Contacts of the strand formed by residues 23 - 27 (chain E) in PDB entry 4WFN
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 23 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20E GLN* 2.7 31.9 + - - +
21E ASP* 4.9 9.0 - - + +
22E GLY* 1.3 81.5 - - - +
24E PHE* 1.3 62.6 + - - +
25E LYS* 5.4 1.9 - - + +
36E PRO* 5.8 5.4 - - + -
37E TYR 5.6 0.9 - - - +
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Residues in contact with PHE 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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18E ASN 3.8 6.3 - - - +
19E ALA* 3.7 30.3 - - + -
20E GLN 3.8 6.5 - - - -
21E ASP 3.0 25.4 - - - -
22E GLY* 3.2 23.3 + - - -
23E VAL* 1.3 76.6 - - - +
25E LYS* 1.3 61.1 + - - +
26E VAL* 6.4 0.2 - - + -
34E THR* 4.8 3.1 - - - -
35E VAL 3.5 23.8 + - - +
36E PRO* 5.0 0.9 - - - +
37E TYR* 3.4 46.3 - + + +
38E ASN 3.9 11.9 - - - -
39E THR* 5.4 1.3 - - - -
41E LEU 5.2 3.6 - - - -
43E VAL* 3.5 34.1 - - + -
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Residues in contact with LYS 25 (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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17E VAL* 4.2 0.7 - - - +
18E ASN* 2.9 54.9 + - + +
20E GLN* 4.5 10.2 + - - +
23E VAL* 4.2 2.2 + - + +
24E PHE* 1.3 75.8 - - - +
26E VAL* 1.3 73.1 + - - +
27E LYS* 3.8 38.3 - - + +
32E GLU* 4.1 2.9 - - - +
34E THR* 3.8 29.6 - - + +
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Residues in contact with VAL 26 (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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15E VAL* 5.5 1.8 - - + -
16E THR 3.6 8.3 - - - +
17E VAL* 3.7 29.4 - - + -
24E PHE* 6.4 0.2 - - + -
25E LYS* 1.3 83.5 - - - +
27E LYS* 1.3 68.9 + - - +
31E GLY 4.4 0.2 - - - +
33E LEU* 3.1 38.0 + - - +
34E THR* 5.0 0.2 - - - +
35E VAL 5.7 0.2 - - - +
37E TYR* 4.8 16.4 - - + +
72E VAL* 5.1 4.7 - - + -
75E ALA* 5.4 4.5 - - + +
76E VAL* 4.1 23.1 - - + +
79E VAL* 4.1 25.8 - - + +
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Residues in contact with LYS 27 (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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15E VAL* 3.7 5.2 - - - +
16E THR* 2.9 42.4 + - - +
18E ASN* 5.6 4.4 + - - +
25E LYS* 3.8 36.6 - - + +
26E VAL* 1.3 81.2 - - - +
28E GLY* 1.3 58.8 + - - +
31E GLY 4.0 4.7 - - - -
32E GLU* 3.5 39.5 - - + +
79E VAL* 5.1 2.2 - - - -
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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