Contacts of the strand formed by residues 79 - 86 (chain B) in PDB entry 1DY5
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 MET 79 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47B VAL* 4.3 1.3 - - + -
49B GLU* 3.3 27.6 - - + +
53B ASP* 3.9 27.1 - - + +
54B VAL* 4.3 4.9 - - - +
57B VAL* 3.9 25.4 - - + -
60B GLN* 5.7 0.4 - - - +
75B SER* 4.3 7.2 - - - +
77B SER* 4.2 16.2 - - - +
78B THR* 1.3 79.0 - - - +
80B SER* 1.3 65.6 + - - +
81B ILE* 3.5 3.7 + - + +
103B ASN* 3.2 8.7 - - - -
104B LYS 2.8 35.6 + - - +
106B ILE* 3.6 37.2 - - + -
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Residues in contact with SER 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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18B SER 2.8 28.5 + - - -
19B ALA* 3.8 7.1 - - - +
47B VAL* 3.8 1.9 - - - +
48B HIS* 2.8 44.7 + - - +
49B GLU* 2.9 15.4 + - - -
79B MET* 1.3 71.4 - - - +
81B ILE* 1.3 60.7 + - - +
102B ALA 3.6 7.9 + - - -
103B ASN* 3.7 13.7 + - - +
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Residues in contact with ILE 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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19B ALA* 5.8 0.7 - - - +
20B ALA 5.5 0.2 + - - -
45B THR* 4.0 16.4 - - + -
46B PHE 3.2 13.0 - - - +
47B VAL* 4.3 9.9 - - + -
48B HIS* 3.9 4.9 - - - -
79B MET 3.8 9.9 - - - +
80B SER* 1.3 80.8 + - - +
82B THR* 1.3 67.8 + - - +
83B ASP* 5.5 3.4 - - + +
101B GLN* 3.8 1.9 - - - -
102B ALA* 2.9 50.3 + - + +
104B LYS* 3.9 27.1 - - + +
106B ILE* 3.7 26.5 - - + -
123B SER* 4.1 17.7 - - - +
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Residues in contact with THR 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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20B ALA* 3.3 19.3 + - + +
25B TYR* 4.0 9.9 - - + -
26B CYS* 3.7 20.9 - - - -
44B ASN 4.0 0.2 - - - +
45B THR* 3.3 9.3 - - - +
46B PHE* 2.8 35.0 + - - -
48B HIS* 2.6 28.5 + - - -
81B ILE* 1.3 74.3 + - - +
83B ASP* 1.3 72.6 + - - +
84B CYS* 3.8 1.8 + - - -
99B THR* 3.8 14.1 - - + -
100B THR 3.4 8.6 + - - +
101B GLN* 4.8 0.7 - - - -
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Residues in contact with ASP 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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26B CYS* 3.7 1.2 - - - -
43B VAL* 4.6 2.6 - - - +
44B ASN 4.6 0.7 - - - -
45B THR* 4.3 13.3 + - - +
81B ILE* 4.2 5.5 - - + +
82B THR* 1.3 72.1 - - - +
84B CYS* 1.3 61.1 + - - +
85B ARG* 2.8 53.9 + - - +
98B LYS* 3.3 6.2 - - - +
99B THR* 3.6 2.3 - - - -
100B THR* 2.9 50.1 + - + +
102B ALA* 5.8 3.7 - - + +
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Residues in contact with CYS 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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25B TYR* 4.8 0.4 - - - -
26B CYS* 2.0 54.3 - - + -
30B MET* 4.1 15.3 - - + -
42B PRO 3.9 0.2 - - - +
43B VAL* 3.3 6.6 - - - +
44B ASN 3.0 36.8 + - - +
46B PHE* 3.7 31.6 - - - -
82B THR* 4.1 3.4 - - - -
83B ASP* 1.3 73.6 - - - +
85B ARG* 1.3 60.6 + - - +
97B TYR* 4.1 5.2 - - + -
98B LYS 3.5 0.9 - - - -
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Residues in contact with ARG 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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42B PRO 3.4 3.6 - - - -
43B VAL* 3.6 31.6 - - + +
83B ASP* 2.8 36.8 + - - +
84B CYS* 1.3 75.0 - - - +
86B GLU* 1.3 74.0 + - + +
97B TYR* 3.6 5.0 - - - -
98B LYS* 2.8 41.6 + - + +
600B ACT 5.6 0.6 + - - -
601B ACT 3.0 25.5 + - - -
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Residues in contact with GLU 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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40B CYS* 5.2 7.4 - - + +
42B PRO* 2.8 50.1 + - + +
43B VAL* 5.9 0.4 - - + -
85B ARG* 1.3 83.8 - - + +
87B THR* 1.3 69.0 + - - +
90B SER* 4.1 15.0 + - - +
96B ALA 3.3 12.3 - - - +
97B TYR* 3.6 7.5 - - + -
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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