Contacts of the strand formed by residues 81 - 90 (chain E) in PDB entry 1C9T
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 GLN 81 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65E VAL 3.0 13.7 - - - +
66E ARG* 3.1 2.1 - - - -
67E LEU* 3.0 39.7 + - + +
70E GLU* 4.7 0.8 + - - -
79E ASN* 5.4 7.4 + - - +
80E GLU* 1.3 82.2 - - - +
82E PHE* 1.3 66.2 + - - +
83E ILE* 3.8 8.5 - - + +
112E ALA* 4.3 10.6 - - - +
113E SER* 2.7 39.0 + - - -
115E ASN* 6.1 0.6 - - - +
118E VAL* 3.2 27.9 - - - +
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Residues in contact with PHE 82 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34E ASN* 5.7 5.4 - - - -
64E GLN* 5.6 16.2 - - + +
65E VAL 3.4 5.4 - - - -
66E ARG* 3.3 45.3 - - + -
70E GLU* 4.2 1.6 - - - -
76E VAL* 6.3 0.4 - - + -
80E GLU* 3.4 32.7 + - + -
81E GLN* 1.3 77.3 - - - +
83E ILE* 1.3 60.6 + - - +
84E SER* 4.4 0.3 + - - -
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Residues in contact with ILE 83 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64E GLN* 3.5 3.9 - - - -
65E VAL* 2.8 44.0 + - - +
67E LEU* 4.0 21.3 - - + -
81E GLN* 4.5 11.9 - - + +
82E PHE* 1.3 78.5 - - - +
84E SER* 1.3 76.6 + - - +
108E LEU* 3.7 22.2 - - + -
109E LYS* 4.5 1.3 - - + -
110E SER* 3.7 41.3 - - - +
111E ALA 4.7 1.3 - - - +
112E ALA* 4.1 14.4 - - + -
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Residues in contact with SER 84 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63E ILE 4.1 5.8 - - - -
64E GLN* 4.6 13.3 + - - +
83E ILE* 1.3 81.1 - - - +
85E ALA* 1.3 56.7 + - - +
108E LEU* 3.6 1.5 - - - -
109E LYS* 2.7 66.9 + - - +
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Residues in contact with ALA 85 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62E GLY* 5.7 3.6 - - - -
63E ILE* 3.3 28.2 + - + +
65E VAL* 4.9 3.1 - - + -
84E SER* 1.3 74.7 - - - +
86E SER* 1.3 64.8 + - - +
87E LYS 4.7 0.2 - - - +
88E SER* 3.9 16.1 + - - +
106E ILE* 3.6 29.2 - - + -
107E LYS 3.3 4.9 - - - +
108E LEU* 4.4 1.8 - - - +
109E LYS* 4.9 1.2 - - - -
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Residues in contact with SER 86 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85E ALA* 1.3 74.7 - - - +
87E LYS* 1.3 83.3 + - - +
88E SER* 4.2 0.5 + - - -
107E LYS* 2.6 20.4 + - - -
108E LEU 4.4 1.8 - - - -
109E LYS* 3.6 27.5 - - - +
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Residues in contact with LYS 87 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51E TRP* 4.9 0.6 - - + -
86E SER* 1.3 100.2 - - - +
88E SER* 1.3 61.6 + - - +
89E ILE* 3.7 24.6 + - + -
105E LEU 4.0 0.2 - - - +
106E ILE* 3.6 1.7 - - - +
107E LYS* 2.8 54.0 + - + +
245E ASN* 3.7 27.9 + - + +
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Residues in contact with SER 88 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59E TYR* 3.6 36.3 - - - -
60E LYS 4.8 4.5 + - - -
62E GLY* 5.6 1.6 + - - -
63E ILE* 4.7 10.8 + - - +
85E ALA* 3.9 19.8 + - - +
86E SER 4.2 1.4 + - - -
87E LYS* 1.3 72.9 + - - +
89E ILE* 1.3 62.1 + - - +
90E VAL 3.5 3.1 + - - -
104E MET* 4.7 3.6 - - - -
105E LEU 3.6 5.6 - - - -
106E ILE* 4.5 11.3 - - - +
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Residues in contact with ILE 89 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51E TRP* 3.8 14.4 - - + -
87E LYS* 4.1 16.4 - - + -
88E SER* 1.3 72.3 - - - +
90E VAL* 1.3 68.3 + - - +
104E MET* 3.5 3.0 - - - -
105E LEU* 2.8 41.5 + - + +
237E TRP* 3.8 10.7 - - + -
241E THR* 3.7 20.9 - - + -
245E ASN* 3.5 37.7 - - + +
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Residues in contact with VAL 90 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56E ALA* 3.8 20.0 - - + +
59E TYR* 3.4 39.5 - - + -
88E SER 3.5 2.0 + - - +
89E ILE* 1.3 83.2 - - - +
91E HIS* 1.3 78.8 + - - +
92E PRO* 3.4 6.4 - - - +
94E TYR* 4.2 12.8 - - + -
104E MET* 3.6 18.8 - - + -
237E TRP* 4.3 0.9 - - - -
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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