Contacts of the strand formed by residues 45 - 53 (chain A) 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 45 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A LEU* 5.7 0.4 - - + -
24A VAL* 3.9 31.4 - - + -
36A LEU* 4.2 14.8 - - + -
38A SER* 3.3 6.3 - - - +
39A TYR* 3.7 22.4 - - + -
43A MET* 3.2 23.3 - - - +
44A ASN* 1.3 78.4 - - - +
46A VAL* 1.3 66.6 + - - +
47A LEU* 4.3 2.0 - - + -
66A VAL* 3.4 7.6 - - - +
67A ILE* 2.8 45.5 + - + +
72A VAL* 4.3 6.3 - - + -
75A ILE* 3.7 33.0 - - + -
10G ALA* 5.7 0.7 - - - -
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Residues in contact with VAL 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A LEU* 3.8 1.6 - - - +
37A ARG* 2.9 40.9 + - + -
38A SER* 3.1 20.3 + - - +
45A LEU* 1.3 80.4 - - - +
47A LEU* 1.3 71.1 + - - +
64A THR* 4.1 11.7 - - + -
65A ILE 3.2 9.4 - - - +
66A VAL* 4.3 13.9 - - + -
9G THR* 4.6 1.8 - - + -
10G ALA* 3.6 37.0 - - + +
13G VAL* 4.0 19.5 - - + -
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Residues in contact with LEU 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A VAL* 3.6 25.6 - - + -
24A VAL* 4.0 12.8 - - + -
32A VAL* 3.8 28.9 - - + +
33A ARG 4.3 1.8 - - - -
34A GLY* 4.0 20.4 - - - +
35A MET 3.2 5.4 - - - +
36A LEU* 3.8 18.2 - - + +
45A LEU* 4.9 2.5 - - + -
46A VAL* 1.3 86.2 - - - +
48A SER* 1.3 59.5 + - - +
50A SER* 4.1 6.5 - - - -
63A GLY 3.6 1.5 - - - +
64A THR* 3.2 4.7 - - - +
65A ILE* 2.9 43.3 + - + +
67A ILE* 4.0 16.8 - - + +
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Residues in contact with SER 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A GLY* 3.6 0.7 - - - -
35A MET* 3.0 29.9 + - - +
37A ARG* 2.8 37.9 + - - +
47A LEU* 1.3 73.1 - - - +
49A ASP* 1.3 83.5 + - - +
50A SER 3.0 3.2 + - - -
63A GLY 3.8 2.7 - - - -
64A THR* 4.0 16.4 - - - -
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Residues in contact with ASP 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A LEU* 5.8 1.5 - - + +
33A ARG 4.1 2.9 - - - +
34A GLY* 4.2 3.6 - - - -
35A MET* 4.3 10.3 - - + +
37A ARG* 4.2 9.7 + - - -
48A SER* 1.3 87.9 + - - +
50A SER* 1.3 61.7 + - - +
51A GLU* 4.2 3.3 + - - +
61A LYS* 5.1 6.2 + - - -
63A GLY* 3.3 13.8 + - - -
64A THR* 4.8 0.4 + - - -
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Residues in contact with SER 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A VAL* 5.2 0.7 - - - -
33A ARG 3.0 15.7 - - - -
34A GLY* 4.2 0.2 - - - -
47A LEU* 4.1 23.1 - - - -
48A SER 3.9 0.9 - - - -
49A ASP* 1.3 78.6 - - - +
51A GLU* 1.3 64.4 + - - +
61A LYS* 3.8 5.2 - - - -
62A LEU* 2.8 37.1 + - - +
63A GLY 2.6 25.3 + - - -
65A ILE* 3.6 17.2 - - - +
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Residues in contact with GLU 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A VAL* 3.3 6.0 - - - -
33A ARG* 2.5 70.7 + - + +
49A ASP 5.1 2.2 - - - +
50A SER* 1.3 78.9 - - - +
52A GLU* 1.3 60.5 + - - +
53A ILE* 3.4 9.7 + - + +
58A SER 5.8 0.2 - - - -
59A GLY* 4.0 18.6 + - - +
60A LYS 3.1 15.3 - - - +
61A LYS* 2.8 29.2 + - - +
62A LEU* 4.1 3.4 - - - +
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Residues in contact with GLU 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A LYS* 5.4 10.1 - - + +
31A GLU 3.6 13.2 - - - +
32A VAL* 4.2 8.3 - - + -
51A GLU* 1.3 69.4 - - - +
53A ILE* 1.3 66.1 + - - +
54A GLN* 2.9 38.6 + - - +
59A GLY* 3.3 1.8 - - - -
60A LYS* 2.7 28.2 + - + +
62A LEU* 3.4 26.7 - - + +
25G LYS* 4.8 15.5 - - - -
31G GLU* 5.8 0.5 - - - +
74G LEU* 6.5 0.4 - - - -
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Residues in contact with ILE 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A LEU* 4.3 16.8 - - + -
31A GLU* 2.9 45.2 + - + +
33A ARG* 3.9 45.3 - - + +
51A GLU* 4.3 11.2 - - + +
52A GLU* 1.3 72.0 - - - +
54A GLN* 1.3 72.9 + - - +
57A GLY* 4.3 13.5 - - - +
58A SER 3.7 6.7 - - - +
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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