Contacts of the strand formed by residues 21 - 26 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20I ASN* 1.3 75.5 - - - +
22I VAL* 1.3 72.2 + - - +
33I ARG* 3.1 37.7 - - + -
34I GLY* 3.3 15.9 - - - +
35I MET* 3.2 33.2 - - + -
49I ASP 5.9 0.9 - - - +
77I PRO* 3.8 1.7 - - - +
78I LEU* 3.0 43.6 + - + +
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Residues in contact with VAL 22 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17I SER* 3.8 28.9 - - - +
20I ASN 3.8 7.0 - - - +
21I LEU* 1.3 81.2 - - - +
23I LEU* 1.3 59.0 + - - +
24I VAL* 4.1 12.7 - - + +
32I VAL 4.1 0.3 - - - +
33I ARG* 3.3 5.9 - - - +
34I GLY 2.9 39.3 + - - +
36I LEU* 4.0 13.0 - - + -
47I LEU* 3.7 24.9 - - + -
75I ILE* 4.2 14.1 - - + -
76I SER 3.3 9.0 - - - +
77I PRO* 4.2 6.7 - - + -
78I LEU* 4.1 5.8 - - - -
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Residues in contact with LEU 23 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22I VAL* 1.3 74.4 - - - +
24I VAL* 1.3 63.9 + - - +
25I LYS* 3.8 39.9 - - + +
31I GLU* 4.2 15.9 - - + +
32I VAL 3.4 20.6 - - - +
33I ARG* 4.1 12.1 - - + +
53I ILE* 4.2 15.5 - - + -
74I LEU* 4.0 2.3 - - + +
75I ILE* 3.5 2.3 - - - -
76I SER* 2.8 38.1 + - - +
78I LEU* 3.9 23.3 - - + +
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Residues in contact with VAL 24 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22I VAL* 4.1 12.8 - - + -
23I LEU* 1.3 81.2 - - - +
25I LYS* 1.3 64.0 + - - +
26I LEU* 3.8 23.1 + - + +
31I GLU* 3.3 3.8 - - - -
32I VAL* 2.8 46.2 + - + +
45I LEU* 3.9 26.2 - - + -
47I LEU* 4.0 20.6 - - + -
67I ILE* 4.6 1.3 - - + -
72I VAL* 4.1 13.7 - - + -
74I LEU 3.5 10.5 - - - +
75I ILE* 4.4 6.3 - - + -
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Residues in contact with LYS 25 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23I LEU* 3.8 14.4 - - + +
24I VAL* 1.3 72.7 - - - +
26I LEU* 1.3 61.9 + - - +
30I LYS 3.7 4.5 - - - +
31I GLU* 3.2 31.6 + - + +
72I VAL* 3.8 3.1 - - - -
73I ILE* 2.8 33.6 + - + -
74I LEU* 3.0 45.5 + - + +
76I SER* 5.7 1.4 - - - -
29J ASN* 3.0 30.7 - - - +
52J GLU* 4.0 15.5 - - - -
62J LEU* 3.9 21.0 - - - +
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Residues in contact with LEU 26 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73H ILE* 4.5 18.4 - - + -
74H LEU* 4.9 8.7 - - + -
24I VAL* 3.9 25.4 - - + +
25I LYS* 1.3 75.3 - - - +
27I LYS* 1.3 71.8 + - - +
29I ASN* 3.7 3.1 + - - -
30I LYS* 2.8 35.5 + - + +
32I VAL* 4.2 25.8 - - + -
67I ILE* 3.8 28.7 - - + -
71I ASN* 3.2 22.4 - - + +
72I VAL* 4.3 1.1 - - + -
73I ILE* 3.4 13.6 - - - +
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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