Contacts of the strand formed by residues 65 - 70 (chain N) in PDB entry 1T6V
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 SER 65 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22N CYS 3.3 9.2 - - - -
23N VAL* 3.7 16.3 - - - +
31N LEU* 4.0 0.3 - - - +
58N THR 4.2 1.6 - - - -
59N VAL* 3.3 6.1 - - - +
60N ASN* 2.9 33.4 + - - +
63N SER* 2.9 32.4 + - - -
64N LYS* 1.3 75.4 - - - +
66N PHE* 1.3 62.3 + - - +
67N SER* 5.5 3.8 - - - -
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Residues in contact with PHE 66 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3N VAL* 3.8 25.1 - - + -
22N CYS* 2.8 52.8 + - + +
24N LEU* 4.4 4.9 - - + -
31N LEU* 4.0 25.6 - - + -
34N THR* 3.6 24.9 - - + -
36N TRP* 3.6 18.4 - + - -
57N GLU* 4.1 9.9 - - - +
58N THR 3.2 7.9 - - - +
59N VAL* 4.2 5.4 - - + -
64N LYS 4.1 5.6 - - - -
65N SER* 1.3 79.1 - - - +
67N SER* 1.4 63.1 + - - +
83N CYS* 3.7 21.1 - - + -
84N GLY 3.8 17.9 - - - -
85N LEU* 4.2 16.2 - - + -
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Residues in contact with SER 67 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19N THR* 4.5 8.1 - - - -
20N ILE 3.1 11.0 - - - -
21N ASN* 2.7 28.6 + - - +
22N CYS 4.4 0.9 + - - -
36N TRP* 3.6 2.9 - - - -
56N VAL 4.4 0.4 - - - -
57N GLU* 3.1 10.4 - - - +
58N THR* 2.8 43.5 + - - -
65N SER* 5.4 3.1 - - - -
66N PHE* 1.4 77.0 + - - +
68N LEU* 1.3 60.2 + - - +
69N ARG 4.3 0.2 - - - -
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Residues in contact with LEU 68 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18N LEU 3.5 2.3 - - - +
19N THR* 3.3 4.8 - - - -
20N ILE* 2.9 36.1 + - + +
36N TRP* 3.6 53.7 - - + -
49N ILE* 4.2 12.8 - - + -
51N LYS* 5.0 5.6 - - + -
55N TYR* 4.1 28.3 - - + -
56N VAL 3.4 26.5 - - - +
57N GLU* 4.0 12.3 - - + +
67N SER* 1.3 73.4 - - - +
69N ARG* 1.3 64.7 + - - +
70N ILE* 4.0 13.7 + - + +
81N TYR* 5.5 1.3 - - + -
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Residues in contact with ARG 69 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17N SER* 3.4 28.7 + - - -
18N LEU 3.3 5.2 - - - +
19N THR* 3.7 23.6 + - + +
54N ARG 3.2 5.7 - - - +
55N TYR* 3.3 3.1 - - - -
56N VAL* 2.7 50.9 + - + +
68N LEU* 1.3 73.5 - - - +
70N ILE* 1.3 63.4 + - - +
71N ASN* 2.6 28.7 + - - +
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Residues in contact with ILE 70 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17N SER* 3.2 6.4 - - - -
18N LEU* 2.7 54.2 + - + +
20N ILE* 4.7 5.2 - - + -
54N ARG* 3.6 18.6 - - - +
55N TYR* 3.8 28.9 - - + -
68N LEU* 4.1 13.0 - - + +
69N ARG* 1.3 75.4 - - - +
71N ASN* 1.3 61.1 + - - +
73N LEU* 3.7 25.0 - - + +
77N ASP* 4.9 2.5 - - - +
81N TYR* 3.5 39.7 - - + +
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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