Contacts of the helix formed by residues 20 - 31 (chain B) in PDB entry 5D4P
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 HIS 20 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16B LEU* 4.4 3.4 - - + +
17B GLU* 3.1 41.4 + - + +
18B GLY 3.1 1.2 - - - -
19B ALA* 1.3 88.8 - - + +
21B LYS* 1.3 64.3 + - - +
22B GLU 3.3 2.9 - - - -
23B PHE* 3.2 12.8 + - + +
24B ALA* 3.2 20.8 + - - +
85B PHE* 3.6 36.3 - + + -
89B HIS* 3.6 34.3 - + - +
90B SER 5.8 0.2 + - - -
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Residues in contact with LYS 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B LEU* 4.7 0.7 - - - -
17B GLU 4.0 0.4 + - - -
18B GLY* 3.1 17.5 + - - +
19B ALA 3.4 1.4 + - - -
20B HIS* 1.3 77.1 - - - +
22B GLU* 1.3 58.9 + - - +
24B ALA* 3.1 7.2 + - - +
25B THR* 2.9 35.8 + - + +
38B ILE* 3.4 34.8 - - + +
64B ILE* 3.7 30.6 - - + +
66B ILE* 4.9 0.4 - - + -
43C SER* 5.1 8.9 + - - -
52C GLU* 5.2 6.9 + - - -
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Residues in contact with GLU 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B ALA 5.0 1.5 + - - +
20B HIS 3.3 0.8 - - - -
21B LYS* 1.3 78.2 - - - +
23B PHE* 1.3 63.9 + - - +
25B THR* 3.3 8.5 + - - +
26B ASP* 2.9 48.8 + - - +
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Residues in contact with PHE 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B HIS* 3.2 18.3 + - + +
22B GLU* 1.3 79.4 - - - +
24B ALA* 1.3 65.9 + - + +
26B ASP* 3.7 6.3 - - + +
27B LEU* 3.1 41.1 + - + +
30B ARG* 6.1 3.8 - - - -
81B GLY 4.3 12.1 - - - -
82B PHE* 4.4 6.1 - + - -
85B PHE* 3.6 49.8 - + + -
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Residues in contact with ALA 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B LEU* 3.8 22.4 - - + -
20B HIS 3.2 2.9 + - - +
21B LYS 3.1 9.0 + - - +
23B PHE* 1.3 83.5 - - + +
25B THR* 1.3 56.7 + - - +
27B LEU* 3.2 4.4 + - - +
28B LEU* 3.0 32.1 + - - +
66B ILE* 3.6 24.5 - - + -
82B PHE* 3.9 21.3 - - + -
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Residues in contact with THR 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B LYS* 2.9 39.5 + - + +
22B GLU* 3.3 12.6 + - - +
24B ALA* 1.3 70.7 - - - +
26B ASP* 1.3 64.3 + - - +
28B LEU* 3.4 8.0 + - + +
29B ASP* 2.9 38.9 + - - +
36B TYR* 3.4 44.5 + - + +
38B ILE* 4.2 5.6 - - + -
66B ILE* 4.5 7.6 - - + -
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Residues in contact with ASP 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B GLU* 2.9 40.7 + - - +
23B PHE* 3.7 6.3 - - - +
25B THR* 1.3 80.3 + - - +
27B LEU* 1.3 55.6 + - - +
29B ASP* 3.3 9.4 + - - +
30B ARG* 2.8 41.2 + - - +
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Residues in contact with LEU 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B PHE* 3.1 26.3 + - + +
24B ALA 3.5 9.0 - - - +
26B ASP* 1.3 76.2 - - - +
28B LEU* 1.3 61.8 + - - +
30B ARG* 3.2 35.7 + - + +
31B ALA* 3.0 29.2 + - + +
77B PRO 5.7 1.3 - - - +
78B LEU* 4.3 9.0 - - + +
81B GLY* 3.5 41.3 - - - +
82B PHE* 3.6 35.2 - - + +
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Residues in contact with LEU 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B LEU* 5.0 0.4 - - + -
14B ILE* 4.3 16.6 - - + -
24B ALA 3.0 20.7 + - - +
25B THR* 3.7 11.0 - - - +
27B LEU* 1.3 77.5 - - - +
29B ASP* 1.3 63.4 + - - +
31B ALA 3.4 0.3 + - - -
32B GLY 3.3 2.9 + - - -
33B VAL* 3.1 47.0 + - + +
36B TYR* 4.1 25.4 - - + -
66B ILE* 3.7 31.0 - - + -
68B ALA* 4.2 15.0 - - + -
78B LEU* 4.0 23.6 - - + -
82B PHE* 4.3 5.8 - - + -
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Residues in contact with ASP 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B THR* 2.9 28.5 + - - +
26B ASP* 3.6 10.9 - - - +
28B LEU* 1.3 76.9 - - - +
30B ARG* 1.3 63.1 + - - +
32B GLY* 3.0 14.7 + - - -
33B VAL 4.5 10.2 - - - +
36B TYR* 3.7 22.8 + - - -
45C LYS* 3.8 27.9 + - - +
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Residues in contact with ARG 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B PHE* 6.1 4.6 - - - -
26B ASP* 2.8 28.0 + - - +
27B LEU* 3.2 40.3 - - - +
29B ASP* 1.3 73.7 - - - +
31B ALA* 1.3 60.2 + - - +
32B GLY* 3.3 1.4 + - - -
81B GLY* 5.8 0.8 - - - -
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Residues in contact with ALA 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B LEU* 3.0 20.9 + - + +
28B LEU 3.9 2.2 - - - +
29B ASP 3.2 0.4 - - - -
30B ARG* 1.3 76.0 - - - +
32B GLY* 1.3 60.0 + - - +
33B VAL* 3.5 2.5 - - + -
74B LEU* 3.8 20.5 - - + +
77B PRO* 5.9 5.4 - - + -
78B LEU* 3.5 30.1 - - + +
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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