Contacts of the strand formed by residues 78 - 83 (chain E) in PDB entry 6DDE
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 THR 78 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21E SER* 3.3 26.9 - - - +
22E CYS 3.4 10.5 - - - +
23E SER* 4.4 10.3 + - - -
29E PHE* 3.9 5.3 - - - -
72E ARG* 3.5 3.6 - - - +
73E ASP* 2.8 36.4 + - - +
76E LYS* 2.7 30.7 + - - +
77E ASN* 1.3 76.8 + - - +
79E LEU* 1.3 60.7 + - - +
80E PHE* 3.5 22.1 - - + -
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Residues in contact with LEU 79 (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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21E SER* 3.5 0.3 + - - -
22E CYS* 2.8 41.8 + - + +
29E PHE* 4.1 12.2 - - + -
34E MET* 3.9 29.2 - - + -
35E HIS 4.7 2.5 - - - +
36E TRP* 3.4 32.9 - - + +
51E ILE* 3.7 21.5 - - + -
70E ILE* 4.1 8.7 - - + -
71E SER 3.3 18.2 - - - +
72E ARG* 4.1 7.0 - - + +
78E THR* 1.3 73.7 - - - +
80E PHE* 1.3 67.1 + - - +
96E CYS* 4.0 19.1 - - - -
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Residues in contact with PHE 80 (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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19E LYS* 3.9 37.5 - - + -
20E LEU 3.3 6.1 - - - +
21E SER* 3.7 16.8 - - - -
36E TRP* 4.5 4.3 - - - -
70E ILE* 3.6 8.0 - - - +
71E SER* 2.8 52.4 + - - +
72E ARG 5.4 0.4 - - - -
73E ASP* 4.4 21.8 - - + -
76E LYS* 5.1 8.3 - - - -
78E THR* 3.5 29.8 - - + -
79E LEU* 1.3 83.5 - - - +
81E LEU* 1.3 61.8 + - - +
82E GLN* 4.9 0.9 - - + +
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Residues in contact with LEU 81 (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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18E ARG 3.8 0.9 - - - +
19E LYS* 3.4 2.4 - - - -
20E LEU* 2.9 42.7 + - + +
36E TRP* 3.8 42.1 - - + +
48E VAL* 4.5 4.5 - - + -
49E ALA* 4.6 7.0 - - + -
68E PHE* 4.3 20.9 - - + -
69E THR 3.3 17.5 - - - +
70E ILE* 3.7 22.4 - - + -
80E PHE* 1.3 72.8 - - - +
82E GLN* 1.3 62.4 + - - +
83E MET* 3.5 30.0 + - + +
94E TYR* 4.9 4.0 - - + -
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Residues in contact with GLN 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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17E SER* 4.0 9.1 - - - -
18E ARG* 3.8 14.0 + - - +
19E LYS* 3.3 34.9 - - + +
67E ARG 4.0 1.7 - - - +
68E PHE* 3.7 0.9 - - - -
69E THR* 2.9 46.2 + - + +
71E SER* 5.6 2.0 + - - +
80E PHE* 4.1 1.7 - - + +
81E LEU* 1.3 70.7 - - - +
83E MET* 1.3 83.9 + - - +
84E THR* 5.3 3.2 - - - +
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Residues in contact with MET 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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17E SER* 3.3 0.7 - - - -
18E ARG* 2.9 44.6 + - + +
20E LEU* 4.1 13.0 - - + -
67E ARG 4.0 3.6 - - - -
68E PHE* 3.5 44.4 - - + -
81E LEU* 4.0 15.7 - - + +
82E GLN* 1.3 84.9 + - - +
84E THR* 1.3 61.2 + - - +
86E LEU* 3.8 15.9 - - + -
94E TYR* 3.5 26.2 - - + -
117E LEU* 3.6 31.2 - - + -
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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