Contacts of the strand formed by residues 43 - 47 (chain J) in PDB entry 5EEZ
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 VAL 43 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55I ILE 3.9 0.3 - - - +
56I LYS* 3.3 8.4 - - - +
57I VAL* 2.9 32.7 + - + +
63I ILE* 4.1 19.3 - - + -
70I ILE* 4.3 5.8 - - + -
71I GLU 4.2 2.7 - - - +
72I SER* 3.6 29.6 - - - +
11J VAL* 4.0 23.1 - - + -
12J ILE 3.2 9.4 - - - +
13J LYS* 4.0 18.2 - - + -
38J LEU* 4.8 1.3 - - - -
41J GLY 3.9 1.1 + - - +
42J GLU* 1.3 78.5 - - - +
44J LEU* 1.3 61.6 + - - +
45J ILE* 4.1 18.2 - - + -
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Residues in contact with LEU 44 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24I LEU* 4.2 23.3 - - + -
54I ALA* 4.4 6.7 - - + -
55I ILE 3.4 19.3 - - - +
56I LYS* 4.2 8.5 - - + -
101I TRP* 5.5 3.1 - - + -
10J VAL 3.7 1.4 - - - +
11J VAL* 3.5 1.9 - - - -
12J ILE* 2.7 40.6 + - + +
21J VAL* 3.7 37.0 - - + -
36J GLU* 4.2 21.3 - - + -
38J LEU* 4.0 19.4 - - + +
43J VAL* 1.3 75.1 - - - +
45J ILE* 1.3 63.2 + - - +
46J ALA* 4.1 15.9 - - + -
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Residues in contact with ILE 45 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10I VAL* 4.1 24.2 - - + -
12I ILE* 6.0 0.2 - - + -
48I PHE* 3.5 23.1 - - + -
54I ALA* 3.1 4.0 - - - +
55I ILE* 2.7 57.2 + - + +
57I VAL* 4.6 11.2 - - + -
63I ILE* 4.8 9.6 - - + -
65I THR* 4.9 2.9 - - + -
9J PHE* 3.4 35.7 - - + -
10J VAL 3.3 4.3 - - - +
11J VAL* 4.4 11.7 - - + -
43J VAL* 4.1 20.0 - - + -
44J LEU* 1.3 76.8 - - - +
46J ALA* 1.3 59.8 + - - +
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Residues in contact with ALA 46 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54I ALA* 4.0 10.5 - - + -
101I TRP* 3.8 28.3 - - + +
9J PHE* 3.3 4.1 - - - -
10J VAL* 2.9 35.4 + - + +
12J ILE* 4.9 7.0 - - + -
21J VAL* 5.2 0.7 - - + -
44J LEU* 4.3 15.3 - - + -
45J ILE* 1.3 76.7 - - - +
47J GLN* 1.3 62.2 + - - +
55J ILE* 4.2 9.0 - - + +
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Residues in contact with GLN 47 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7I SER* 5.1 2.8 + - - -
8I ASP* 5.6 2.4 - - - +
26I ARG* 2.8 32.3 + - - +
48I PHE* 3.4 42.0 - - + +
53I SER* 3.0 23.3 + - - +
101I TRP* 2.9 22.9 + - - -
7J SER* 3.5 29.6 + - - +
8J ASP 3.4 7.9 - - - +
9J PHE* 4.0 9.6 - - + -
46J ALA* 1.3 73.6 - - - +
48J PHE* 1.3 72.3 + - - +
49J THR* 3.5 4.3 - - + +
52J THR* 4.7 1.7 - - - +
55J ILE* 4.2 5.7 - - - +
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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