Contacts of the strand formed by residues 86 - 91 (chain A) in PDB entry 1Z09
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 86 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A MET* 3.8 17.9 - - + -
4A VAL* 6.0 4.9 - - + -
5A GLU* 4.0 17.0 - - - +
8A LEU* 6.4 0.9 - - + -
22A VAL* 5.5 9.6 - - + -
23A VAL 3.8 3.8 - - - +
24A ASN* 3.2 32.1 - - + +
25A THR* 5.8 0.4 - - + -
30A ILE* 3.3 19.7 - - + +
83A ASP* 3.0 34.1 + - + +
84A LYS 3.2 2.8 + - - +
85A ASP* 1.3 128.9 + - + +
87A PHE* 1.3 68.2 + - - +
88A LEU* 5.3 1.6 - - + -
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Residues in contact with PHE 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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22A VAL* 5.4 0.9 - - - +
23A VAL* 2.5 65.0 + - + +
24A ASN 2.7 35.2 - - - -
25A THR* 3.8 8.5 - - + -
47A HIS* 3.5 26.9 - + - -
50A ILE* 4.2 29.8 - - + -
51A LEU* 5.8 4.7 - - + -
80A VAL* 4.7 0.9 - - + -
81A ALA 3.7 6.1 - - - -
82A PRO* 3.4 27.8 - - + -
83A ASP 5.5 0.2 - - - +
84A LYS 6.0 0.4 - - - -
85A ASP 5.4 0.4 - - - -
86A TYR* 1.3 82.1 - - - +
88A LEU* 1.3 66.5 + - - +
89A ILE* 5.9 0.2 - - + -
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Residues in contact with LEU 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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8A LEU* 3.3 32.3 - - + -
11A LEU* 3.0 35.9 - - + -
20A ILE* 5.2 5.2 - - + -
21A ILE 3.3 15.3 - - - +
22A VAL* 3.7 14.4 - - + -
23A VAL* 4.1 0.4 - - - +
80A VAL* 3.0 27.0 - - - +
81A ALA* 3.2 24.3 + - + +
83A ASP* 5.6 4.5 - - + -
86A TYR* 5.2 1.8 - - + +
87A PHE* 1.3 84.3 - - - +
89A ILE* 1.3 60.8 + - - +
90A VAL* 3.6 11.9 + - + +
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Residues in contact with ILE 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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20A ILE* 4.1 1.0 - - - +
21A ILE* 3.0 41.3 + - + +
23A VAL* 4.8 6.3 - - + -
42A TYR* 4.6 1.1 - - + -
43A ALA* 4.1 18.8 - - - +
46A MET* 2.9 58.8 - - + -
47A HIS* 4.8 0.4 - - - +
50A ILE* 4.0 5.2 - - + -
78A ILE* 5.4 0.7 - - + -
79A MET 3.5 11.9 - - - +
80A VAL* 3.7 18.6 - - + -
88A LEU* 1.3 71.9 - - - +
90A VAL* 1.3 62.0 + - - +
91A ILE* 3.5 28.6 + - + +
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Residues in contact with VAL 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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11A LEU* 3.6 39.0 - - + +
19A GLY 4.6 0.7 - - - -
20A ILE* 5.1 9.6 - - + +
77A GLU* 4.0 7.1 - - - +
79A MET* 2.6 47.7 + - + +
80A VAL* 5.4 0.4 - - - -
81A ALA* 5.5 2.5 - - + +
88A LEU* 3.6 16.2 - - + +
89A ILE* 1.3 74.6 - - - +
91A ILE* 1.3 60.0 + - - +
92A GLN* 2.7 41.2 + - + +
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Residues in contact with ILE 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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17A VAL* 3.8 1.4 - - - -
18A GLN* 2.8 45.8 + - + +
19A GLY 2.6 46.8 + - - +
20A ILE* 4.3 3.3 - - - +
21A ILE* 4.0 11.0 - - + -
34A MET* 3.9 16.4 - - + -
42A TYR* 5.0 13.7 - - + -
46A MET* 5.8 0.4 - - - -
76A ASN* 3.5 24.7 - - - +
77A GLU 4.1 8.1 - - - +
78A ILE* 5.8 4.3 - - + -
89A ILE* 3.6 34.1 - - + +
90A VAL* 1.3 71.6 - - - +
92A GLN* 1.3 62.2 + - - +
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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