Contacts of the strand formed by residues 73 - 78 (chain E) in PDB entry 4JFF
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 GLN 73 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22E GLU* 2.6 33.4 + - + +
23E CYS 3.4 6.1 - - - +
24E THR* 4.7 5.6 - - + +
33E LEU* 4.7 0.4 - - - -
68E ARG* 3.4 6.0 - - - +
69E PRO* 3.3 29.5 - - + +
70E GLN* 3.2 40.4 + - + +
71E ASP 3.5 0.4 + - - -
72E ARG* 1.3 79.1 - - - +
74E PHE* 1.3 61.7 + - - +
75E ILE* 4.0 15.0 - - + +
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Residues in contact with PHE 74 (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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22E GLU* 3.6 0.5 - - - +
23E CYS* 2.7 50.3 + - + +
33E LEU* 3.5 50.3 - - + -
34E TYR 3.7 4.9 - - - -
35E TRP* 3.0 43.6 - + - -
48E PHE* 4.7 2.9 - - + -
50E TRP* 3.7 46.9 - + + -
66E ALA* 4.4 3.4 - - + -
67E SER 3.3 19.1 - - - -
68E ARG* 4.0 9.4 - - + -
73E GLN* 1.3 74.2 - - - +
75E ILE* 1.3 66.3 + - - +
91E CYS* 4.2 9.4 - - - -
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Residues in contact with ILE 75 (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 SER* 4.6 11.0 - - - +
21E LEU 3.3 10.8 - - - +
22E GLU* 4.6 9.0 - - + +
35E TRP* 3.5 7.1 + - - -
66E ALA* 3.2 5.2 - - - -
67E SER* 2.7 49.0 + - - +
69E PRO* 3.8 26.5 - - + -
73E GLN* 4.0 15.7 - - - +
74E PHE* 1.3 80.1 - - - +
76E LEU* 1.3 65.3 + - - +
77E SER* 3.4 21.8 - - - +
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Residues in contact with LEU 76 (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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19E LEU* 4.2 5.1 - - + +
20E SER* 3.5 3.5 + - - -
21E LEU* 2.9 48.8 + - + +
35E TRP* 3.6 32.6 - - + -
47E LEU* 4.1 7.2 - - + -
48E PHE* 3.6 37.0 - - + -
64E LEU* 4.4 15.9 - - + -
65E SER 3.5 8.1 - - - +
75E ILE* 1.3 72.9 - - - +
77E SER* 1.3 63.6 + - - +
89E TYR* 3.5 37.2 - - + -
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Residues in contact with SER 77 (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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19E LEU* 3.1 15.8 + - - -
20E SER* 5.0 2.3 + - - -
64E LEU* 3.5 6.2 - - - +
65E SER* 2.8 45.1 + - - -
66E ALA 6.0 0.2 - - - -
67E SER* 5.1 1.7 + - - -
75E ILE* 3.4 18.7 - - - +
76E LEU* 1.3 75.2 + - - +
78E SER* 1.3 67.0 + - - +
302E SO4 4.9 2.0 - - - -
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Residues in contact with SER 78 (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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18E PRO* 3.1 6.1 - - - +
19E LEU* 2.8 44.3 + - - +
63E ASN* 2.8 41.6 + - - -
64E LEU* 4.2 4.7 - - - -
77E SER* 1.3 78.1 - - - +
79E LYS* 1.3 60.5 + - - +
80E LYS 3.4 7.3 + - - -
81E LEU* 3.8 11.1 + - - +
302E SO4 3.8 5.2 - - - -
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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