Contacts of the helix formed by residues 50 - 59 (chain E) in PDB entry 3J8B
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 MET 50 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45E LEU* 4.9 6.3 + - - +
48E THR* 3.5 7.7 - - - +
49E ASN* 1.3 77.4 - - - +
51E VAL* 1.3 58.9 + - - +
52E ASP* 3.4 2.7 - - + +
53E PHE* 3.8 18.0 + - + +
54E ALA* 3.1 22.6 + - - +
73E LYS* 6.1 0.4 - - - -
140E GLU 3.4 14.3 + - - +
141E CYS 4.1 14.8 - - - +
142E GLY* 4.3 6.7 - - - +
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Residues in contact with VAL 51 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49E ASN 3.6 4.8 + - - +
50E MET* 1.3 70.9 - - - +
52E ASP* 1.3 56.3 + - - +
53E PHE 3.4 0.4 - - - -
54E ALA* 3.2 10.7 - - + -
55E MET* 2.3 39.1 + - - +
70E LEU* 5.2 17.0 - - + +
73E LYS* 5.2 12.5 - - + +
74E ARG* 5.9 4.5 - - + +
141E CYS 5.1 1.2 + - - -
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Residues in contact with ASP 52 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50E MET* 3.4 1.8 - - + -
51E VAL* 1.3 73.6 - - - +
53E PHE* 1.3 64.2 + - - +
55E MET* 3.2 7.7 + - - +
56E ASP* 3.0 22.0 + - - +
141E CYS 5.6 5.1 + - - +
142E GLY* 6.1 3.1 - - - +
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Residues in contact with PHE 53 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20E PHE* 6.5 0.9 - - + -
45E LEU* 4.8 13.0 - - + +
50E MET* 3.8 20.0 + - + +
52E ASP* 1.3 79.1 - - - +
54E ALA* 1.3 57.7 + - - +
56E ASP* 3.1 10.1 + - - +
57E VAL* 2.9 26.6 + - - +
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Residues in contact with ALA 54 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45E LEU* 4.8 13.2 - - + +
46E SER* 6.0 2.0 - - - +
50E MET 3.1 19.8 + - - +
51E VAL* 3.3 13.5 - - + +
53E PHE* 1.3 78.2 - - - +
55E MET* 1.3 56.4 + - - +
57E VAL* 3.2 10.2 + - - +
58E TYR* 2.9 26.7 + - - +
70E LEU* 6.3 2.7 - - + -
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Residues in contact with MET 55 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51E VAL* 2.3 30.7 + - + +
52E ASP* 3.2 9.4 + - - +
54E ALA* 1.3 68.3 - - - +
56E ASP* 1.3 61.5 + - - +
58E TYR* 3.1 11.3 + - - +
59E LYS* 3.1 20.4 + - - +
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Residues in contact with ASP 56 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52E ASP 3.0 11.9 + - - +
53E PHE* 3.4 11.7 - - - +
55E MET* 1.3 74.0 - - - +
57E VAL* 1.3 65.9 + - - +
59E LYS* 3.0 22.1 + - - +
60E ASN 5.0 0.5 - - - +
62E TYR* 3.2 7.0 - - - +
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Residues in contact with VAL 57 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41E LYS 5.7 0.7 - - - -
42E LEU* 4.4 24.9 - - + +
45E LEU* 5.4 3.8 - - + -
53E PHE 2.9 13.1 + - - +
54E ALA* 3.2 12.5 + - - +
56E ASP* 1.3 71.8 - - - +
58E TYR* 1.3 56.3 + - - +
62E TYR* 1.7 52.1 - - + +
63E SER* 2.9 6.9 - - - +
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Residues in contact with TYR 58 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54E ALA 2.9 12.8 + - - +
55E MET* 3.1 17.2 + - - +
57E VAL* 1.3 78.5 - - - +
59E LYS* 1.3 59.5 + - - +
60E ASN* 3.9 0.3 + - - -
62E TYR 4.6 1.9 - - - +
63E SER 3.5 13.4 - - - +
64E ASP* 4.9 1.2 - - - -
65E ASP* 3.5 35.2 + - + +
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Residues in contact with LYS 59 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55E MET 3.1 10.9 + - - +
56E ASP* 3.0 15.9 + - - +
57E VAL 3.0 0.7 - - - +
58E TYR* 1.3 77.2 - - - +
60E ASN* 1.3 64.2 + - - +
62E TYR* 2.6 34.5 + - - +
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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