Contacts of the strand formed by residues 73 - 78 (chain L) in PDB entry 6D2P
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 73 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22L SER* 3.8 16.4 - - - -
23L CYS 3.5 2.2 - - - -
24L THR* 3.2 29.5 - - + +
69L LYS* 3.3 4.4 - - - +
70L SER* 2.7 41.3 + - - -
71L GLY 3.3 1.2 - - - -
72L ASN* 1.3 89.8 + - - +
74L ALA* 1.3 73.4 + - - +
75L SER* 3.9 8.4 + - - +
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Residues in contact with ALA 74 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23L CYS* 2.7 44.4 + - - +
35L LEU* 6.0 1.1 - - + -
36L VAL* 3.7 37.5 - - + +
38L TRP* 3.8 5.1 - - + +
54L GLY* 6.3 1.1 - - - -
68L SER 3.5 10.1 - - - +
69L LYS* 3.9 11.4 - - + -
72L ASN 4.2 0.4 + - - -
73L THR* 1.3 71.3 - - - +
75L SER* 1.3 65.4 + - - +
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Residues in contact with SER 75 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20L THR* 3.7 25.3 - - - +
21L ILE 3.3 5.4 + - - -
22L SER* 4.1 3.6 - - - -
38L TRP* 3.8 7.0 + - - -
66L SER 3.9 0.5 - - - +
67L GLY* 3.6 4.5 - - - -
68L SER* 2.9 49.3 + - - +
69L LYS* 5.7 0.4 - - - -
73L THR* 3.9 13.6 + - - +
74L ALA* 1.3 79.6 + - - +
76L LEU* 1.3 60.0 + - - +
77L THR* 4.1 1.9 + - - -
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Residues in contact with LEU 76 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19L ILE 3.8 0.9 - - - +
20L THR* 3.3 2.3 - - - -
21L ILE* 2.8 45.1 + - + +
38L TRP* 3.5 43.6 - - + +
50L MET* 5.2 2.7 - - + -
51L ILE* 3.9 25.1 - - + -
65L PHE* 4.4 18.8 - - + -
66L SER 3.7 9.9 - - - +
75L SER* 1.3 73.0 - - - +
77L THR* 1.3 64.6 + - - +
78L ILE* 4.7 9.6 - - + +
89L TYR* 3.7 36.3 - - + -
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Residues in contact with THR 77 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18L SER* 4.8 10.1 - - - -
19L ILE 3.4 7.2 - - - +
20L THR* 2.7 29.8 + - - +
64L ARG 2.9 5.1 - - - +
65L PHE* 3.5 1.3 - - - -
66L SER* 2.9 51.8 + - - +
68L SER* 5.2 3.5 + - - -
75L SER* 4.1 3.7 + - - -
76L LEU* 1.3 76.0 + - - +
78L ILE* 1.3 71.0 + - - +
79L SER* 4.7 2.9 - - - +
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Residues in contact with ILE 78 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17L GLN 3.9 1.9 - - - +
18L SER* 3.3 1.9 - - - -
19L ILE* 3.0 41.6 + - + +
21L ILE* 5.3 3.8 - - + -
64L ARG* 3.4 12.6 - - + -
65L PHE* 3.6 40.4 - - + -
76L LEU* 4.7 9.9 - - + +
77L THR* 1.3 75.2 - - - +
79L SER* 1.3 65.4 + - - +
80L GLY 4.8 0.4 - - - +
81L LEU* 4.2 9.5 + - + +
85L ASP* 3.7 22.2 - - + +
89L TYR* 3.8 16.2 - - + +
106L LEU* 3.8 29.2 - - + -
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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