Contacts of the strand formed by residues 32 - 37 (chain A) in PDB entry 40ER
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 32 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23A THR* 3.5 5.7 - - - +
24A LEU* 2.7 40.4 + - + -
25A GLY 2.9 29.1 + - - +
27A GLY* 5.4 0.2 - - - -
30A GLY 4.2 2.5 - - - +
31A LYS* 1.3 81.1 - - - +
33A LYS* 1.3 57.4 + - - +
45A ALA* 5.8 0.9 - - + -
46A VAL 3.1 18.8 - - - +
47A LYS* 3.6 24.0 - - + -
48A ILE* 4.1 0.7 - - - -
601A STU 3.8 39.5 - - + +
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Residues in contact with LYS 33 (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 VAL* 6.0 3.6 - - - -
20A LEU* 4.8 14.8 - - + -
21A GLY 3.4 24.0 - - - +
22A ASP 3.4 8.5 - - - +
23A THR* 3.0 27.4 + - - +
24A LEU* 3.9 5.9 - - - +
31A LYS* 3.3 29.5 - - - +
32A VAL* 1.3 79.0 - - - +
34A VAL* 1.3 68.1 + - - +
45A ALA* 3.6 4.2 - - - -
46A VAL* 3.0 40.9 + - + +
48A ILE* 4.0 11.9 - - + +
108B SEP 4.5 16.0 + - - -
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Residues in contact with VAL 34 (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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20A LEU* 3.5 3.1 - - - -
21A GLY* 2.6 35.8 + - - -
22A ASP* 3.0 34.0 + - + +
24A LEU* 3.5 35.0 - - + -
33A LYS* 1.3 73.9 - - - +
35A GLY* 1.3 61.8 + - - +
36A LYS* 6.2 0.9 - - + -
43A LYS* 4.5 17.9 - - - +
44A VAL 3.5 5.2 - - - +
46A VAL* 5.0 1.3 - - - -
97A TYR* 4.0 19.3 - - + +
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Residues in contact with GLY 35 (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 TYR* 4.0 11.0 - - - -
19A ILE 3.3 10.5 - - - -
20A LEU* 4.5 6.1 - - - -
33A LYS 4.0 0.4 + - - -
34A VAL* 1.3 74.8 - - - +
36A LYS* 1.3 60.4 - - - +
43A LYS* 3.5 13.2 - - - -
44A VAL* 2.6 42.3 + - - -
46A VAL* 4.9 3.6 - - - +
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Residues in contact with LYS 36 (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 TYR* 3.4 5.0 - - - -
19A ILE* 2.9 51.1 + - + +
34A VAL* 6.2 0.9 - - + -
35A GLY* 1.3 74.6 - - - +
37A HIS* 1.3 70.0 + - - +
38A GLU 3.3 1.4 + - - -
41A GLY* 4.2 18.6 - - - -
42A HIS 3.3 8.3 - - - +
43A LYS* 4.2 24.5 - - + +
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Residues in contact with HIS 37 (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 HIS* 3.3 30.0 - + + +
18A TYR* 3.1 36.8 - + + -
36A LYS* 1.3 74.1 - - - +
38A GLU* 1.3 65.4 + - - +
39A LEU* 3.1 46.9 + - + -
40A THR* 3.3 32.3 + - + +
41A GLY* 3.2 15.1 + - - -
42A HIS* 3.0 13.7 + - + +
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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