Contacts of the helix formed by residues 23 - 31 (chain Q) in PDB entry 5L4K
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 Q).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12Q ALA* 3.4 28.9 + - - +
15Q LEU* 3.8 16.3 + - - -
16Q LEU* 4.3 9.1 - - - +
20Q ARG 3.6 10.9 + - - -
21Q GLU 3.3 0.8 - - - -
22Q ALA* 1.3 75.6 - - - +
24Q ILE* 1.3 61.6 + - - +
25Q ASP 3.4 0.7 - - - -
26Q ILE* 3.7 13.3 - - - +
27Q LEU* 3.6 18.0 - - - +
56Q LEU* 3.5 26.3 - - - +
59Q LYS* 5.0 1.1 - - - -
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Residues in contact with ILE 24 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20Q ARG* 3.6 19.1 - - - +
21Q GLU* 3.4 32.7 + - - +
22Q ALA 3.3 0.6 - - - -
23Q SER* 1.3 78.8 - - - +
25Q ASP* 1.3 62.5 + - - +
26Q ILE 3.5 0.7 - - - -
27Q LEU* 4.2 6.2 - - + +
28Q HIS* 2.8 58.3 + - + +
59Q LYS* 3.8 14.4 - - - +
62Q GLN* 3.8 27.4 - - + +
64Q ALA* 5.9 0.2 - - + -
65Q GLU* 3.6 29.2 - - + +
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Residues in contact with ASP 25 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1Q MET* 4.8 1.2 - - - +
21Q GLU* 3.0 20.3 - - - +
22Q ALA* 3.7 13.9 + - - +
23Q SER 3.4 0.2 - - - -
24Q ILE* 1.3 85.8 - - - +
26Q ILE* 1.3 61.8 + - + +
27Q LEU 3.6 0.2 - - - -
28Q HIS* 4.2 6.8 + - - +
29Q SER* 2.9 22.3 + - - -
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Residues in contact with ILE 26 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1Q MET* 3.8 27.2 - - + +
8Q GLU* 3.0 32.7 - - - +
11Q ARG* 4.0 5.6 - - + +
12Q ALA* 3.5 32.8 - - + -
15Q LEU* 3.7 25.6 - - + -
22Q ALA 3.6 13.0 - - - +
23Q SER* 3.7 17.3 - - - +
25Q ASP* 1.3 79.3 - - + +
27Q LEU* 1.3 69.5 + - - +
28Q HIS 3.3 0.2 - - - -
29Q SER* 3.3 10.2 + - - -
30Q ILE* 3.4 18.0 + - - +
56Q LEU* 5.5 0.2 - - + -
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Residues in contact with LEU 27 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8Q GLU* 4.2 5.2 - - - -
23Q SER 3.6 15.5 - - - +
24Q ILE* 4.2 5.2 - - + +
26Q ILE* 1.3 83.9 - - - +
28Q HIS* 1.3 70.1 + - + +
30Q ILE* 3.7 3.5 + - - +
31Q VAL* 3.0 54.4 + - + +
52Q GLU* 3.8 26.7 - - - +
53Q LEU* 4.2 9.2 - - + +
56Q LEU* 3.9 17.7 - - + -
57Q LEU* 3.8 41.7 - - + +
59Q LYS* 6.2 0.2 - - - +
65Q GLU* 4.0 7.9 - - - +
72Q TYR* 5.5 1.8 - - + -
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Residues in contact with HIS 28 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24Q ILE* 2.8 42.2 + - + +
25Q ASP* 4.2 6.7 + - - +
26Q ILE 3.3 0.4 - - - -
27Q LEU* 1.3 83.6 - - + +
29Q SER* 1.3 59.0 + - - +
31Q VAL 4.4 1.6 - - - -
32Q LYS* 3.3 37.0 - - - +
57Q LEU* 3.6 21.7 - - + +
64Q ALA* 5.0 15.0 + - + -
65Q GLU* 4.8 4.3 - - + -
68Q GLY* 5.9 1.4 - - - -
72Q TYR* 3.5 33.1 - + - +
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Residues in contact with SER 29 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1Q MET* 3.5 33.7 + - - +
25Q ASP 2.9 17.5 + - - -
26Q ILE 3.3 4.8 + - - -
27Q LEU 3.2 0.8 - - - -
28Q HIS* 1.3 81.1 - - - +
30Q ILE* 1.3 59.3 + - - +
31Q VAL 3.6 0.2 - - - -
32Q LYS* 4.8 1.1 - - - +
33Q ARG 3.2 18.5 + - - +
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Residues in contact with ILE 30 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1Q MET* 3.4 13.5 - - + +
2Q ALA 3.2 24.9 - - - +
3Q ALA 4.9 1.8 - - - +
4Q ALA 3.8 13.2 - - - +
5Q ALA* 4.2 12.3 - - + -
8Q GLU* 4.2 18.8 - - + +
26Q ILE 3.5 15.7 - - - +
27Q LEU 3.8 2.9 - - - +
29Q SER* 1.3 77.5 - - - +
31Q VAL* 1.3 67.1 + - + +
33Q ARG 3.8 3.3 - - - +
34Q ASP* 3.4 20.5 - - + +
36Q GLN* 5.3 0.7 - - - +
43Q VAL* 3.2 25.1 - - + +
49Q SER* 5.1 3.4 - - - +
52Q GLU* 3.3 24.5 - - - +
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Residues in contact with VAL 31 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27Q LEU* 3.0 44.5 + - + +
29Q SER 3.6 0.2 - - - -
30Q ILE* 1.3 81.9 - - + +
32Q LYS* 1.3 72.1 + - - +
33Q ARG 3.2 0.3 + - - -
42Q ALA* 4.0 2.6 - - - +
43Q VAL* 3.1 27.2 - - + +
49Q SER* 5.2 5.6 - - - +
52Q GLU* 4.5 7.2 - - + +
53Q LEU* 4.5 23.3 - - + -
72Q TYR* 3.9 32.3 - - + +
76Q PHE* 4.4 12.1 - - + -
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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