Contacts of the strand formed by residues 56 - 59 (chain E) in PDB entry 3JUT
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 TYR 56 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17E ILE* 4.5 0.4 - - - -
39E SER* 5.7 0.4 - - - -
47E TYR* 3.8 45.3 - + + -
48E ILE 3.7 3.6 - - - +
49E LYS* 3.3 32.2 - - + +
54E GLY 3.3 19.3 - - - -
55E GLN* 1.3 72.7 - - - +
57E LEU* 1.3 66.7 + - - +
58E ALA 3.3 0.5 + - - -
67E GLY* 3.6 2.8 - - - -
68E SER* 2.8 38.9 + - - +
69E GLN 4.4 3.8 - - - -
70E THR 4.0 0.9 - - - -
71E PRO* 3.6 45.9 - - + +
75E CYS* 3.7 18.2 - - + -
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Residues in contact with LEU 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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15E LEU* 4.0 22.4 - - + -
17E ILE* 3.8 16.2 - - + +
23E VAL* 3.8 38.6 - - + -
48E ILE* 2.8 42.7 + - + +
56E TYR* 1.3 73.6 - - - +
58E ALA* 1.3 68.3 + - - +
65E LEU* 4.3 6.3 - - + -
66E TYR 3.8 2.7 - - - +
75E CYS* 3.3 22.0 - - - +
77E PHE* 3.5 27.5 - - + -
101E VAL* 4.1 15.9 - - + -
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Residues in contact with ALA 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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56E TYR 4.0 2.2 - - - +
57E LEU* 1.3 76.7 - - - +
59E MET* 1.3 61.8 + - - +
65E LEU* 3.2 7.8 - - - +
66E TYR* 2.9 63.8 + - + +
74E GLU 3.2 15.0 - - - +
75E CYS* 3.7 16.8 - - - -
77E PHE* 4.0 5.4 - - - -
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Residues in contact with MET 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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58E ALA* 1.3 74.5 - - - +
60E ASP* 1.3 67.8 + - - +
63E GLY* 3.7 33.9 - - - +
64E LEU 3.4 4.5 - - - +
65E LEU* 3.7 23.1 - - + -
66E TYR* 4.0 3.4 - - - -
74E GLU* 3.0 27.9 + - - +
77E PHE* 4.3 12.3 - - + -
91E SER* 3.9 17.7 + - - -
93E LYS* 5.5 0.3 - - - +
94E HIS* 4.7 7.1 - - + -
99E TRP* 3.7 30.7 - - + +
100E PHE 3.4 33.0 - - - +
101E VAL 4.1 1.3 - - - +
110E LYS 5.6 0.2 - - - +
112E GLY* 4.2 2.9 - - - +
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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