Contacts of the strand formed by residues 78 - 84 (chain K) in PDB entry 1I9R
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 78 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21K SER* 4.2 4.7 - - - +
22K CYS 3.3 16.6 - - - +
23K LYS* 3.8 16.1 - - + +
29K PHE* 3.3 7.9 - - - -
72K VAL* 3.2 5.0 - - - +
73K ASP* 2.7 31.2 + - - -
76K ALA* 2.6 28.6 + - - +
77K SER* 1.3 75.3 + - - +
79K ALA* 1.3 70.7 + - - +
80K TYR* 3.0 38.7 + - + +
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Residues in contact with ALA 79 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22K CYS* 2.8 35.6 + - + +
29K PHE* 4.1 6.2 - - + -
34K MET* 4.3 22.0 - - + -
36K TRP* 3.9 20.2 - - + +
51K ILE* 4.8 1.8 - - + -
71K THR 3.4 9.6 - - - +
72K VAL* 4.0 9.9 - - + +
78K THR* 1.3 79.1 - - - +
80K TYR* 1.3 66.9 + - - +
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Residues in contact with TYR 80 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19K LYS* 3.5 45.8 - - + -
20K LEU 3.0 7.0 - - - +
21K SER* 3.8 23.6 - - - -
36K TRP* 3.9 6.9 + - - -
69K THR 3.5 3.1 - - - +
70K LEU* 3.6 3.8 - - - +
71K THR* 2.8 48.1 + - + +
72K VAL* 4.3 1.6 - - - -
73K ASP* 4.1 19.2 + - + +
76K ALA* 4.9 2.1 - - - +
78K THR* 3.0 39.6 - - + +
79K ALA* 1.3 77.5 - - - +
81K MET* 1.3 60.2 + - - +
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Residues in contact with MET 81 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18K VAL 3.7 0.7 - - - +
19K LYS* 3.2 3.1 - - - -
20K LEU* 2.5 61.1 + - + +
36K TRP* 3.3 46.4 - - + -
48K ILE* 3.7 20.6 - - + -
68K ALA* 4.3 10.8 - - + -
69K THR 3.7 3.1 - - - -
70K LEU* 4.0 9.9 - - + -
71K THR* 5.9 0.2 - - - -
80K TYR* 1.3 75.0 - - - +
82K GLU* 1.3 62.9 + - - +
83K LEU* 3.8 20.8 + - + -
94K TYR* 3.3 32.3 - - + -
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Residues in contact with GLU 82 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17K SER* 5.2 7.8 - - - -
18K VAL 3.2 14.1 - - - +
19K LYS* 3.8 29.7 - - + +
67K LYS 3.0 11.8 - - - +
69K THR* 3.1 43.6 + - - +
71K THR* 5.7 3.4 - - + +
81K MET* 1.3 76.0 - - - +
83K LEU* 1.3 68.6 - - - +
84K SER* 3.8 6.6 + - - +
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Residues in contact with LEU 83 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17K SER* 3.2 4.2 - - - -
18K VAL* 2.9 44.1 + - + +
20K LEU* 4.2 9.2 - - + -
38K LYS* 5.8 0.9 - - - +
48K ILE* 5.1 2.5 - - + -
64K PHE* 5.7 2.0 - - + -
67K LYS* 3.0 25.6 - - + +
68K ALA* 4.2 8.3 - - + -
81K MET* 3.8 35.6 - - + -
82K GLU* 1.3 74.8 - - - +
84K SER* 1.3 59.8 + - - +
86K LEU* 3.7 21.8 - - + -
94K TYR* 3.7 44.0 - - + +
114K VAL* 4.5 1.6 - - + -
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Residues in contact with SER 84 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16K ALA 4.0 0.2 - - - -
17K SER* 2.8 17.9 - - - -
66K SER 4.1 9.2 + - - -
67K LYS* 3.1 26.8 + - - +
69K THR* 4.7 4.7 + - - -
82K GLU* 4.2 10.0 + - - +
83K LEU* 1.3 75.9 - - - +
85K SER* 1.3 83.7 + - - +
86K LEU* 3.2 3.6 + - - +
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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