Contacts of the strand formed by residues 81 - 90 (chain C) in PDB entry 1T7C
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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66C VAL 3.3 4.7 - - - +
67C VAL* 3.4 1.6 - - - -
68C ALA* 2.9 43.9 + - + +
80C ILE* 1.3 77.8 - - - +
82C LYS* 1.3 61.7 + - - +
83C LEU* 3.5 16.3 + - + +
111C ALA 4.7 0.3 - - - +
112C ALA* 3.7 8.0 - - - -
113C SER* 2.8 56.3 + - - -
115C SER* 4.6 3.0 + - - -
118C VAL* 3.6 23.2 - - + +
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Residues in contact with LYS 82 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C GLN* 5.6 3.4 - - - -
65C VAL* 5.4 12.1 - - + -
66C VAL 3.5 4.7 - - - -
67C VAL* 4.3 14.1 - - + +
80C ILE* 4.1 29.3 + - + +
81C GLN* 1.3 71.9 - - - +
83C LEU* 1.3 66.5 + - - +
84C LYS* 4.1 3.4 + - - +
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Residues in contact with LEU 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46C LEU* 5.1 0.9 - - + -
65C VAL* 3.6 4.7 - - - +
66C VAL* 2.6 58.0 + - + +
68C ALA* 4.4 9.0 - - + -
81C GLN* 3.9 21.8 - - + +
82C LYS* 1.3 79.9 - - - +
84C LYS* 1.3 64.6 + - - +
108C LEU* 3.7 20.6 - - + -
110C THR* 3.7 29.2 - - + +
111C ALA 3.9 11.4 - - - +
112C ALA* 3.5 29.6 - - + -
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Residues in contact with LYS 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62C THR 5.9 1.1 - - - +
64C ASP 4.8 0.4 - - - +
65C VAL* 4.6 18.2 - - + -
82C LYS 4.1 3.5 + - - +
83C LEU* 1.3 75.5 - - - +
85C ILE* 1.3 60.8 + - - +
108C LEU* 3.5 7.8 - - - +
109C SER* 3.0 40.6 + - - +
110C THR* 4.2 4.5 + - - +
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Residues in contact with ILE 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C LEU* 5.7 0.9 - - + -
60C VAL* 3.5 29.8 - - + -
61C THR 3.8 2.0 - - - +
62C THR* 3.7 25.7 + - - +
64C ASP* 3.5 30.7 + - + +
65C VAL* 4.3 1.1 - - - +
66C VAL* 4.0 21.8 - - + -
83C LEU 4.5 0.7 - - - +
84C LYS* 1.3 78.1 - - - +
86C ALA* 1.3 64.5 + - - +
87C LYS 3.7 25.6 - - - +
88C VAL* 4.0 12.3 - - + -
106C LEU* 4.0 20.4 - - + -
107C LYS 3.8 5.6 - - - +
108C LEU* 4.5 3.6 - - + +
109C SER* 4.2 2.0 - - - -
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Residues in contact with ALA 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62C THR* 3.5 12.2 - - - +
85C ILE* 1.3 74.0 - - - +
87C LYS* 1.3 63.5 + - + +
107C LYS* 2.7 24.5 + - + +
108C LEU 3.9 2.5 - - - +
109C SER* 3.6 29.9 - - - +
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Residues in contact with LYS 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62C THR* 4.1 5.4 - - + -
85C ILE* 3.6 5.0 - - - +
86C ALA* 1.3 84.5 - - + +
88C VAL* 1.3 73.5 + - - +
89C PHE* 3.4 42.4 - - + -
106C LEU* 3.8 0.3 - - - -
107C LYS* 2.9 34.9 + - + +
245C ASN* 4.9 3.8 + - - -
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Residues in contact with VAL 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60C VAL 3.7 27.8 - - - +
61C THR* 3.9 22.2 - - - -
62C THR* 4.0 6.7 - - + +
85C ILE* 4.0 11.7 - - + -
87C LYS* 1.3 85.4 - - - +
89C PHE* 1.3 65.7 + - - +
90C LYS* 3.9 9.8 + - + +
104C THR* 3.6 24.2 - - + -
105C LEU 3.7 2.2 - - - -
106C LEU* 4.0 8.3 - - + -
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Residues in contact with PHE 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51C TRP* 3.6 27.6 - + - -
87C LYS* 3.4 55.4 - - + -
88C VAL* 1.3 75.2 - - - +
90C LYS* 1.3 60.8 + - - +
104C THR* 4.0 1.1 - - - -
105C LEU* 2.8 39.9 + - + +
107C LYS* 4.0 6.7 - - + -
237C TRP* 3.3 13.9 - - + -
241C THR* 3.7 24.7 - - + -
245C ASN* 3.4 38.4 - - + -
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Residues in contact with LYS 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56C ALA* 4.2 13.8 + - + +
88C VAL* 3.8 9.3 + - + +
89C PHE* 1.3 74.5 - - - +
91C ASN* 1.3 74.5 + - - +
92C SER* 3.1 5.6 + - - -
94C TYR* 3.3 39.9 - - - -
96C SER* 5.9 1.4 - - - -
104C THR* 3.4 23.1 - - + +
237C TRP* 4.0 0.7 - - - -
1606C SO4 3.4 7.8 + - - -
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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