Contacts of the strand formed by residues 50 - 55 (chain A) in PDB entry 4AG1
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 SER 50 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A GLU 4.0 0.2 - - - +
20A ILE* 3.5 0.5 - - - +
21A VAL* 2.8 51.2 + - - +
48A GLY 3.4 0.4 - - - -
49A ARG* 1.3 83.7 - - - +
51A ILE* 1.3 69.9 + - - +
71A GLU* 6.1 0.9 - - - -
72A VAL 5.9 2.7 - - - -
75A GLN* 4.3 4.9 - - - +
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Residues in contact with ILE 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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18A LEU* 4.1 22.0 - - + -
19A GLU 3.4 9.2 - - - +
20A ILE* 3.8 16.4 - - + -
46A CYS 4.1 16.2 - - - +
48A GLY 4.4 0.7 - - - +
50A SER* 1.3 84.7 - - - +
52A THR* 1.3 72.5 + - - +
53A VAL* 4.4 0.4 - - + -
71A GLU* 3.7 5.9 - - - +
72A VAL* 3.0 48.9 + - + +
75A GLN* 3.6 32.3 - - - +
91A MET* 4.4 4.0 - - + -
93A LEU* 3.8 22.0 - - + -
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Residues in contact with THR 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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17A TYR 3.7 1.0 - - - +
18A LEU* 3.5 2.8 - - - -
19A GLU* 2.9 44.3 + - - +
21A VAL* 6.1 1.4 - - - +
51A ILE* 1.3 73.5 - - - +
53A VAL* 1.3 64.8 + - - +
54A THR* 4.9 1.0 + - - +
69A LYS* 3.5 41.3 - - + -
70A LEU 3.6 10.3 - - - +
71A GLU* 2.6 30.7 + - - +
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Residues in contact with VAL 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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16A ALA* 3.8 25.4 - - + -
17A TYR 3.4 3.4 - - - +
18A LEU* 4.1 19.5 - - + -
40A VAL* 4.2 8.7 - - + -
51A ILE* 4.4 0.4 - - + -
52A THR* 1.3 77.1 - - - +
54A THR* 1.3 64.3 + - - +
55A LEU* 3.8 21.3 - - + -
68A GLN 3.6 1.2 - - - +
69A LYS* 3.3 2.9 - - - +
70A LEU* 2.8 43.5 + - + +
72A VAL* 3.8 24.2 - - + -
93A LEU* 4.4 5.4 - - + -
95A LEU* 3.9 14.8 - - + -
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Residues in contact with THR 54 (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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15A MET 4.1 1.2 - - - +
16A ALA* 3.6 2.3 - - - -
17A TYR* 2.8 44.4 + - - +
52A THR* 4.9 1.0 + - - +
53A VAL* 1.3 72.6 - - - +
55A LEU* 1.3 69.5 + - - +
57A ALA* 4.0 16.4 - - + +
60A ILE* 4.0 16.1 - - + +
67A TRP* 3.7 35.0 - - + -
68A GLN 3.6 4.3 - - - +
69A LYS* 3.6 26.3 - - + +
128A TRP* 5.2 0.5 - - - -
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Residues in contact with LEU 55 (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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13A PRO 5.5 1.8 - - - +
14A TYR 4.8 1.1 - - - +
15A MET 4.0 9.2 - - - +
16A ALA* 3.7 28.3 - - + -
34A LEU* 4.1 29.8 - - + -
40A VAL* 4.7 0.2 - - + -
53A VAL* 3.8 10.3 - - + -
54A THR* 1.3 76.4 - - - +
56A GLY* 1.3 64.5 + - - +
57A ALA 3.3 2.8 + - - -
67A TRP* 3.3 3.6 - - - -
68A GLN* 2.9 37.5 + - + +
70A LEU* 4.2 15.7 - - + -
95A LEU* 4.5 4.0 - - + -
99A ALA* 3.6 31.0 - - + -
105A VAL* 4.0 19.3 - - + -
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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