Contacts of the strand formed by residues 30 - 35 (chain E) in PDB entry 4PJO
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 ARG 30 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28E ARG 3.9 0.8 + - - -
29E SER* 1.3 74.3 + - - +
31E ILE* 1.3 62.0 - - - +
44E GLU* 2.9 40.5 + - - +
45E GLY* 3.8 15.0 - - - +
46E CYS* 4.0 12.6 - - - +
60E ASP* 3.2 34.5 + - - +
62E GLU* 2.6 41.2 + - - +
89E SER* 3.4 1.6 - - - -
90E VAL* 2.7 50.3 + - + +
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Residues in contact with ILE 31 (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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24E TYR* 3.4 41.3 - - + -
29E SER* 4.1 11.0 - - - +
30E ARG* 1.3 74.6 - - - +
32E GLN* 1.3 67.2 + - - +
33E VAL* 4.4 5.3 - - + +
43E ILE 4.2 0.2 - - - +
44E GLU* 3.0 4.5 - - - +
45E GLY 2.7 45.0 + - - +
47E ILE* 3.8 31.2 - - + -
58E LEU* 5.2 1.5 - - + +
87E LEU* 3.9 30.5 - - + -
88E GLN 3.2 19.1 - - - +
89E SER* 3.8 7.2 - - - +
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Residues in contact with GLN 32 (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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30E ARG 4.1 0.6 + - - -
31E ILE* 1.3 74.6 - - - +
33E VAL* 1.3 63.0 - - - +
34E TRP* 4.1 1.2 + - + -
42E ARG* 2.9 41.7 + - - -
43E ILE 3.5 6.3 - - - +
44E GLU* 3.7 16.7 + - + +
64E ILE* 3.1 31.3 - - - +
71E ARG* 4.9 4.4 - - - +
86E LEU 3.6 2.1 - - - +
87E LEU* 3.6 0.7 - - - -
88E GLN* 2.9 62.9 + - + +
90E VAL 5.2 7.0 + - - -
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Residues in contact with VAL 33 (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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31E ILE* 4.4 6.1 - - + +
32E GLN* 1.3 73.9 - - - +
34E TRP* 1.3 67.1 + - - +
35E LEU* 4.2 14.5 - - + +
42E ARG* 3.3 10.4 - - - +
43E ILE* 2.6 59.5 + - + +
44E GLU* 5.9 0.2 - - - -
56E LEU* 4.1 17.0 - - + -
58E LEU* 5.0 6.7 - - + -
79E LEU* 4.2 12.3 - - + -
84E ILE* 4.8 4.3 - - + -
86E LEU 3.3 4.3 - - - +
87E LEU* 3.1 29.2 - - + -
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Residues in contact with TRP 34 (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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32E GLN* 4.4 3.4 - - + -
33E VAL* 1.3 80.1 - - - +
35E LEU* 1.3 61.5 + - - +
42E ARG* 3.2 33.7 - - - +
84E ILE* 3.8 5.0 - - - -
85E THR* 2.9 28.0 + - + -
86E LEU* 2.8 52.8 + - + +
88E GLN* 2.6 26.8 + - - -
21G LEU* 4.4 3.4 - - + -
25G ARG* 4.0 42.4 - - + +
26G HIS 5.3 0.2 - - - -
27G VAL* 3.5 32.3 - - + -
47G GLU* 3.1 34.5 - - + -
57G ILE* 4.0 7.4 - - + -
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Residues in contact with LEU 35 (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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33E VAL* 4.2 21.5 - - + +
34E TRP* 1.3 81.8 - - - +
36E TYR* 1.3 54.6 + - - +
37E GLU 3.3 0.9 + - - -
38E GLN* 3.7 23.4 + - + +
41E MET* 3.6 52.2 + - + +
42E ARG* 4.2 5.1 - - - +
43E ILE* 4.5 6.5 - - + -
79E LEU* 4.3 8.1 - - + -
83E ASN* 3.2 26.7 - - + +
84E ILE 5.0 0.2 - - - +
85E THR* 3.7 2.5 - - - -
70F LEU* 4.3 13.0 - - + -
25G ARG* 2.6 40.0 + - - +
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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