Contacts of the strand formed by residues 38 - 43 (chain A) in PDB entry 4BGQ
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 ILE 38 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A LEU* 4.1 16.4 - - + -
29A LYS* 4.2 18.6 - - + +
30A CYS 3.3 12.1 - - - +
31A ARG* 4.4 14.1 - - + +
36A HIS 3.4 8.0 + - - +
37A GLU* 1.3 82.4 - - - +
39A VAL* 1.3 68.7 + - - +
76A LYS* 5.5 0.3 - - - -
90A GLU* 5.5 0.5 - - - -
91A TYR* 3.8 38.9 + - + +
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Residues in contact with VAL 39 (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 PHE* 3.6 34.3 - - + -
28A LEU 3.8 0.2 - - - +
29A LYS* 3.7 3.8 - - - -
30A CYS* 2.9 39.3 + - + +
37A GLU* 4.1 17.0 - - + +
38A ILE* 1.3 80.0 - - - +
40A ALA* 1.3 59.5 + - - +
41A ILE* 3.9 9.4 - - + -
76A LYS* 4.0 17.3 - - + -
88A VAL* 3.7 22.7 - - + -
89A PHE 3.5 12.6 - - - +
91A TYR* 3.7 10.2 - - - +
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Residues in contact with ALA 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A VAL* 5.3 0.4 - - + -
27A VAL* 4.0 9.2 - - + -
28A LEU 3.4 4.9 - - - +
39A VAL* 1.3 73.3 - - - +
41A ILE* 1.3 61.6 + - - +
87A LEU 3.6 1.9 - - - +
88A VAL* 3.7 0.2 - - - -
89A PHE* 2.8 39.3 + - - +
90A GLU 3.8 4.5 - - - +
91A TYR* 3.8 10.4 - - + +
1000A 38R 3.5 45.8 - - + +
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Residues in contact with ILE 41 (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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10A MET* 4.3 7.0 - - + -
13A PHE* 3.7 37.0 - - + -
26A VAL 3.7 0.2 - - - +
27A VAL* 3.4 3.7 - - - -
28A LEU* 2.7 45.7 + - + +
30A CYS* 3.7 28.9 - - + -
39A VAL* 3.9 11.2 - - + -
40A ALA* 1.3 76.0 - - - +
42A LYS* 1.3 63.9 + - - +
43A LYS 3.7 2.0 + - - +
79A PHE* 4.4 4.9 - - + -
86A TYR* 3.9 35.7 - - + -
87A LEU 3.3 9.0 - - - +
88A VAL* 4.2 13.2 - - + -
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Residues in contact with LYS 42 (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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24A TYR* 3.3 30.8 + - - +
26A VAL 3.5 10.1 - - - +
27A VAL* 4.4 10.8 - - + +
40A ALA 3.9 1.4 + - - -
41A ILE* 1.3 73.7 - - - +
43A LYS* 1.3 64.0 + - - +
44A PHE* 3.8 32.2 - - + -
60A GLU* 5.1 8.5 + - - -
85A LEU 3.8 1.2 - - - +
86A TYR* 3.4 5.9 - - - -
87A LEU* 2.8 41.9 + - + +
89A PHE* 4.3 17.3 - - + -
153A ASP* 5.6 1.8 + - - -
1000A 38R 3.5 38.0 + - + +
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Residues in contact with LYS 43 (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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10A MET* 5.2 0.9 - - - -
25A GLY* 4.2 2.3 - - - -
26A VAL* 2.9 53.8 + - + +
28A LEU* 4.1 27.4 - - + +
41A ILE 3.7 1.4 + - - +
42A LYS* 1.3 76.4 - - - +
44A PHE* 1.3 74.9 + - - +
45A LYS 4.1 0.5 + - - -
84A LYS* 5.7 4.3 - - + -
85A LEU 4.0 5.4 - - - +
86A TYR* 3.6 39.3 - - + +
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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