Contacts of the strand formed by residues 72 - 77 (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 VAL 72 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24I VAL* 4.1 13.0 - - + -
25I LYS 3.9 3.1 - - - -
26I LEU* 4.3 0.9 - - + -
43I MET* 3.7 32.1 - - + +
45I LEU* 4.3 3.8 - - + -
67I ILE* 4.0 21.5 - - + -
69I GLY* 3.0 15.5 + - - +
71I ASN* 1.3 77.8 - - - +
73I ILE* 1.3 64.1 + - - +
74I LEU* 3.8 13.9 - - - +
75I ILE* 3.9 27.8 - - + -
68J ARG* 2.7 31.2 + - - +
71J ASN* 3.0 7.0 + - - -
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Residues in contact with ILE 73 (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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25I LYS* 2.8 17.8 + - + +
26I LEU* 3.4 29.2 - - - +
27I LYS* 3.9 13.0 - - + +
72I VAL* 1.3 78.1 - - - +
74I LEU* 1.3 65.9 + - + +
26J LEU* 4.2 25.4 - - + -
27J LYS 4.2 4.5 - - - +
28J GLY* 3.4 28.0 - - - +
29J ASN* 4.2 15.7 - - + +
67J ILE* 3.7 3.8 - - - +
68J ARG 3.0 23.7 + - - -
71J ASN* 3.4 28.2 + - + +
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Residues in contact with LEU 74 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23I LEU* 4.8 1.8 - - + +
24I VAL* 3.5 5.4 - - - +
25I LYS* 3.0 73.5 + - + +
72I VAL* 3.8 2.4 - - - -
73I ILE* 1.3 87.2 - - + +
75I ILE* 1.3 75.5 + - - +
76I SER* 4.5 4.7 - - - +
26J LEU* 4.6 11.4 - - + -
29J ASN* 4.2 10.1 - - - +
32J VAL* 5.0 1.3 - - + -
62J LEU* 4.5 11.0 - - + -
65J ILE* 4.3 25.1 - - + -
66J VAL 3.1 15.9 - - - +
67J ILE* 4.3 5.8 - - + -
68J ARG 4.8 0.2 - - - +
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Residues in contact with ILE 75 (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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14I LEU* 4.0 26.2 - - + -
17I SER* 5.8 0.4 - - - +
22I VAL* 4.2 24.7 - - + -
23I LEU 3.5 4.9 - - - +
24I VAL* 4.4 7.6 - - + -
36I LEU* 5.5 4.0 - - + -
43I MET* 4.2 23.3 - - + -
45I LEU* 3.8 35.4 - - + -
72I VAL* 3.9 12.8 - - + -
74I LEU* 1.3 80.8 - - - +
76I SER* 1.3 64.8 + - - +
77I PRO* 4.1 3.6 - - + +
65J ILE* 3.4 2.8 - - - -
66J VAL* 2.9 42.5 + - + +
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Residues in contact with SER 76 (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* 4.3 3.4 - - - -
23I LEU* 2.8 48.9 + - - -
25I LYS* 5.7 1.3 - - - -
74I LEU* 4.5 6.3 - - - -
75I ILE* 1.3 76.4 - - - +
77I PRO* 1.3 70.1 + - - +
78I LEU* 3.4 7.1 + - - +
62J LEU* 3.0 20.5 + - - -
64J THR 2.9 16.8 + - - -
65J ILE* 3.8 11.4 - - - -
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Residues in contact with PRO 77 (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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13I VAL* 3.8 21.1 - - + +
17I SER* 3.0 29.2 - - - +
20I ASN* 6.6 0.2 - - + -
21I LEU 3.8 7.9 - - - +
22I VAL* 4.2 4.9 - - + -
75I ILE* 4.1 5.8 - - + +
76I SER* 1.3 90.9 + - - +
78I LEU* 1.3 63.9 + - - +
62J LEU 5.1 1.4 - - - +
64J THR* 3.3 27.8 + - + +
66J VAL* 5.7 0.2 - - + -
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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