Contacts of the helix formed by residues 22 - 35 (chain P) in PDB entry 3UCZ
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 LYS 22 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20P LYS 3.8 2.1 + - - +
21P ILE* 1.3 81.0 - - - +
23P LYS* 1.3 65.8 + - - +
24P ASP* 3.3 17.0 - - + +
25P GLU* 4.1 12.8 - - + +
26P LEU* 3.1 23.1 + - - +
47P ARG* 3.4 17.9 - - - +
33R A 5.1 8.5 + - - -
34R A 5.6 6.7 - - - -
61R A 4.3 20.1 + - - +
62R A 3.4 28.0 + - - +
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Residues in contact with LYS 23 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22P LYS* 1.3 70.0 - - - +
24P ASP* 1.3 75.8 + - - +
26P LEU* 3.3 5.0 + - - +
27P LYS* 3.1 49.6 + - - +
45P VAL* 3.4 40.8 + - + +
46P SER* 4.9 4.3 - - - +
47P ARG* 3.3 25.7 - - - +
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Residues in contact with ASP 24 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22P LYS* 4.8 14.6 - - + +
23P LYS* 1.3 87.4 + - - +
25P GLU* 1.3 64.8 + - + +
27P LYS* 4.0 4.0 - - - +
28P LYS* 3.4 23.1 + - - +
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Residues in contact with GLU 25 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21P ILE* 4.1 16.8 - - + -
22P LYS* 3.7 11.6 + - + +
23P LYS 3.3 0.2 - - - -
24P ASP* 1.3 83.2 - - + +
26P LEU* 1.3 56.6 + - - +
28P LYS* 3.2 19.4 + - - +
29P SER* 2.8 41.4 + - - -
78P TYR* 4.4 10.1 + - - +
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Residues in contact with LEU 26 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17P LEU* 4.4 24.5 - - + -
18P ASN 5.1 6.3 - - - +
21P ILE* 3.9 27.0 - - + +
22P LYS 3.1 21.1 + - - +
23P LYS* 3.7 3.4 - - - +
25P GLU* 1.3 77.0 - - - +
27P LYS* 1.3 63.5 + - - +
29P SER* 3.7 3.6 - - - -
30P LEU* 3.0 46.1 + - + +
45P VAL* 3.5 28.9 - - + -
47P ARG* 5.8 4.9 - - + -
53P GLY* 6.2 2.0 - - - +
54P GLN 5.0 2.5 - - - +
77P PHE* 4.1 19.5 - - + -
78P TYR* 5.1 1.8 - - + -
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Residues in contact with LYS 27 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23P LYS* 3.1 43.9 + - - +
24P ASP* 4.0 4.5 - - - +
26P LEU* 1.3 77.9 - - - +
28P LYS* 1.3 53.9 + - - +
30P LEU* 3.3 8.6 + - - +
31P HIS* 2.8 36.8 + - - +
42P ASP* 4.2 11.0 + - - +
43P ILE* 3.1 40.7 + - + +
44P LEU* 5.1 2.0 - - - +
45P VAL* 4.1 21.7 - - + +
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Residues in contact with LYS 28 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24P ASP 3.4 13.5 + - - +
25P GLU* 3.2 26.1 + - - +
27P LYS* 1.3 78.8 - - - +
29P SER* 1.3 57.8 + - - +
31P HIS* 3.5 7.5 + - - +
32P ALA* 3.1 27.0 + - - +
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Residues in contact with SER 29 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25P GLU* 2.8 22.7 + - - -
26P LEU 3.7 1.3 - - - -
28P LYS* 1.3 70.3 - - - +
30P LEU* 1.3 60.3 + - - +
32P ALA* 3.0 9.1 + - - +
33P ILE* 2.9 34.9 + - - +
77P PHE* 3.6 22.4 - - - -
78P TYR* 2.7 28.7 + - - -
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Residues in contact with LEU 30 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14P ILE* 3.8 14.8 - - + -
17P LEU* 4.7 4.7 - - + -
26P LEU* 3.0 39.4 + - + +
27P LYS 3.7 3.4 - - - +
29P SER* 1.3 75.3 - - - +
31P HIS* 1.3 52.5 + - - +
33P ILE* 3.3 4.9 + - - -
34P PHE* 2.8 66.3 + - + +
43P ILE* 4.1 15.3 - - + -
45P VAL* 4.1 7.2 - - + -
55P ALA* 3.6 26.7 - - + -
57P VAL* 5.0 0.9 - - + -
77P PHE* 3.9 24.2 - - + -
82P MET* 4.4 5.6 - - - -
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Residues in contact with HIS 31 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27P LYS 2.8 19.1 + - - +
28P LYS* 3.5 8.9 + - - +
30P LEU* 1.3 76.1 - - - +
32P ALA* 1.3 63.7 + - - +
35P SER* 3.0 37.1 + - - -
40P ILE* 3.9 19.1 + - + +
43P ILE* 3.7 17.0 - - + +
99P MG 2.6 30.2 - - - -
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Residues in contact with ALA 32 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28P LYS 3.1 13.7 + - - +
29P SER* 3.0 12.6 + - - +
31P HIS* 1.3 77.6 + - - +
33P ILE* 1.3 64.9 + - + +
35P SER* 3.9 10.8 + - - -
36P ARG* 4.2 9.4 + - - +
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Residues in contact with ILE 33 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29P SER 2.9 18.6 + - - +
30P LEU* 3.6 6.1 - - - +
31P HIS 3.1 0.2 - - - -
32P ALA* 1.3 81.8 - - + +
34P PHE* 1.3 79.3 + - + +
35P SER 3.7 0.3 + - - -
36P ARG* 3.2 38.9 + - - +
37P PHE* 4.0 7.6 - - - -
72P MET* 3.6 24.9 - - - -
75P PHE* 4.4 19.7 - - + -
77P PHE* 3.8 23.6 - - + -
82P MET* 4.6 8.1 - - + -
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Residues in contact with PHE 34 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12P ILE* 3.6 18.6 - - + -
14P ILE* 3.7 25.4 - - + -
30P LEU* 2.8 45.2 + - + +
31P HIS 3.9 0.4 - - - -
33P ILE* 1.3 84.7 - - + +
35P SER* 1.3 59.7 + - - +
36P ARG 3.1 6.3 + - - -
37P PHE* 3.6 15.0 + + - -
38P GLY 4.1 0.3 - - - +
40P ILE* 3.9 11.6 - - + +
57P VAL* 4.3 12.3 - - + -
59P PHE* 3.5 27.8 - + + -
68P ALA* 3.7 29.8 - - + -
72P MET* 4.6 6.5 - - - -
82P MET* 3.6 25.4 - - + -
84P ILE* 3.9 14.6 - - + -
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Residues in contact with SER 35 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31P HIS* 3.0 27.3 + - - -
32P ALA* 3.9 10.6 + - - -
33P ILE 3.5 0.4 - - - -
34P PHE* 1.3 74.7 - - - +
36P ARG* 1.3 61.5 + - - +
37P PHE 3.0 7.4 + - - -
38P GLY* 3.6 19.2 + - - +
40P ILE* 4.1 8.5 - - - -
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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