Contacts of the helix formed by residues 20 - 29 (chain A) in PDB entry 2LQB
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 20 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18A CYS 5.2 0.4 - - - -
19A GLN* 1.3 75.8 - - - +
21A CYS* 1.3 62.0 + - - +
22A VAL* 2.9 14.3 + - - +
23A SER* 3.4 17.7 + - - -
24A SER* 4.3 0.9 + - - -
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Residues in contact with CYS 21 (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 MET* 5.0 5.5 - - - -
19A GLN* 3.6 13.7 - - + +
20A SER* 1.3 74.3 - - - +
22A VAL* 1.3 66.2 + - - +
23A SER 3.1 0.4 - - - -
24A SER* 2.8 30.7 + - - -
25A ILE* 2.8 23.5 + - + +
68A MET 5.5 0.2 - - - -
70A PHE* 3.4 44.0 - - + -
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Residues in contact with VAL 22 (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 MET* 4.3 15.7 - - + -
19A GLN 5.8 0.4 - - - +
20A SER* 2.9 7.8 - - - +
21A CYS* 1.3 78.8 - - - +
23A SER* 1.3 63.4 + - - +
25A ILE* 3.3 11.5 + - - +
26A GLU* 3.1 26.1 + - + +
40A VAL* 3.5 48.9 - - + +
42A LEU* 4.6 24.2 - - + +
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Residues in contact with SER 23 (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 SER* 3.4 12.3 + - - -
21A CYS 3.1 0.6 - - - -
22A VAL* 1.3 79.9 - - - +
24A SER* 1.3 62.1 + - - +
26A GLU* 3.3 24.8 + - - +
27A GLY 3.6 4.3 + - - -
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Residues in contact with SER 24 (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 SER 4.3 0.6 + - - -
21A CYS* 2.8 29.2 + - - -
23A SER* 1.3 78.1 - - - +
25A ILE* 1.3 63.2 + - - -
27A GLY* 3.2 11.3 + - - -
28A LYS* 3.6 21.6 + - - +
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Residues in contact with ILE 25 (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 0.2 - - + -
16A MET* 4.5 21.1 - - + -
21A CYS* 2.8 40.1 + - + +
22A VAL* 3.7 9.6 - - - +
24A SER* 1.3 76.5 - - - +
26A GLU* 1.3 63.4 + - - +
28A LYS* 3.2 24.0 - - + +
29A VAL 3.9 1.7 + - - -
38A VAL* 4.8 14.0 - - + +
40A VAL* 4.5 17.5 - - + -
68A MET* 3.2 51.6 - - + -
70A PHE* 4.6 7.4 - - + -
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Residues in contact with GLU 26 (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* 3.1 17.3 + - + +
23A SER* 3.3 18.9 + - - +
24A SER 3.1 0.2 - - - -
25A ILE* 1.3 78.7 - - - +
27A GLY* 1.3 57.2 + - - +
29A VAL* 2.8 33.1 + - + +
38A VAL* 4.0 24.9 - - - +
39A LYS* 5.6 5.0 - - - +
40A VAL* 5.7 5.6 - - + +
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Residues in contact with GLY 27 (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 SER 3.6 4.5 + - - -
24A SER* 3.2 9.0 + - - -
26A GLU* 1.3 76.8 - - - +
28A LYS* 1.3 56.6 + - - +
29A VAL* 4.8 0.7 - - - -
30A ARG* 2.8 37.2 + - - +
31A LYS* 3.9 3.5 + - - +
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Residues in contact with LYS 28 (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 SER* 3.6 23.6 + - - +
25A ILE* 3.2 22.3 + - + +
26A GLU 3.2 0.2 - - - -
27A GLY* 1.3 75.7 - - - +
29A VAL* 1.3 51.9 + - - +
31A LYS* 2.7 35.2 + - + +
32A LEU* 3.2 18.4 + - + +
38A VAL* 6.4 0.2 - - + -
64A HIS* 5.0 13.7 - - + +
67A ASP* 4.9 10.8 + - + -
68A MET* 4.6 32.6 + - + +
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Residues in contact with VAL 29 (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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25A ILE 3.9 1.4 + - - -
26A GLU* 2.8 25.4 + - + +
27A GLY* 3.0 0.9 - - - +
28A LYS* 1.3 78.8 - - - +
30A ARG* 1.3 62.4 + - + +
32A LEU* 3.0 31.9 + - - +
35A VAL* 3.2 29.4 - - + +
36A VAL 4.0 5.4 - - - +
37A ARG* 3.5 38.4 - - + +
38A VAL* 3.8 19.2 - - + +
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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