Contacts of the helix formed by residues 79 - 90 (chain B) in PDB entry 1ZTD
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 SER 79 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73B TRP* 4.8 4.3 - - - +
78B ILE* 1.3 79.0 - - - +
80B GLU* 1.3 65.3 + - - +
81B ARG* 3.6 8.7 + - - +
82B GLU* 3.2 24.3 + - - +
83B ALA* 3.1 23.2 + - - +
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Residues in contact with GLU 80 (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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73A TRP* 4.5 11.6 - - - -
80A GLU* 5.1 4.7 - - - +
17B PHE* 3.7 21.3 - - + -
18B LEU* 3.6 26.2 - - + -
21B LEU* 3.8 19.8 - - + +
73B TRP* 4.5 13.8 - - - +
79B SER* 1.3 72.9 - - - +
81B ARG* 1.3 69.1 + - - +
83B ALA* 3.2 3.9 + - - +
84B VAL* 2.9 35.7 + - + +
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Residues in contact with ARG 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B SER* 3.3 8.2 + - - +
80B GLU* 1.3 87.8 + - - +
82B GLU* 1.3 62.1 + - - +
84B VAL* 3.4 6.8 + - - +
85B GLU* 3.1 36.9 + - + +
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Residues in contact with GLU 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B ILE* 3.6 10.3 - - + +
79B SER* 3.2 18.3 + - - +
81B ARG* 1.3 77.4 - - - +
83B ALA* 1.3 66.8 + - - +
85B GLU* 3.4 7.5 + - + +
86B ILE* 3.1 42.7 + - + +
115B ILE* 5.7 0.7 - - - +
119B ARG* 2.7 47.8 + - - -
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Residues in contact with ALA 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B LEU* 4.0 26.5 - - + -
73B TRP* 6.5 0.7 - - + -
78B ILE* 4.0 15.5 - - + +
79B SER 3.1 17.5 + - - +
80B GLU* 3.6 4.0 - - - +
82B GLU* 1.3 77.3 - - - +
84B VAL* 1.3 63.0 + - - +
86B ILE* 3.4 3.1 + - - +
87B ILE* 3.1 30.0 + - - +
112B LEU* 4.0 20.7 - - + +
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Residues in contact with VAL 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B LEU* 4.0 16.4 - - + +
21B LEU* 3.8 32.3 - - + -
22B ALA* 3.9 23.6 - - - +
25B GLU* 4.4 15.0 - - - +
80B GLU* 2.9 26.8 + - + +
81B ARG* 3.7 6.7 - - - +
83B ALA* 1.3 76.6 - - - +
85B GLU* 1.3 58.4 + - + +
87B ILE* 3.4 8.9 + - - +
88B LYS* 3.0 34.0 + - + +
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Residues in contact with GLU 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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25B GLU* 4.7 2.3 - - - +
81B ARG* 3.1 30.4 + - + +
82B GLU* 3.7 7.6 - - - +
83B ALA 3.3 0.2 - - - -
84B VAL* 1.3 76.9 - - + +
86B ILE* 1.3 64.7 + - + +
88B LYS* 3.5 27.3 + - - +
89B LYS* 3.1 52.5 + - - +
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Residues in contact with ILE 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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78B ILE* 4.1 6.5 - - + -
82B GLU* 3.1 36.1 + - + +
83B ALA 3.7 5.2 - - - +
84B VAL 3.3 0.2 - - - -
85B GLU* 1.3 77.5 - - + +
87B ILE* 1.3 62.7 + - - +
89B LYS* 3.6 6.5 + - - +
90B ASN* 2.8 29.3 + - - +
108B ALA 4.5 1.0 - - - +
111B PRO* 4.1 12.1 - - + -
112B LEU* 3.7 49.1 - - + +
115B ILE* 3.5 31.2 - - + -
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Residues in contact with ILE 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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15B ILE* 4.5 2.2 - - + -
18B LEU* 4.1 36.3 - - + +
19B TYR* 4.0 24.0 - - + +
22B ALA* 3.8 14.6 - - + -
83B ALA 3.1 17.6 + - - +
84B VAL* 3.7 5.4 - - - +
85B GLU 3.3 0.2 - - - -
86B ILE* 1.3 75.7 - - - +
88B LYS* 1.3 63.9 + - - +
90B ASN* 2.9 16.6 + - - +
91B LEU* 3.2 19.2 + - + +
108B ALA* 4.2 10.3 - - + +
109B LEU* 4.2 23.3 - - + -
112B LEU* 4.2 20.4 - - + -
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Residues in contact with LYS 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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22B ALA* 3.4 26.5 - - + +
25B GLU* 2.7 52.0 + - + +
26B PHE* 4.3 12.3 - - + +
84B VAL* 3.0 21.6 + - + +
85B GLU* 3.8 32.5 + - - +
87B ILE* 1.3 74.7 - - - +
89B LYS* 1.3 63.9 + - + +
90B ASN 3.0 1.4 + - - -
91B LEU* 3.1 27.0 + - + +
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Residues in contact with LYS 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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85B GLU* 3.1 38.6 + - - +
86B ILE* 3.9 7.6 - - - +
87B ILE 3.3 0.2 - - - -
88B LYS* 1.3 76.6 - - + +
90B ASN* 1.3 66.5 + - - +
91B LEU 3.6 1.8 - - - +
92B TYR* 5.2 3.6 + - - -
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Residues in contact with ASN 90 (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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86B ILE* 2.8 25.1 + - - +
87B ILE 2.9 10.0 + - - +
89B LYS* 1.3 89.0 - - - +
91B LEU* 1.3 58.1 + - - +
92B TYR* 3.2 30.3 + - + -
104B ALA 5.0 0.2 - - - +
107B ARG 4.4 2.2 - - - +
108B ALA* 3.4 31.5 + - - +
111B PRO* 3.6 34.0 - - + +
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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