Contacts of the strand formed by residues 18 - 24 (chain E) in PDB entry 3P92
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 ILE 18 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41A PHE* 4.0 23.3 - - + -
57A HIS 5.2 5.4 - - - +
58A CYS* 5.7 0.7 - - - +
59A TYR 5.8 1.8 - - - +
60A LYS* 3.6 33.0 - - + +
16E ALA* 4.0 15.7 - - + -
17E GLY* 1.3 74.5 - - - +
19E ILE* 1.3 66.8 + - - +
20E ARG* 3.3 30.7 + - - +
33E PHE 3.7 0.6 - - - +
34E VAL* 4.7 1.3 - - - -
35E TYR* 2.8 49.1 + - + +
37E GLY* 4.4 11.9 - - - -
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Residues in contact with ILE 19 (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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37A SER 6.1 1.6 - - - +
39A SER* 4.6 12.6 - - - +
60A LYS* 5.7 0.4 - - - +
193A ARG* 4.2 22.2 - - - +
17E GLY 4.1 1.5 + - - +
18E ILE* 1.3 75.2 - - - +
20E ARG* 1.3 71.8 + - - +
21E TYR* 5.5 4.9 - - + -
32E THR* 4.2 27.6 - - + -
33E PHE 3.7 6.1 - - - +
34E VAL* 5.1 2.9 - - + +
46E LYS 5.2 3.5 - - - +
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Residues in contact with ARG 20 (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 ILE* 3.3 17.8 + - + +
19E ILE* 1.3 80.3 + - - +
21E TYR* 1.3 65.7 + - - +
32E THR* 3.2 6.4 - - - -
33E PHE* 2.9 47.7 + - + -
35E TYR* 3.7 41.3 - - + -
44E ASN* 2.8 47.3 + - - +
45E PHE 3.5 14.8 - - - -
46E LYS* 3.8 38.7 - - - +
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Residues in contact with TYR 21 (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 ILE* 5.5 4.7 - - + -
20E ARG* 1.3 77.3 - - - +
22E PHE* 1.3 60.1 + - - +
30E CYS* 4.3 8.5 - - + -
31E GLN* 3.2 24.7 - - - -
32E THR* 3.5 25.0 - - + +
33E PHE* 3.7 2.8 - - - -
44E ASN* 3.4 8.1 - - - -
45E PHE* 2.9 36.5 + - + +
46E LYS 4.5 3.1 - - - -
47E SER* 3.4 20.2 - - - +
48E ALA* 3.3 46.0 - - + +
51E CYS* 4.1 11.4 - - + -
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Residues in contact with PHE 22 (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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7E GLU 5.1 0.2 - - - -
9E PRO* 3.6 39.7 - - + -
21E TYR* 1.3 74.1 - - - +
23E TYR* 1.3 76.6 + - - +
24E ASN* 3.5 24.7 + - + -
30E CYS* 3.3 1.9 - - - -
31E GLN* 2.9 64.4 + - + -
32E THR 3.7 17.0 - - - -
33E PHE* 3.6 23.3 - + + -
43E ASN* 3.5 28.3 - - - +
45E PHE* 4.5 0.2 - - - -
51E CYS* 3.6 6.5 - - - -
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Residues in contact with TYR 23 (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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1E ARG* 3.2 39.4 + - - -
5E CYS* 3.4 29.9 - - + +
6E LEU* 5.0 0.2 - - + -
7E GLU 4.6 1.2 - - - +
22E PHE* 1.3 78.2 - - - +
24E ASN* 1.3 56.5 + - - +
25E ALA* 3.4 30.2 + - + -
28E GLY* 3.5 19.9 + - - -
29E LEU 3.7 26.5 - - - -
30E CYS* 4.0 2.5 - - - -
43E ASN* 2.8 31.2 + - - +
51E CYS* 3.6 6.4 - - - -
55E CYS* 3.4 35.0 - - + -
56E GLY 3.7 19.5 - - - -
57E GLY* 4.4 1.2 + - - -
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Residues in contact with ASN 24 (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 PHE* 3.5 19.1 + - + -
23E TYR* 1.3 71.1 - - - +
25E ALA* 1.3 59.2 + - - +
26E LYS* 3.0 23.6 + - - +
27E ALA* 3.1 15.9 + - + +
28E GLY 2.8 24.4 + - - -
29E LEU 3.0 21.9 + - - +
31E GLN* 2.9 32.3 + - + +
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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