Contacts of the helix formed by residues 22 - 27 (chain N) 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 PHE 22 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18N GLN* 3.2 35.9 + - + +
19N LEU* 4.8 1.6 - - - +
21N GLU* 1.3 77.9 - - + +
23N ALA* 1.3 58.3 + - - +
25N HIS* 4.1 11.0 - - + +
26N LYS* 3.5 14.2 + - - +
124T LEU* 3.5 31.2 - - + -
125T GLU* 4.1 25.4 - - + -
127T ASN* 4.1 23.1 - - - -
129T LEU* 3.7 31.1 - - + +
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Residues in contact with ALA 23 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8N ILE* 4.5 12.6 - - + +
11N LEU* 5.3 13.7 - - + -
19N LEU* 3.2 21.4 + - + +
20N LYS* 3.7 7.2 - - - +
21N GLU 3.0 0.8 - - - -
22N PHE* 1.3 75.7 - - - +
24N LEU* 1.3 60.9 + - + +
25N HIS 3.0 4.5 - - - -
26N LYS* 3.3 4.7 + - - +
27N LEU* 2.9 33.3 + - - +
44N LYS* 4.9 15.0 - - - +
129T LEU* 5.8 0.2 - - - -
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Residues in contact with LEU 24 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20N LYS 3.1 19.6 + - - +
21N GLU* 3.3 5.8 + - - +
23N ALA* 1.3 76.9 - - + +
25N HIS* 1.3 64.3 + - + +
27N LEU* 4.4 17.5 - - + -
28N ASN* 3.1 21.6 - - - +
44N LYS* 5.9 4.9 - - - -
45N ILE* 4.8 14.8 - - + -
48N LEU* 4.2 24.0 - - + -
56N SER* 3.9 26.2 - - - +
59N PHE* 3.9 18.4 - - + +
60N ALA* 4.2 11.4 - - + +
63N VAL* 4.2 22.6 - - + +
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Residues in contact with HIS 25 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21N GLU* 2.8 37.5 + - + +
22N PHE* 4.3 13.0 + - + +
23N ALA 3.0 1.0 - - - -
24N LEU* 1.3 87.3 - - - +
26N LYS* 1.3 58.6 + - - +
27N LEU 3.3 1.6 - - - -
28N ASN* 3.9 8.8 - - - +
29N ALA* 3.2 27.4 + - - +
59N PHE* 3.7 39.9 - + - -
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Residues in contact with LYS 26 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8N ILE* 4.2 18.8 - - + +
22N PHE 3.5 15.4 + - - +
23N ALA* 3.3 5.0 + - - +
25N HIS* 1.3 77.5 - - - +
27N LEU* 1.3 59.0 + - - +
29N ALA* 4.0 4.2 + - + +
30N VAL* 3.1 39.6 - - + +
34N PHE* 6.2 2.0 - - - -
129T LEU* 3.8 30.1 - - + -
130T PRO* 3.7 29.1 + - + +
132T THR* 3.5 28.4 - - - +
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Residues in contact with LEU 27 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5N ALA* 4.4 12.8 - - + -
8N ILE* 4.1 16.9 - - + +
9N ILE* 4.4 9.6 - - + -
23N ALA 2.9 16.4 + - - +
24N LEU* 4.4 11.2 - - + -
26N LYS* 1.3 73.9 - - - +
28N ASN* 1.3 67.2 + - - +
29N ALA 3.0 1.8 - - - -
30N VAL* 2.9 20.2 + - + +
31N VAL* 3.2 19.3 + - + +
34N PHE* 5.0 2.5 - - + -
38N ILE* 3.5 34.3 - - + -
45N ILE* 4.2 12.8 - - + -
63N VAL* 3.7 28.7 - - + -
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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