Contacts of the strand formed by residues 79 - 85 (chain O) 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 GLY 79 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38O ARG* 5.4 0.4 - - - -
39O LYS 3.3 11.0 - - - -
40O LYS* 4.3 0.2 - - - -
41O SER* 3.4 19.1 + - - -
77O ASP 3.6 1.2 + - - -
78O GLY* 1.3 76.0 - - - -
80O THR* 1.3 63.6 + - - -
81O TYR* 4.2 6.7 - - - -
108O THR 3.6 0.7 - - - +
109O ALA* 3.6 1.4 - - - -
110O VAL* 2.8 34.5 + - - +
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Residues in contact with THR 80 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38O ARG* 3.3 4.5 - - - +
39O LYS* 2.8 55.7 + - + +
46O GLU* 5.5 3.0 - - - +
79O GLY* 1.3 77.5 + - - -
81O TYR* 1.3 73.7 + - - +
82O ARG* 4.5 15.5 - - - +
106O ASP 5.4 0.7 - - - +
107O GLY* 4.4 7.2 - - - -
108O THR 3.2 15.7 - - - +
109O ALA* 4.0 12.1 - - + +
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Residues in contact with TYR 81 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5O GLN* 3.0 5.4 + - - -
20O ILE* 3.9 20.4 - - + -
36O TRP* 5.3 4.0 - - + -
37O TYR 3.2 4.7 - - - +
38O ARG* 3.1 38.5 + - + -
46O GLU* 5.4 0.2 - - - -
49O ILE* 3.6 25.4 - - + -
55O TYR* 4.6 4.9 + + - -
68O LEU* 4.6 2.0 - - + -
70O ILE* 3.6 29.2 - - + +
77O ASP* 2.6 40.9 + - - +
79O GLY 4.1 8.5 - - - -
80O THR* 1.3 77.6 - - - +
82O ARG* 1.3 61.3 + - - +
107O GLY* 3.2 2.5 - - - -
108O THR 2.7 32.2 + - - +
110O VAL* 3.7 29.2 - - + -
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Residues in contact with ARG 82 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5O GLN* 3.6 5.8 - - - +
36O TRP* 3.4 8.4 - - - -
37O TYR* 2.8 42.4 + - + +
39O LYS* 5.5 3.6 - - - +
46O GLU* 2.9 37.0 + - - +
80O THR* 4.5 14.1 - - - +
81O TYR* 1.3 74.7 - - - +
83O CYS* 1.3 65.6 + - - +
94O TYR* 3.5 26.3 + - - -
97O CYS* 4.0 3.1 - - - -
104O CYS* 3.9 13.9 - - + -
105O GLY 3.1 35.9 + - - +
106O ASP* 3.3 23.3 + - - +
107O GLY* 4.2 2.2 - - - +
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Residues in contact with CYS 83 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3O VAL* 3.5 15.9 - - - -
5O GLN* 3.3 13.2 + - - -
22O CYS* 2.0 50.3 - - - -
35O CYS 3.3 5.6 - - - -
36O TRP* 3.5 20.3 - - + -
37O TYR* 4.9 1.6 - - - -
66O PHE* 3.6 10.8 - - + -
82O ARG* 1.3 74.3 - - - +
84O GLY* 1.3 60.0 + - - +
104O CYS* 3.2 7.1 - - - +
105O GLY 2.7 27.7 + - - -
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Residues in contact with GLY 84 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3O VAL* 5.3 0.7 - - - -
34O THR* 3.5 4.5 - - - -
35O CYS* 2.7 41.5 + - - -
37O TYR* 4.5 1.3 - - - -
66O PHE* 3.8 12.5 - - - -
83O CYS* 1.3 78.3 - - - +
85O LEU* 1.3 62.5 + - - -
103O GLU 3.4 11.9 - - - -
104O CYS* 3.8 11.2 - - - -
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Residues in contact with LEU 85 (chain O).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102M GLY* 4.2 20.6 - - - +
103M ASN* 4.6 1.8 - - + +
3O VAL* 4.3 13.9 - - + -
24O LEU* 4.3 9.4 - - + -
29O TYR* 3.8 22.9 - - + +
31O LEU* 3.7 31.0 - - + -
32O GLY 5.5 1.6 - - - +
33O SER 3.7 6.3 - - - +
35O CYS* 4.1 3.3 - - - +
37O TYR* 4.8 1.2 + - - -
66O PHE* 4.5 5.4 - - + -
84O GLY* 1.3 75.2 - - - -
86O GLY* 1.3 67.9 + - - +
96O LEU* 3.9 8.0 - - - +
102O ALA* 3.4 18.3 - - + +
103O GLU* 2.9 43.2 + - + +
104O CYS* 5.4 1.4 - - - -
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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