Contacts of the strand formed by residues 79 - 87 (chain A) in PDB entry 6O4P
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 LEU 79 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71A ILE* 4.1 18.2 - - + -
72A CYS 3.2 26.5 - - - +
73A GLN* 4.1 23.3 - - + +
77A GLY 3.7 4.7 + - - +
78A ALA* 1.3 70.6 - - - +
80A GLY* 1.3 62.8 + - - +
81A GLY* 3.3 28.8 - - - +
82A THR* 5.1 2.5 - - - +
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Residues in contact with GLY 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A CYS* 4.3 6.3 - - - -
27A PRO* 3.5 6.5 - - - +
28A GLY* 3.3 47.6 + - - -
72A CYS 3.6 8.7 + - - -
73A GLN* 4.5 2.2 - - - +
74A THR 5.0 0.4 - - - +
78A ALA 3.3 4.6 + - - -
79A LEU* 1.3 77.1 - - - +
81A GLY* 1.3 57.0 + - - +
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Residues in contact with GLY 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A PRO* 3.9 11.8 - - - +
71A ILE* 4.2 0.3 - - - -
72A CYS* 3.4 28.8 + - - +
79A LEU* 3.3 14.7 - - - +
80A GLY* 1.3 78.7 - - - +
82A THR* 1.3 63.8 + - - -
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Residues in contact with THR 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A GLY* 3.8 15.4 - - - +
27A PRO* 5.0 2.8 - - - +
69A THR* 3.5 25.6 - - + -
70A TYR 3.2 17.0 - - - +
71A ILE* 4.0 18.0 - - + +
79A LEU* 5.1 2.6 - - - +
81A GLY* 1.3 76.2 + - - -
83A VAL* 1.3 65.8 + - - +
84A THR* 5.4 2.0 - - - +
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Residues in contact with VAL 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A GLY* 3.6 4.5 - - - +
14A GLN* 3.4 39.3 - - + +
24A LEU* 4.2 18.8 - - + -
25A CYS 3.4 22.0 - - - +
27A PRO* 3.7 17.9 - - + -
37A TRP* 4.8 3.8 - - + -
69A THR* 3.6 0.3 - - - -
70A TYR* 2.6 52.9 + - + +
72A CYS* 4.8 6.1 - - - -
81A GLY 4.4 0.2 + - - -
82A THR* 1.3 79.9 - - - +
84A THR* 1.3 64.8 + - - +
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Residues in contact with THR 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A GLY 3.0 15.8 + - - -
13A VAL* 3.3 19.6 - - + +
14A GLN* 2.7 33.1 + - - +
68A GLY* 3.3 16.2 - - - +
69A THR* 4.2 14.1 + - - +
82A THR* 5.4 1.6 - - - +
83A VAL* 1.3 76.9 + - - +
85A LEU* 1.3 66.7 + - - +
86A GLN* 5.7 1.8 - - + +
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Residues in contact with LEU 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A GLN 3.4 9.9 - - - +
15A TYR 4.2 10.8 - - - -
16A GLY* 4.3 1.6 - - - +
22A VAL* 4.0 27.8 - - + -
24A LEU* 3.7 23.3 - - + -
59A LEU* 4.3 5.4 - - + -
62A ALA* 5.6 1.6 - - + -
63A ASP 5.7 0.2 - - - +
66A ASP* 3.7 24.9 - - + +
67A GLU* 3.2 24.2 - - - +
68A GLY* 2.8 16.4 + - - +
70A TYR* 3.8 24.7 - - + +
83A VAL 4.1 1.4 + - - -
84A THR* 1.3 76.6 - - - +
86A GLN* 1.3 73.7 + - - +
87A LEU* 5.0 9.2 - - + -
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Residues in contact with GLN 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A VAL* 3.8 21.3 - - + -
14A GLN 2.9 6.5 + - - -
15A TYR* 3.2 21.7 - - + +
16A GLY 3.0 24.4 + - - -
67A GLU* 4.0 17.4 + - - +
84A THR* 3.8 1.9 + - + +
85A LEU* 1.3 77.7 - - - +
87A LEU* 1.3 87.7 + - - +
117A GLY 5.3 0.8 + - - -
118A LEU* 4.6 7.9 - - + +
115B ILE* 4.3 28.4 - - + +
504B SO4 4.2 21.2 + - - -
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Residues in contact with LEU 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A GLY* 3.5 7.9 - - - -
17A GLN 4.0 3.6 - - - -
18A PRO* 3.8 31.6 - - + -
22A VAL* 4.6 3.6 - - + -
62A ALA* 3.9 25.1 - - + -
63A ASP* 3.5 36.8 - - - +
64A SER* 4.0 4.9 - - - +
67A GLU* 3.6 26.5 + - + +
85A LEU* 5.0 7.9 - - + -
86A GLN* 1.3 98.5 + - - +
88A GLY* 1.3 58.2 + - - +
118A LEU* 3.7 8.1 - - - +
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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