Contacts of the helix formed by residues 21 - 32 (chain A) in PDB entry 5LPN
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 GLY 21 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A GLY 3.2 0.6 - - - -
20A VAL* 1.3 81.0 - - - +
22A LYS* 1.3 56.0 + - - +
24A CYS* 2.9 4.3 + - - +
25A VAL* 2.7 36.9 + - - +
88A VAL* 5.5 0.7 - - - -
122A ASN* 3.5 10.9 + - - -
202A GNP 3.0 38.2 + - - -
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Residues in contact with LYS 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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14A LEU* 3.8 17.6 - - + +
15A ILE* 3.5 30.7 - - - +
16A GLY* 2.8 25.4 + - - +
17A ASP 3.3 4.8 + - - -
20A VAL* 4.0 12.8 - - + -
21A GLY* 1.3 76.6 - - - +
23A THR* 1.3 64.1 + - - +
24A CYS 3.1 0.2 + - - -
25A VAL* 3.2 7.2 + - - +
26A LEU* 2.9 24.8 + - - +
64A ASP* 3.6 10.5 - - - +
65A THR* 3.6 32.8 - - - -
67A GLY* 3.7 2.0 - - - +
88A VAL* 4.0 13.7 - - + -
202A GNP 2.9 40.8 + - - +
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Residues in contact with THR 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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22A LYS* 1.3 75.7 - - - +
24A CYS* 1.3 59.1 + - - +
26A LEU* 3.6 3.9 + - - +
27A PHE* 2.9 33.4 + - + +
39A ILE 4.9 5.5 + - - +
41A THR* 3.0 3.3 + - - +
64A ASP* 2.7 21.3 + - - +
201A MG 1.9 35.0 - - - -
202A GNP 2.8 16.4 + - - +
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Residues in contact with CYS 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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21A GLY 2.9 8.1 + - - +
23A THR* 1.3 79.2 - - - +
25A VAL* 1.3 60.0 + - - +
27A PHE* 3.9 7.5 - - - +
28A ARG* 2.9 23.0 + - - +
33A ALA 4.7 1.2 - - - +
34A PHE* 4.4 8.0 - - + +
35A ASN* 3.7 27.6 - - - -
37A THR 5.4 3.6 - - - -
153A ALA* 3.3 17.7 - - + +
202A GNP 3.1 44.6 + - + +
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Residues in contact with VAL 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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14A LEU* 5.3 4.7 - - + -
21A GLY 2.7 21.5 + - - +
22A LYS* 3.6 9.4 - - - +
24A CYS* 1.3 73.6 - - - +
26A LEU* 1.3 62.8 + - - +
28A ARG* 3.5 2.8 - - - +
29A PHE* 2.9 21.7 + - - +
88A VAL* 5.1 8.3 - - + -
120A LEU* 4.6 13.9 - - + -
122A ASN* 3.7 31.4 - - + +
151A THR* 4.4 4.5 - - - +
153A ALA* 4.0 5.8 - - + -
159A ILE* 3.7 24.8 - - + +
163A PHE* 3.8 24.5 - - + -
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Residues in contact with LEU 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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14A LEU* 3.9 9.2 - - + -
22A LYS 2.9 16.1 + - - +
23A THR* 3.8 5.8 - - - +
25A VAL* 1.3 79.7 - - - +
27A PHE* 1.3 51.2 + - - +
29A PHE* 3.3 10.2 + - + -
30A SER* 2.4 40.9 + - - +
47A LYS* 3.6 35.7 - - + +
62A ILE* 3.8 54.3 - - + +
64A ASP* 4.1 22.0 - - + -
163A PHE* 4.6 3.4 - - + -
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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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23A THR* 2.9 24.5 + - + +
24A CYS* 3.9 9.9 - - - +
25A VAL 3.2 0.4 - - - -
26A LEU* 1.3 74.6 - - - +
28A ARG* 1.3 59.9 + - - +
30A SER* 3.3 7.2 - - - -
31A ASP* 2.9 51.6 + - + -
32A ASP 3.5 2.9 + - - -
33A ALA* 4.1 27.8 + - + +
34A PHE* 4.8 4.9 - - - -
35A ASN* 4.9 17.5 - - + -
47A LYS* 6.0 9.0 - - + -
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Residues in contact with ARG 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 CYS 2.9 18.5 + - - +
25A VAL 3.5 3.4 - - - +
27A PHE* 1.3 77.0 - - - +
29A PHE* 1.3 59.3 + - - +
32A ASP* 2.9 47.3 + - - +
33A ALA* 3.3 38.9 + - - +
34A PHE* 4.5 4.0 - - - +
153A ALA* 2.9 23.4 + - - +
154A LYS* 2.5 31.7 + - - +
155A ALA 4.0 0.2 - - - -
156A ASN* 3.1 42.8 - - - +
159A ILE* 3.5 28.7 - - + -
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Residues in contact with PHE 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 VAL 2.9 16.7 + - - +
26A LEU* 3.7 7.2 - - + +
27A PHE 3.2 0.2 - - - -
28A ARG* 1.3 78.6 - - - +
30A SER* 1.3 56.1 + - - +
32A ASP* 4.5 1.0 + - - +
49A LYS* 2.1 68.6 + - + -
51A VAL* 4.4 8.3 - - + -
60A LEU* 4.0 16.6 - - + -
62A ILE* 3.8 28.7 - - + -
159A ILE* 3.6 12.1 - - + -
160A GLU* 4.1 30.7 - - + -
163A PHE* 3.7 44.9 - + + -
164A LEU* 4.7 4.5 - - + -
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Residues in contact with SER 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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26A LEU* 2.4 34.5 + - - +
27A PHE* 3.3 15.1 + - - -
29A PHE* 1.3 79.0 - - - +
31A ASP* 1.3 72.0 + - - +
47A LYS* 4.8 19.2 - - - +
48A ILE 5.2 6.5 - - - -
49A LYS* 4.1 20.9 + - - +
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Residues in contact with ASP 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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27A PHE* 2.9 43.7 + - + +
30A SER* 1.3 94.2 - - - +
32A ASP* 1.3 72.5 + - - +
33A ALA* 3.3 8.1 + - + +
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Residues in contact with ASP 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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27A PHE 3.5 0.2 + - - -
28A ARG* 2.9 27.8 + - - +
29A PHE 4.5 0.8 + - - +
30A SER 3.7 1.0 - - - -
31A ASP* 1.3 78.7 - - - +
33A ALA* 1.3 58.8 + - - +
156A ASN* 2.9 29.8 + - - -
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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