Contacts of the helix formed by residues 23 - 36 (chain A) in PDB entry 3PLV
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 23 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A GLU 3.6 3.0 + - - -
22A ASP* 1.3 76.3 - - - +
24A VAL* 1.3 55.0 + - - +
25A GLY* 3.5 2.4 + - - -
26A ASP* 2.9 35.4 + - - +
27A PHE* 2.8 33.4 + - - +
53A ASP 3.4 14.1 - - - -
54A HIS* 4.1 11.0 - - - -
55A ILE 3.5 7.6 - - - -
56A SER* 4.0 3.4 - - - +
57A LEU* 4.8 0.2 - - - -
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Residues in contact with VAL 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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22A ASP 3.8 0.6 + - - -
23A SER* 1.3 71.6 - - - +
25A GLY* 1.3 56.4 + - - +
27A PHE* 3.3 7.5 + - - +
28A LYS* 2.8 53.3 + - + +
44A LEU* 4.7 5.4 - - + -
51A LEU* 3.8 40.8 - - + +
52A LYS 3.4 20.0 - - - +
53A ASP* 3.4 5.8 + - - +
55A ILE 2.9 21.2 + - - +
56A SER 4.8 0.2 - - - -
57A LEU* 4.1 11.4 - - + +
60A TYR* 3.9 12.8 - - + -
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Residues in contact with GLY 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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23A SER* 3.1 2.4 - - - -
24A VAL* 1.3 76.3 - - - +
26A ASP* 1.3 63.4 + - - +
28A LYS* 3.3 6.9 + - - +
29A LYS* 3.2 27.3 + - - +
39A PRO* 5.3 1.0 - - - +
53A ASP* 2.9 36.0 + - - -
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Residues in contact with ASP 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 ASP* 4.7 10.0 - - + +
23A SER* 2.9 29.4 + - - +
25A GLY* 1.3 72.9 - - - +
27A PHE* 1.3 66.3 + - - +
29A LYS* 3.4 35.1 + - - +
30A VAL* 3.5 17.0 + - - +
52C LEU* 3.5 34.0 - - + +
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Residues in contact with PHE 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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4A VAL* 3.8 17.7 - - + -
6A VAL* 3.7 28.7 - - + -
16A VAL* 3.6 31.6 - - + -
18A CYS* 3.8 22.7 - - + -
22A ASP* 4.7 5.2 - - + +
23A SER 2.8 13.3 + - - +
24A VAL* 3.3 12.3 + - - +
26A ASP* 1.3 76.8 - - - +
28A LYS* 1.3 56.7 + - - +
30A VAL* 3.2 5.9 + - + +
31A LEU* 2.9 33.1 + - + +
44A LEU* 3.7 31.9 - - + -
57A LEU* 3.7 28.9 - - + -
68A LEU* 4.0 8.5 - - + -
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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 VAL* 2.8 30.5 + - - +
25A GLY* 3.6 6.3 - - - +
27A PHE* 1.3 73.7 - - - +
29A LYS* 1.3 53.9 + - - +
31A LEU* 3.7 7.1 - - - +
32A SER* 2.7 38.8 + - - -
39A PRO* 4.2 28.8 + - + +
42A ILE* 3.6 29.9 + - + +
43A VAL* 4.5 4.6 - - - +
44A LEU* 3.9 32.7 - - + +
50A VAL* 6.2 0.6 - - - +
51A LEU 4.3 10.3 + - - -
53A ASP* 2.8 34.1 + - - +
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Residues in contact with LYS 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 GLY 3.2 12.7 + - - +
26A ASP* 3.5 31.4 + - - +
27A PHE 3.2 0.4 - - - -
28A LYS* 1.3 78.2 - - - +
30A VAL* 1.3 61.2 + - - +
32A SER* 3.5 2.9 + - - -
33A LEU* 3.4 25.1 + - - +
39A PRO* 4.0 19.7 - - + -
50C LEU* 3.9 36.9 + - + +
52C LEU* 5.4 3.0 - - + +
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Residues in contact with VAL 30 (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 VAL* 3.9 12.3 - - + -
17A LYS 4.8 1.6 - - - +
18A CYS* 6.4 1.1 - - + -
26A ASP 3.5 10.0 + - - +
27A PHE* 3.2 8.3 + - + +
29A LYS* 1.3 73.9 - - - +
31A LEU* 1.3 67.7 + - - +
33A LEU* 3.2 8.3 + - - +
34A GLN* 3.1 38.1 + - - +
43C THR* 4.5 16.8 - - + -
46C LEU* 4.5 13.2 - - + -
47C ARG* 4.3 17.9 - - + +
50C LEU* 3.8 21.5 - - + -
52C LEU* 4.0 13.9 - - + -
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Residues in contact with LEU 31 (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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6A VAL* 4.0 22.0 - - + -
14A VAL* 4.5 2.5 - - + -
16A VAL* 3.7 30.8 - - + +
27A PHE* 2.9 23.1 + - + +
28A LYS* 3.7 4.7 - - - +
30A VAL* 1.3 77.2 - - - +
32A SER* 1.3 57.4 + - - +
34A GLN* 3.0 5.5 + - - +
35A ILE* 3.0 52.3 + - + +
42A ILE* 3.9 23.6 - - + -
44A LEU* 4.1 30.7 - - + -
70A LEU* 4.1 4.7 - - + -
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Residues in contact with SER 32 (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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28A LYS 2.7 24.2 + - - -
29A LYS 3.7 4.9 - - - -
30A VAL 3.2 0.2 - - - -
31A LEU* 1.3 75.1 - - - +
33A LEU* 1.3 59.1 + - - +
36A GLY* 2.9 26.3 + - - -
37A THR* 3.0 44.9 + - - +
38A GLN 3.5 2.6 - - - -
39A PRO* 3.2 29.3 - - - +
42A ILE* 3.9 5.0 - - - +
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Residues in contact with LEU 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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29A LYS 3.4 16.1 + - - +
30A VAL* 3.2 9.2 + - - +
32A SER* 1.3 78.5 - - - +
34A GLN* 1.3 61.2 - - - +
35A ILE 3.6 0.2 + - - -
36A GLY* 4.2 4.3 + - - -
46C LEU* 4.2 32.1 - - + +
50C LEU* 3.8 32.3 - - + -
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Residues in contact with GLN 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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14A VAL* 3.8 8.2 - - + +
15A ARG 2.9 24.8 + - - -
16A VAL* 3.6 29.5 - - - +
17A LYS 4.6 2.3 + - - -
30A VAL* 3.1 18.6 + - - +
31A LEU* 3.0 11.0 + - - +
33A LEU* 1.3 78.8 - - - +
35A ILE* 1.3 65.0 + - + +
36A GLY 3.7 0.2 - - - -
37C SER* 3.1 27.0 + - - +
38C LEU* 3.7 37.0 - - + +
43C THR* 4.7 2.8 + - - -
46C LEU* 4.5 3.6 - - + -
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Residues in contact with ILE 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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14A VAL* 3.9 29.4 - - + -
31A LEU* 3.0 44.2 + - + +
32A SER* 4.2 0.2 - - - -
34A GLN* 1.3 80.9 - - - +
36A GLY* 1.3 62.2 + - - +
37A THR* 3.6 25.7 - - + -
70A LEU* 3.7 31.9 - - + -
72A TYR* 3.8 15.6 + - + +
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Residues in contact with GLY 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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32A SER 2.9 10.4 + - - -
33A LEU 4.2 3.4 + - - -
34A GLN 3.7 1.6 - - - -
35A ILE* 1.3 79.1 - - - +
37A THR* 1.3 58.0 + - - -
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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