Contacts of the strand formed by residues 20 - 26 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18B LYS* 3.7 22.5 - - + +
19B ALA* 1.3 79.0 - - - +
21B LYS* 1.3 69.8 + - - +
22B ARG* 3.1 32.2 + - - +
36B ASP* 3.5 9.5 - - - +
37B TYR* 3.0 31.2 + - + +
39B GLY* 3.8 13.7 + - - -
101B SO4 2.4 35.7 + - - -
47D PHE* 4.1 0.9 - - - -
52D ASP* 3.4 35.2 - - + +
55D ARG* 4.0 1.1 - - - +
56D THR* 5.0 0.2 - - - +
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Residues in contact with LYS 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B GLU* 1.3 76.2 - - - +
22B ARG* 1.3 77.6 + - - +
23B ILE* 6.0 0.2 - - - -
34B ARG* 3.7 43.6 - - + +
35B PHE* 3.3 11.7 - - - +
36B ASP* 2.7 31.9 + - - +
48B ARG* 5.5 2.4 - - - +
52D ASP* 4.5 0.8 + - - +
55D ARG* 3.3 30.1 - - - +
111D SO4 3.5 22.2 + - - +
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Residues in contact with ARG 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B GLU* 3.1 38.0 + - - +
21B LYS* 1.3 85.6 + - - +
23B ILE* 1.3 67.2 + - - +
34B ARG* 3.4 5.7 - - - +
35B PHE* 2.9 53.1 + - + -
37B TYR* 3.5 35.2 - - + +
39B GLY* 5.1 0.6 + - - -
46B ASN* 3.2 25.4 + - - +
47B PHE 3.6 11.4 - - - -
48B ARG* 3.1 58.5 - - - +
101B SO4 3.4 3.6 + - - -
52D ASP* 4.4 5.5 + - - -
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Residues in contact with ILE 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B LYS 6.0 0.2 - - - -
22B ARG* 1.3 81.8 - - - +
24B TYR* 1.3 61.6 + - - +
32B CYS* 3.7 17.3 - - + +
33B LEU 3.3 13.7 - - - +
34B ARG* 4.2 16.8 - - + -
35B PHE* 3.8 1.3 - - - -
46B ASN* 3.5 2.4 - - - -
47B PHE* 2.7 56.6 + - + +
48B ARG 4.4 6.5 - - - +
49B ARG 4.1 0.9 - - - -
50B THR* 3.5 37.0 - - + +
53B CYS* 3.5 25.1 - - + -
99B SO4 5.6 0.7 - - - +
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Residues in contact with TYR 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B LEU 4.9 0.9 - - - -
10B PRO* 5.6 0.4 - - + -
11B ALA* 3.6 31.6 - - + -
23B ILE* 1.3 75.2 - - - +
25B TYR* 1.3 69.6 + - - +
26B ASN* 3.0 40.5 + - + -
32B CYS* 3.5 0.7 - - - -
33B LEU* 2.9 59.6 + - + +
34B ARG 3.9 3.1 - - - -
35B PHE* 3.4 35.0 - + + -
45B ASN* 3.3 31.0 - - - +
53B CYS* 4.0 5.2 - - - -
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Residues in contact with TYR 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3B ARG* 2.9 34.4 + - - -
7B CYS* 3.4 29.7 - - + +
9B LEU 4.1 3.5 - - - +
24B TYR* 1.3 76.0 - - - +
26B ASN* 1.3 61.2 + - - +
27B SER* 3.6 24.0 + - - -
30B LYS* 3.7 20.1 - - - +
31B GLN 3.7 13.7 - - - -
32B CYS* 3.8 14.6 - - - -
45B ASN* 2.8 38.2 + - - +
53B CYS* 3.8 6.8 - - - -
57B CYS* 3.3 40.2 + - + -
58B LEU* 3.7 26.7 - - + +
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Residues in contact with ASN 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B TYR* 3.0 36.0 + - + +
25B TYR* 1.3 71.8 - - - +
27B SER* 1.3 61.5 + - - +
28B ALA* 3.2 14.9 + - - +
29B ARG* 3.1 39.7 + - + +
30B LYS* 3.2 18.2 + - - -
31B GLN 3.1 21.8 + - - +
33B LEU* 4.2 9.6 - - + +
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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