +
82B ASP* 3.3 17.0 - - + +
84B ALA* 1.3 78.0 - - - +
86B LEU* 1.3 64.6 + - + +
87B LEU 3.4 0.5 + - - -
88B HIS* 3.5 19.6 + - - +
89B ASP* 4.2 4.5 + - - +
215D ARG* 5.7 2.9 + - - -
558D GLN 4.7 12.4 - - - +
559D PRO* 5.6 4.5 - - + -
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Residues in contact with LEU 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B CYS* 3.3 7.6 - - - -
12B HIS* 3.0 62.8 + - + +
15B ALA* 4.3 20.4 - - + -
82B ASP* 3.1 17.9 + - + +
83B LEU* 3.4 16.6 - - + +
84B ALA 3.2 0.4 - - - -
85B ALA* 1.3 81.4 - - + +
87B LEU* 1.3 57.9 + - - +
89B ASP* 4.2 5.0 - - - +
557D ARG* 5.8 5.8 - - - +
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Residues in contact with LEU 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B CYS* 3.9 7.2 - - - +
9B LEU* 4.0 27.6 - - + -
12B HIS* 4.6 4.9 - - + -
16B LEU* 4.2 16.8 - - + -
68B TYR* 2.6 44.4 + - + +
71B PHE* 4.0 23.8 - - + -
72B TYR* 4.3 15.3 - - + -
75B LEU* 3.7 25.1 - - + -
83B LEU 3.3 13.5 + - - +
84B ALA 2.9 8.7 + - - +
86B LEU* 1.3 79.2 - - - +
88B HIS* 1.3 54.0 + - - +
89B ASP 3.0 3.1 - - - -
90B GLY 2.8 16.9 + - - -
91B ILE 3.7 1.2 + - - -
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Residues in contact with HIS 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B TYR* 3.1 25.0 + - + +
84B ALA 2.7 15.6 + - - +
85B ALA* 3.5 17.9 + - - +
87B LEU* 1.3 71.4 - - - +
89B ASP* 1.3 65.3 + - - +
90B GLY 3.3 0.7 + - - -
91B ILE* 3.3 37.7 + - + +
108B SER* 6.4 0.2 - - - -
558D GLN* 3.1 43.5 - - + +
559D PRO* 4.0 22.3 - - + +
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Residues in contact with ASP 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B LYS* 5.5 5.4 - - - +
8B CYS* 4.0 19.5 - - - +
11B GLN* 5.9 1.0 + - - -
12B HIS* 5.4 4.0 - - + -
85B ALA 4.2 3.2 + - - +
86B LEU 4.2 7.6 - - - +
88B HIS* 1.3 83.3 - - - +
90B GLY* 1.3 57.1 + - - +
91B ILE 3.6 3.3 + - - +
212D PHE* 4.5 0.9 - - - -
213D SER* 2.8 51.3 + - - +
214D GLN* 3.4 11.1 + - - +
215D ARG* 4.7 1.3 + - + +
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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