Contacts of the helix formed by residues 46 - 59 (chain Z) in PDB entry 5JPQ
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 46 (chain Z).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44Z GLY 3.7 1.8 + - - +
45Z LEU* 1.3 77.0 - - - +
47Z ASP* 1.3 66.2 + - - +
48Z TYR* 4.3 8.1 - - + +
49Z GLU* 3.0 20.7 + - + +
50Z VAL* 3.2 10.9 + - - +
93Z SER* 6.4 1.6 - - - -
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Residues in contact with ASP 47 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46Z LYS* 1.3 71.8 - - - +
48Z TYR* 1.3 56.2 + - - +
50Z VAL* 3.3 9.5 + - - +
51Z SER* 2.9 29.8 + - - -
91Z PRO* 4.9 13.6 - - + +
93Z SER* 5.7 5.4 - - - -
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Residues in contact with TYR 48 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46Z LYS* 3.2 6.2 - - + +
47Z ASP* 1.3 78.1 - - - +
49Z GLU* 1.3 56.3 + - - +
51Z SER* 3.7 8.7 - - - -
52Z PHE* 3.0 26.3 + - - +
91Z PRO* 5.2 6.7 - - + +
93Z SER* 4.6 16.0 - - - +
94Z LYS* 3.9 28.7 - - + +
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Residues in contact with GLU 49 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17Z PHE* 5.5 10.5 - - + -
45Z LEU* 4.3 10.5 - - + -
46Z LYS* 3.0 22.9 + - + +
48Z TYR* 1.3 74.6 - - - +
50Z VAL* 1.4 61.6 + - - +
52Z PHE* 3.3 8.2 + - - +
53Z LEU* 3.0 26.3 + - - +
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Residues in contact with VAL 50 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45Z LEU* 4.8 8.6 - - + +
46Z LYS 3.2 11.0 + - - +
47Z ASP* 3.6 11.0 - - - +
49Z GLU* 1.4 75.7 - - - +
51Z SER* 1.4 55.0 + - - +
53Z LEU* 3.0 10.4 + - - +
54Z ARG* 3.0 27.1 + - - +
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Residues in contact with SER 51 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47Z ASP 2.9 17.0 + - - -
48Z TYR* 3.7 9.6 - - - -
50Z VAL* 1.4 74.5 - - - +
52Z PHE* 1.3 56.5 + - - +
54Z ARG* 3.2 10.3 + - - +
55Z LEU* 3.0 27.8 + - - +
89Z ILE 5.1 11.0 - - - -
90Z CYS* 5.8 1.3 - - - -
91Z PRO* 5.2 11.4 - - - -
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Residues in contact with PHE 52 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18Z ARG* 6.1 6.1 - - + -
48Z TYR 3.0 18.5 + - - +
49Z GLU* 3.5 8.7 - - - +
51Z SER* 1.3 76.1 - - - +
53Z LEU* 1.4 56.6 + - - +
55Z LEU* 3.3 9.8 + - - +
56Z ILE* 3.0 27.4 + - - +
98Z TYR 6.1 1.1 - - - +
99Z PHE* 6.1 8.3 - - + -
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Residues in contact with LEU 53 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49Z GLU 3.0 13.0 + - - +
50Z VAL* 3.0 11.4 + - - +
52Z PHE* 1.4 72.3 - - - +
54Z ARG* 1.3 60.4 + - - +
56Z ILE* 3.3 9.8 + - - +
57Z GLU* 3.0 26.5 + - - +
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Residues in contact with ARG 54 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50Z VAL 3.0 12.2 + - - +
51Z SER* 3.5 11.9 - - - +
53Z LEU* 1.3 73.7 - - - +
55Z LEU* 1.4 57.4 + - - +
57Z GLU* 3.3 9.6 + - - +
58Z SER* 3.0 28.2 + - - -
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Residues in contact with LEU 55 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51Z SER 3.0 13.2 + - - +
52Z PHE* 3.4 13.2 - - - +
54Z ARG* 1.4 76.6 - - - +
56Z ILE* 1.4 61.8 + - - +
58Z SER* 3.2 17.2 + - - +
59Z VAL* 3.2 14.6 + - - +
88Z HIS* 5.3 12.8 - - + -
99Z PHE* 5.7 9.4 - - + +
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Residues in contact with ILE 56 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21Z ILE* 6.0 6.7 - - + -
52Z PHE 3.0 12.7 + - - +
53Z LEU* 3.3 13.7 + - - +
55Z LEU* 1.4 74.3 - - - +
57Z GLU* 1.4 61.3 + - - +
59Z VAL* 3.4 4.7 + - - +
60Z THR* 3.2 27.4 + - - -
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Residues in contact with GLU 57 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53Z LEU 3.0 13.7 + - - +
54Z ARG* 3.5 12.6 - - - +
55Z LEU 3.3 0.2 - - - -
56Z ILE* 1.4 74.7 - - - +
58Z SER* 1.4 58.4 + - - +
60Z THR* 3.0 25.2 - - - +
63Z SER* 5.5 9.0 - - - -
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Residues in contact with SER 58 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54Z ARG 3.0 13.4 + - - -
55Z LEU* 3.2 11.3 + - - -
57Z GLU* 1.4 77.3 - - - +
59Z VAL* 1.4 57.2 + - - +
60Z THR 3.6 2.0 - - - +
83Z GLY 4.2 9.0 - - - +
86Z SER* 5.1 16.4 - - - -
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Residues in contact with VAL 59 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55Z LEU 3.2 13.3 + - - +
56Z ILE* 3.4 3.5 + - - +
57Z GLU 3.3 0.2 - - - -
58Z SER* 1.4 76.5 - - - +
60Z THR* 1.3 52.8 + - - +
81Z ILE* 3.7 4.2 - - - +
82Z VAL* 2.8 29.3 + - - -
83Z GLY* 2.8 26.2 + - - +
106Z LEU* 6.4 1.6 - - + -
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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