Contacts of the strand formed by residues 36 - 42 (chain I) in PDB entry 1YI5
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 36 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139D LYS* 5.6 5.1 - - - +
183D VAL* 3.1 37.5 - - - +
184D THR 3.1 20.4 - - - +
185D TYR* 3.6 40.0 + - + -
186D SER 4.2 0.2 - - - +
163E GLU* 5.8 1.6 + - - -
164E TYR* 6.2 1.8 - - - -
24I THR* 3.3 5.7 - - - -
25I TRP* 2.8 79.3 + - + +
27I ASP* 4.9 5.2 + - - +
30I CYS* 4.6 0.2 - - - -
34I GLY 3.6 1.8 + - - -
35I LYS* 1.3 73.9 - - - +
37I VAL* 1.3 60.0 + - - +
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Residues in contact with VAL 37 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184D THR* 3.6 31.1 + - + +
186D SER* 3.0 35.5 - - - +
6I THR* 4.1 1.6 + - - +
22I THR* 5.2 0.4 - - + -
23I LYS 3.4 14.1 - - - +
24I THR* 3.9 14.8 - - + -
25I TRP* 4.7 1.3 - - - -
35I LYS 3.8 0.4 + - - -
36I ARG* 1.3 73.9 - - - +
38I ASP* 1.3 57.8 + - - +
39I LEU* 3.3 32.8 + - + -
65I PHE* 4.0 22.4 - - + -
66I PRO* 5.4 7.9 - - + -
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Residues in contact with ASP 38 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184D THR* 5.6 1.2 + - - -
6I THR* 3.1 26.6 - - - +
21I TYR* 3.5 22.3 + - - -
23I LYS* 2.7 55.0 + - + +
25I TRP* 4.1 15.4 - - + -
37I VAL* 1.3 70.8 - - - +
39I LEU* 1.3 65.1 + - - +
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Residues in contact with LEU 39 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4I PHE* 3.5 23.3 - - + +
5I ILE* 5.0 1.6 - - - +
6I THR* 3.5 34.5 + - - +
8I ASP 6.0 1.3 - - - +
21I TYR* 3.7 9.0 + - - +
22I THR* 3.8 33.4 - - + +
37I VAL* 3.3 31.4 - - + -
38I ASP* 1.3 83.6 - - - +
40I GLY* 1.3 59.4 + - - +
63I ASN* 4.0 17.3 - - - +
64I PRO 4.4 12.3 - - - +
65I PHE* 4.4 13.0 - - + +
66I PRO* 5.9 0.7 - - + -
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Residues in contact with GLY 40 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3I CYS* 4.2 2.4 - - - +
4I PHE 3.3 12.7 + - - -
5I ILE* 4.0 12.1 - - - -
20I CYS* 3.5 4.3 - - - -
21I TYR* 2.9 44.1 + - - -
39I LEU* 1.3 77.8 - - - +
41I CYS* 1.3 60.5 + - - -
63I ASN* 3.5 4.2 + - - +
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Residues in contact with CYS 41 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3I CYS* 3.8 14.8 - - + -
5I ILE* 4.2 20.4 - - - +
14I CYS* 2.0 52.5 - - + -
17I GLY* 4.7 2.5 - - - +
19I VAL 3.2 13.9 - - - +
21I TYR* 3.8 8.7 + - - -
40I GLY* 1.3 73.5 - - - -
42I ALA* 1.3 65.4 + - - +
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Residues in contact with ALA 42 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17I GLY* 2.9 28.0 - - - -
18I HIS 2.9 2.6 + - - -
19I VAL* 3.1 14.4 + - + +
21I TYR* 3.8 20.0 - - + -
41I CYS* 1.3 78.6 - - - +
43I ALA* 1.3 63.2 + - - +
44I THR 3.4 16.4 - - - +
46I PRO* 5.9 1.1 - - + -
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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