Contacts of the helix formed by residues 48 - 58 (chain T) 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 PHE 48 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8T GLU* 5.5 11.0 - - + -
12T GLY 6.1 1.6 - - - +
13T ALA* 5.3 2.9 - - + -
38T GLU* 5.0 18.3 + - + -
42T ASN* 5.9 1.6 - - - +
46T ILE 3.8 1.2 + - - -
47T PRO* 1.3 79.8 - - - +
49T SER* 1.3 64.0 + - - +
50T ALA* 3.2 9.2 - - + +
51T THR* 3.3 28.5 + - - +
52T VAL* 3.3 10.9 + - - +
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Residues in contact with SER 49 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38T GLU* 5.6 2.2 - - - +
47T PRO 3.7 1.4 + - - -
48T PHE* 1.3 71.6 - - - +
50T ALA* 1.3 64.6 + - - +
52T VAL* 3.4 8.8 + - - +
53T GLU* 3.3 20.8 + - - +
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Residues in contact with ALA 50 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12T GLY* 4.9 4.5 - - - -
13T ALA* 3.8 13.1 - - + +
26T ILE* 4.0 29.0 - - + +
27T THR 5.0 5.2 - - - +
28T ASN* 5.1 7.0 - - + -
48T PHE* 3.2 7.3 - - + +
49T SER* 1.3 78.3 - - - +
51T THR* 1.3 56.9 + - - +
53T GLU* 3.6 6.7 + - - +
54T LEU* 3.1 26.7 + - - +
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Residues in contact with THR 51 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8T GLU* 6.0 3.8 - - - -
13T ALA* 3.7 17.6 - - - +
47T PRO* 4.5 9.2 - - - -
48T PHE* 3.3 26.7 + - - +
49T SER 3.2 0.2 - - - -
50T ALA* 1.3 77.8 - - - +
52T VAL* 1.3 59.2 + - - +
54T LEU* 3.2 3.3 + - - +
55T LEU* 3.0 31.1 + - - +
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Residues in contact with VAL 52 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47T PRO* 5.4 3.9 - - + +
48T PHE 3.3 9.4 + - - +
49T SER* 3.7 12.3 - - - +
50T ALA 3.4 0.2 - - - -
51T THR* 1.3 80.8 - - - +
53T GLU* 1.3 59.5 + - - +
55T LEU* 3.5 6.1 + - - +
56T LYS* 3.5 17.5 + - - +
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Residues in contact with GLU 53 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26T ILE* 5.2 7.0 - - + -
49T SER 3.3 10.4 + - - +
50T ALA* 3.8 9.9 - - - +
51T THR 3.3 0.4 - - - -
52T VAL* 1.3 78.4 - - - +
54T LEU* 1.3 61.2 + - - +
56T LYS* 3.3 7.9 + - - +
57T LYS* 3.2 21.8 + - - +
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Residues in contact with LEU 54 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13T ALA* 4.6 16.4 - - + +
14T VAL 6.3 0.2 - - - -
15T ALA* 5.9 6.5 - - + +
24T ASP* 5.7 5.3 - - + +
25T TYR* 5.4 2.9 - - - -
26T ILE* 4.7 10.9 - - + +
50T ALA 3.1 17.8 + - - +
51T THR* 3.2 8.5 + - - +
53T GLU* 1.3 73.8 - - - +
55T LEU* 1.3 58.1 + - - +
56T LYS 3.0 8.7 + - - -
57T LYS* 3.4 6.4 + - - +
58T VAL* 3.2 25.8 + - - +
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Residues in contact with LEU 55 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51T THR 3.0 16.9 + - - +
52T VAL* 3.5 6.9 + - - +
53T GLU 3.4 0.2 - - - -
54T LEU* 1.3 74.9 - - - +
56T LYS* 1.3 53.5 + - - +
58T VAL* 2.8 18.9 - - - +
59T ASN* 4.6 2.8 - - - -
60T PRO 5.1 1.7 - - - -
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Residues in contact with LYS 56 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52T VAL 3.5 10.1 + - - +
53T GLU* 3.3 11.6 + - - +
54T LEU 3.0 0.6 - - - -
55T LEU* 1.3 76.4 - - - +
57T LYS* 1.3 67.4 + - - +
58T VAL 3.0 9.1 - - - +
59T ASN* 4.6 4.7 - - - +
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Residues in contact with LYS 57 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24T ASP* 5.8 7.2 - - + -
53T GLU 3.2 12.4 + - - +
54T LEU* 3.4 6.9 + - - +
56T LYS* 1.3 80.8 - - - +
58T VAL* 1.3 58.5 + - - +
59T ASN* 4.0 1.6 + - - +
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Residues in contact with VAL 58 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15T ALA* 5.6 8.7 - - + -
23T VAL* 6.4 1.8 - - + -
24T ASP* 5.3 13.6 - - + +
54T LEU 3.2 11.0 + - - +
55T LEU* 2.8 26.9 - - - +
56T LYS 3.0 4.7 - - - +
57T LYS* 1.3 78.3 - - - +
59T ASN* 1.3 61.1 + - - +
60T PRO* 3.7 10.1 - - + -
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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