Contacts of the strand formed by residues 37 - 46 (chain F) in PDB entry 5USJ
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 GLU 37 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65E SER* 4.6 7.8 + - - +
35F THR* 3.6 1.4 - - - +
36F ILE* 1.3 85.1 - - + +
38F ASP* 1.3 69.7 + - - +
56F LEU* 3.8 33.2 - - + +
57F ASP 3.6 9.2 - - - +
58F THR* 4.7 4.7 - - - -
59F ALA 5.4 0.2 - - - +
67F MET* 3.6 33.1 - - + +
70F GLN* 4.9 9.8 + - - +
71F TYR* 3.2 32.6 - - + +
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Residues in contact with ASP 38 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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0B HIS* 4.9 9.0 + - - +
102E ARG* 5.0 6.8 + - - -
35F THR* 3.7 18.2 + - + +
36F ILE 5.2 0.7 + - - -
37F GLU* 1.3 81.5 - - - +
39F SER* 1.3 62.4 + - - +
40F TYR* 3.8 29.5 + - + +
55F ILE 3.7 0.2 - - - +
56F LEU* 3.6 5.9 - - - +
57F ASP* 2.9 39.2 + - + +
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Residues in contact with SER 39 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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0B HIS* 3.1 26.2 + - - -
102E ARG* 5.3 2.8 + - - -
38F ASP* 1.3 77.6 - - - +
40F TYR* 1.3 62.1 + - - +
41F ARG* 5.9 0.4 - - - -
54F ASP* 4.2 13.4 + - - -
55F ILE 3.2 7.4 - - - -
56F LEU* 4.0 15.9 - - - -
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Residues in contact with TYR 40 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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-1B SER* 3.1 40.4 - - - +
0B HIS* 3.5 34.7 - + - +
20F THR* 3.6 27.4 - - + -
21F ILE* 4.4 17.1 - - + +
24F ILE* 3.8 19.1 - - + -
38F ASP* 3.8 31.2 + - + +
39F SER* 1.3 74.7 - - - +
41F ARG* 1.3 64.6 + - - +
53F LEU 3.6 0.5 - - - +
54F ASP* 3.4 5.4 - - - +
55F ILE* 2.8 45.1 + - + +
57F ASP* 4.2 14.1 + - + -
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Residues in contact with ARG 41 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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-1B SER 5.2 1.3 + - - +
0B HIS* 6.1 0.8 - - - +
1B MET* 4.2 29.3 + - + +
3B GLU* 3.8 12.0 + - - -
41B ARG* 3.0 38.5 - - - +
52B LEU* 3.7 12.3 - - - -
3F GLU* 3.6 17.2 + - - -
24F ILE* 3.7 11.6 - - - +
39F SER 5.9 0.7 - - - -
40F TYR* 1.3 78.4 - - - +
42F LYS* 1.3 64.8 + - - +
52F LEU* 3.2 33.6 + - + +
53F LEU 3.2 6.1 - - - +
54F ASP* 3.7 37.6 + - - +
55F ILE* 6.0 0.2 - - - -
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Residues in contact with LYS 42 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B MET* 4.8 3.8 - - - -
23F LEU* 3.5 43.3 + - + +
24F ILE* 3.8 28.7 + - + -
26F ASN* 5.5 1.6 + - - -
41F ARG* 1.3 78.6 - - - +
43F GLN* 1.3 68.0 + - - +
44F VAL* 3.4 27.8 - - + -
52F LEU* 3.7 6.4 - - - +
53F LEU* 2.8 44.3 + - + +
55F ILE* 5.3 1.3 - - + -
149F ARG* 5.6 0.8 - - - +
153F ASP* 6.0 0.2 - - - -
157F TYR* 5.7 1.1 - - - -
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Residues in contact with GLN 43 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B GLN* 3.6 53.2 - - - +
1F MET* 3.1 34.1 - - - +
42F LYS* 1.3 81.8 - - - +
44F VAL* 1.3 64.3 + - - +
50F THR* 3.6 23.3 - - + +
51F CYS 3.3 15.0 - - - +
52F LEU* 3.8 8.2 - - + +
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Residues in contact with VAL 44 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23F LEU* 5.7 1.1 - - + -
42F LYS* 3.4 37.2 - - + +
43F GLN* 1.3 73.0 - - - +
45F VAL* 1.3 64.5 + - - +
46F ILE* 3.6 30.3 - - + -
49F GLU 3.7 0.2 - - - +
50F THR* 3.3 5.6 - - - +
51F CYS* 2.9 39.0 + - - -
53F LEU* 4.0 22.9 - - + -
157F TYR* 4.3 22.9 - - + +
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Residues in contact with VAL 45 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44F VAL* 1.3 77.3 - - - +
46F ILE* 1.3 67.7 + - - +
47F ASP 4.2 0.6 + - - -
48F GLY* 3.8 31.2 - - - +
49F GLU 3.5 4.9 - - - +
50F THR* 3.9 17.0 - - + +
157F TYR* 4.3 13.7 + - - -
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Residues in contact with ILE 46 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44F VAL* 3.6 25.8 - - + -
45F VAL* 1.3 79.2 - - - +
47F ASP* 1.3 75.7 + - - +
48F GLY 3.1 0.2 - - - -
49F GLU 3.0 16.0 + - - -
51F CYS* 4.1 4.0 - - - -
53F LEU* 4.8 1.1 - - + -
157F TYR* 3.8 35.4 - - + +
160F VAL* 3.7 33.9 - - + -
161F ARG* 4.0 26.2 - - + +
164F ARG* 3.3 30.1 + - - +
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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