Contacts of the strand formed by residues 45 - 50 (chain E) in PDB entry 4WCI
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 45 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15E ASP 3.5 22.8 + - - -
16E ASP* 3.9 10.5 + - - +
17E GLU 3.4 23.1 + - - -
18E LEU* 3.6 17.0 - - + +
19E THR 5.2 1.8 - - - +
41E GLU* 3.3 5.1 - - - +
42E LEU 2.8 37.5 + - - +
43E ASN* 3.4 2.9 - - + +
44E GLY* 1.3 79.8 - - - +
46E ARG* 1.3 85.5 + - - +
47E GLY* 4.1 0.4 - - - -
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Residues in contact with ARG 46 (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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21A ARG* 6.3 2.2 - - + -
22A VAL* 4.0 7.9 + - - +
18E LEU* 3.9 0.9 - - - -
28E ASN* 2.9 51.6 + - - +
30E LYS* 3.8 14.5 - - - +
39E GLU* 2.7 44.7 + - - +
40E GLY* 3.2 14.9 - - - +
41E GLU* 3.9 17.2 - - + +
45E ARG* 1.3 99.5 + - - +
47E GLY* 1.3 58.4 + - - +
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Residues in contact with GLY 47 (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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16E ASP 3.3 11.7 - - - -
18E LEU* 3.6 19.6 - - - +
39E GLU* 3.3 8.9 + - - -
40E GLY 3.0 33.1 + - - +
45E ARG* 4.1 1.1 - - - -
46E ARG* 1.3 76.2 - - - +
48E MET* 1.3 66.3 + - - -
49E PHE* 3.9 0.2 - - - -
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Residues in contact with MET 48 (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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10E TYR* 5.5 0.2 - - - -
16E ASP* 2.8 39.2 + - + +
17E GLU* 3.4 10.3 - - + +
18E LEU 2.9 24.4 + - - +
32E LEU* 4.3 16.8 - - + +
34E GLU* 4.0 19.7 - - + +
37E TRP* 3.9 34.3 - - + +
38E LEU 3.2 23.6 - - - +
39E GLU* 3.5 26.7 - - + -
47E GLY* 1.3 72.1 - - - -
49E PHE* 1.3 62.7 + - - +
388F ARG* 3.8 7.6 - - - +
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Residues in contact with PHE 49 (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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4E TYR* 4.5 4.0 - + + -
18E LEU* 4.0 12.6 - - + +
20E ILE* 4.5 8.3 - - + -
26E ILE* 3.6 35.7 - - + -
29E VAL* 3.9 20.6 - - + -
37E TRP* 3.3 6.9 - - - -
38E LEU* 2.9 59.0 + - + -
39E GLU 3.7 20.2 - - - -
47E GLY 3.9 6.3 - - - -
48E MET* 1.3 80.1 - - - +
50E PRO* 1.3 76.2 - - + +
54E VAL* 3.6 43.1 - - + -
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Residues in contact with PRO 50 (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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10E TYR* 4.1 23.3 - - + -
20E ILE* 4.6 3.8 - - + -
36E GLY 3.8 6.3 - - - +
37E TRP* 3.4 17.9 - - + -
49E PHE* 1.3 89.5 - - + +
51E ASP* 1.3 64.7 + - - +
52E ASN* 3.2 8.5 + - - +
53E PHE* 3.2 48.8 + - + +
54E VAL* 3.8 7.1 - - - +
385F ALA* 3.9 9.6 - - + -
386F PRO* 3.8 14.1 - - + -
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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