Contacts of the strand formed by residues 68 - 74 (chain A) in PDB entry 5THH
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 GLU 68 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35A GLU* 4.7 14.7 - - + +
36A LEU 2.9 13.6 + - - +
37A LYS* 3.2 42.2 + - + +
38A ILE* 2.9 26.3 + - - +
66A GLY 3.7 0.2 + - - -
67A CYS* 1.3 69.9 - - - +
69A VAL* 1.3 59.9 + - - +
70A THR* 4.1 1.5 + - - -
114A LYS* 3.9 25.4 - - + +
116A LYS* 6.0 0.5 + - - -
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Residues in contact with VAL 69 (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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38A ILE* 3.3 13.5 - - + +
39A TYR* 5.1 1.3 - - - -
40A TRP* 5.4 1.1 - - + +
59A ILE* 4.3 21.8 - - + +
62A PHE* 3.7 28.9 - - + -
63A LEU* 3.5 24.0 - - + -
67A CYS* 3.6 8.9 + - + +
68A GLU* 1.3 77.4 - - - +
70A THR* 1.3 71.1 + - - +
71A ILE* 4.8 1.1 - - + -
114A LYS 3.1 11.5 + - - +
115A LEU* 3.4 22.4 - - + +
116A LYS* 2.9 24.8 + - - +
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Residues in contact with THR 70 (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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38A ILE 3.0 7.7 + - - -
39A TYR* 3.2 18.5 - - + +
40A TRP 3.1 23.9 + - - -
68A GLU 5.2 1.0 + - - -
69A VAL* 1.3 77.3 + - - +
71A ILE* 1.3 68.1 + - - +
72A LEU 4.4 0.9 - - - +
116A LYS* 3.3 33.9 + - + +
118A ILE* 3.6 29.6 - - + -
177A LEU* 4.4 16.1 + - + -
179A VAL* 4.8 7.8 - - - +
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Residues in contact with ILE 71 (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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40A TRP* 3.5 25.8 - - + +
56A MET* 4.7 0.4 - - - -
59A ILE* 3.9 30.1 - - + -
69A VAL* 4.3 1.5 - - + -
70A THR* 1.3 78.4 - - - +
72A LEU* 1.3 63.2 + - - +
73A PHE* 3.7 28.8 + - + -
101A ILE* 4.0 20.6 - - + -
105A LEU* 4.2 9.4 - - + -
115A LEU* 4.1 17.0 - - + -
116A LYS 2.8 9.5 + - - -
117A PHE* 3.6 21.5 - - + -
118A ILE* 2.9 26.9 + - - +
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Residues in contact with LEU 72 (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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39A TYR* 4.1 15.2 - - + -
40A TRP 3.0 7.7 + - - +
41A GLY* 3.4 8.4 - - - -
42A THR* 3.0 31.7 + - - +
70A THR* 4.0 1.6 + - - +
71A ILE* 1.3 72.2 - - - +
73A PHE* 1.3 60.1 + - - +
74A ALA* 3.5 11.5 + - + +
118A ILE* 3.5 20.6 - - + +
120A GLY* 3.6 28.5 - - - +
123A TYR* 3.6 21.5 - - + +
124A GLN* 4.5 1.8 - - - +
173A ASP* 3.6 12.6 - - - +
177A LEU* 4.3 5.4 - - + -
401A TYR* 3.4 37.7 - - + +
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Residues in contact with PHE 73 (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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42A THR* 3.8 13.5 - - + -
44A THR* 3.9 12.6 - - + -
71A ILE* 3.7 22.0 - - + -
72A LEU* 1.3 70.2 - - - +
74A ALA* 1.3 60.1 + - - +
75A ASP* 3.0 6.7 + - - +
94A VAL* 4.6 6.5 - - + -
97A TYR* 3.8 30.5 - - + -
98A GLU* 3.4 41.3 - - + -
101A ILE* 3.6 27.8 - - + -
117A PHE* 3.6 30.5 - + + -
118A ILE 2.8 20.4 + - - +
119A LYS* 3.2 10.8 - - + +
120A GLY 2.8 24.5 + - - -
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Residues in contact with ALA 74 (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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42A THR 2.9 17.4 + - - +
43A ALA* 3.5 10.6 - - - -
44A THR* 3.6 3.1 + - - +
72A LEU* 3.5 13.0 + - + +
73A PHE* 1.3 68.1 - - - +
75A ASP* 1.3 60.1 + - - +
76A LEU 3.5 2.5 - - - -
77A HIS* 3.6 17.5 - - + +
78A ALA 3.1 19.1 + - - -
120A GLY* 4.4 4.3 - - - +
124A GLN* 5.4 0.4 - - - -
401A TYR* 3.6 33.7 - - + -
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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