Contacts of the strand formed by residues 20 - 26 (chain E) in PDB entry 1Y62
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 20 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18E LYS* 3.4 32.4 + - + +
19E ALA* 1.3 78.4 - - - +
21E LYS* 1.3 69.4 + - - +
22E ARG* 3.6 11.8 + - - +
36E ASP* 3.4 12.4 + - - +
37E TYR* 2.8 42.8 + - + +
39E GLY* 3.3 22.5 + - - -
102E SO4 2.6 38.3 + - - +
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Residues in contact with LYS 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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20E GLU* 1.3 80.3 - - - +
22E ARG* 1.3 74.5 + - - +
34E ARG* 3.8 43.1 - - + +
35E PHE 3.6 10.3 - - - +
36E ASP* 3.3 27.9 + - - +
48E ARG* 5.5 2.1 - - - +
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Residues in contact with ARG 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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20E GLU* 3.6 8.2 + - + +
21E LYS* 1.3 81.8 + - - +
23E ILE* 1.3 67.1 + - - +
34E ARG* 3.2 8.1 - - - +
35E PHE* 3.1 50.3 + - + -
37E TYR* 3.3 47.2 - - + -
39E GLY* 5.1 1.2 - - - -
46E ASN* 3.3 23.5 + - - +
47E PHE 3.7 8.5 - - - +
48E ARG* 3.0 48.5 - - - +
102E SO4 2.9 37.2 + - - -
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Residues in contact with ILE 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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22E ARG* 1.3 75.9 - - - +
24E TYR* 1.3 64.7 + - - +
32E CYS* 3.5 34.1 - - + +
33E LEU 3.3 11.0 - - - +
34E ARG* 3.5 33.2 - - + +
35E PHE* 3.7 1.2 - - - -
46E ASN* 3.4 6.6 - - - -
47E PHE* 2.8 47.3 + - + +
48E ARG 4.7 4.5 - - - +
49E ARG 4.2 0.7 - - - -
50E THR* 3.6 35.9 - - - +
53E CYS* 3.8 11.4 - - + -
109E SO4 5.3 1.8 - - - +
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Residues in contact with TYR 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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9E LEU 5.1 0.4 - - - -
11E ALA* 3.7 27.1 - - + -
23E ILE* 1.3 74.0 - - - +
25E TYR* 1.3 70.0 + - - +
26E ASN* 3.4 37.4 + - + -
32E CYS* 3.3 1.6 - - - -
33E LEU* 2.9 67.6 + - + +
34E ARG 3.4 20.4 - - - -
35E PHE* 3.5 25.6 - + + -
45E ASN* 3.4 31.6 - - - +
47E PHE* 4.7 0.4 - - - -
53E CYS* 3.8 6.1 - - - -
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Residues in contact with TYR 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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3E ARG* 5.0 11.0 + - - -
7E CYS* 3.5 28.3 - - + +
8E ASP* 5.1 1.1 - - - -
9E LEU 4.4 1.2 - - - +
24E TYR* 1.3 77.5 - - - +
26E ASN* 1.3 57.3 - - - +
27E SER* 3.5 23.7 + - - -
30E LYS* 3.6 51.4 - - - +
31E GLN 3.5 10.8 - - - -
32E CYS* 4.0 10.8 - - - -
45E ASN* 2.8 32.0 + - - +
53E CYS* 3.7 9.5 - - - -
57E CYS* 3.4 50.8 + - + -
58E LEU* 4.0 13.2 - - + +
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Residues in contact with ASN 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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24E TYR* 3.4 26.5 + - + -
25E TYR* 1.3 71.9 - - - +
27E SER* 1.3 51.3 + - - +
28E ALA* 3.0 13.7 + - - +
29E ARG* 2.9 43.8 + - + +
30E LYS* 2.7 36.0 + - - -
31E GLN 2.8 16.5 + - - +
33E LEU* 3.7 13.7 - - + -
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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