Contacts of the strand formed by residues 21 - 26 (chain F) in PDB entry 1TH7
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 21 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20F ASN* 1.3 76.5 - - - +
22F VAL* 1.3 59.2 + - - +
34F GLY* 3.6 15.9 - - - +
35F MET* 3.3 30.5 - - + -
49F ASP* 5.9 1.1 - - + +
77F PRO* 3.6 1.9 - - - +
78F LEU* 2.7 55.2 + - + +
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Residues in contact with VAL 22 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17F SER* 3.9 26.7 - - - -
20F ASN 3.9 7.9 - - - +
21F LEU* 1.3 81.6 - - - +
23F LEU* 1.3 62.3 + - - +
24F VAL* 4.2 11.7 - - + -
33F ARG* 3.4 5.0 - - - +
34F GLY 2.9 40.6 + - - +
36F LEU* 4.1 11.7 - - + -
47F LEU* 3.9 23.3 - - + -
75F ILE* 4.3 12.1 - - + -
76F SER 3.3 10.1 - - - +
77F PRO* 4.1 8.3 - - + -
78F LEU* 3.8 7.6 - - - +
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Residues in contact with LEU 23 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22F VAL* 1.3 74.4 - - - +
24F VAL* 1.3 66.8 + - - +
25F LYS* 4.0 33.0 - - + +
31F GLU* 3.9 13.5 - - - +
32F VAL 3.5 5.6 - - - -
33F ARG* 3.9 13.9 - - + +
74F LEU* 4.2 3.6 - - + -
75F ILE* 3.5 1.2 - - - +
76F SER* 2.9 50.4 + - - +
78F LEU* 3.3 34.7 - - + +
62G LEU* 4.8 13.9 - - + +
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Residues in contact with VAL 24 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22F VAL* 4.2 11.0 - - + -
23F LEU* 1.3 81.6 - - - +
25F LYS* 1.3 64.6 + - - +
26F LEU* 3.7 22.9 + - + +
31F GLU* 3.4 5.5 - - - +
32F VAL* 2.8 42.1 + - + +
45F LEU* 3.9 27.6 - - + -
47F LEU* 4.1 20.2 - - + -
67F ILE* 4.8 1.3 - - + -
72F VAL* 4.0 14.6 - - + -
74F LEU 3.5 9.6 - - - +
75F ILE* 4.3 6.5 - - + -
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Residues in contact with LYS 25 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23F LEU* 4.0 16.9 - - + +
24F VAL* 1.3 72.3 - - - +
26F LEU* 1.3 59.6 + - - +
30F LYS 3.7 5.2 - - - +
31F GLU* 2.8 31.7 + - + +
72F VAL* 3.7 1.4 - - - -
73F ILE* 2.8 40.0 + - + -
74F LEU* 2.9 43.8 + - + +
30G LYS* 4.7 15.9 - - - +
52G GLU* 4.0 20.8 + - - -
60G LYS* 6.0 3.0 - - - +
62G LEU* 4.4 17.2 - - - +
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Residues in contact with LEU 26 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73E ILE* 4.3 20.9 - - + -
74E LEU* 4.9 6.1 - - + -
24F VAL* 3.7 32.8 - - + +
25F LYS* 1.3 75.6 - - - +
27F LYS* 1.3 71.0 + - - +
29F ASN* 3.5 4.9 + - - -
30F LYS* 2.8 36.3 + - + +
31F GLU 4.8 0.4 - - - +
32F VAL* 4.2 27.1 - - + -
67F ILE* 4.1 20.9 - - + -
71F ASN* 3.2 22.4 - - + +
72F VAL* 4.2 1.1 - - - -
73F ILE* 3.6 9.9 - - - +
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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