Contacts of the strand formed by residues 19 - 25 (chain F) 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 VAL 19 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1F ILE* 4.9 0.2 - - - -
3F CYS* 4.0 5.4 - - - -
17F GLY 3.0 1.8 + - - +
18F HIS* 1.3 85.1 - - + +
20F CYS* 1.3 63.2 + - - +
21F TYR* 4.1 4.2 + - + -
41F CYS* 3.2 9.0 - - - +
42F ALA* 3.1 48.0 + - + +
44F THR* 3.4 30.3 - - - +
45F CYS* 3.9 14.6 - - + +
56F CYS* 4.3 18.2 - - + -
57F CYS 3.7 10.5 - - - +
58F SER* 5.7 1.1 - - - +
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Residues in contact with CYS 20 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1F ILE* 4.1 12.3 - - - -
2F ARG 4.1 5.6 - - - -
3F CYS* 2.0 49.1 - - - -
19F VAL* 1.3 72.4 - - - +
21F TYR* 1.3 59.9 + - - +
40F GLY 3.6 2.7 - - - -
55F GLN 3.7 0.3 - - - +
56F CYS* 3.4 5.0 - - - -
57F CYS* 3.1 40.2 + - - -
59F THR 4.2 1.6 - - - -
62F CYS* 3.9 16.4 - - - -
63F ASN* 3.5 22.2 - - - +
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Residues in contact with TYR 21 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19F VAL* 4.9 3.8 - - + -
20F CYS* 1.3 73.7 - - - +
22F THR* 1.3 64.8 + - - +
23F LYS* 3.4 45.2 + - + -
38F ASP* 4.0 11.5 + - - -
39F LEU* 3.6 4.1 - - - -
40F GLY* 2.9 32.7 + - - -
41F CYS 3.8 12.4 + - - -
42F ALA* 3.4 33.0 - - + -
46F PRO* 4.4 24.9 - - + -
54F ILE* 5.0 2.2 - - + -
55F GLN 3.5 3.4 - - - +
56F CYS* 4.2 17.5 - - - -
63F ASN* 3.3 16.2 + - - -
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Residues in contact with THR 22 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21F TYR* 1.3 76.4 + - - +
23F LYS* 1.3 70.1 + - - +
24F THR* 3.7 13.5 + - + +
37F VAL* 5.0 2.5 - - + -
38F ASP 4.5 0.2 - - - -
39F LEU* 3.7 19.3 - - + -
53F ASP 3.5 5.5 - - - +
54F ILE* 3.5 2.8 - - - -
55F GLN* 3.0 45.4 + - + +
63F ASN* 3.3 28.0 + - - +
64F PRO 5.3 3.4 - - - +
66F PRO* 5.9 5.6 - - + -
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Residues in contact with LYS 23 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21F TYR* 3.4 36.1 + - + -
22F THR* 1.3 74.1 - - - +
24F THR* 1.3 67.4 + - - +
25F TRP* 4.4 21.7 - - + -
36F ARG 4.5 0.2 - - - -
37F VAL* 3.4 19.7 - - - +
38F ASP* 3.6 38.8 + - + +
46F PRO* 5.4 4.7 - - + -
52F VAL* 5.6 9.0 - - + -
53F ASP 3.7 4.5 - - - -
54F ILE* 4.0 18.6 - - + -
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Residues in contact with THR 24 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186A SER* 5.7 1.1 - - - -
22F THR* 3.7 15.0 + - + +
23F LYS* 1.3 81.4 - - - +
25F TRP* 1.3 61.9 + - - +
35F LYS* 3.8 21.1 + - + -
36F ARG 3.3 7.0 - - - +
37F VAL* 3.8 21.5 - - + -
52F VAL* 4.9 0.8 - - - +
53F ASP* 2.9 54.0 + - - +
54F ILE 5.3 0.5 - - - -
66F PRO* 5.9 6.1 - - + -
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Residues in contact with TRP 25 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163B GLU* 4.5 21.4 + - - +
23F LYS* 4.4 18.6 - - + -
24F THR* 1.3 82.7 - - - +
26F CYS* 1.3 72.7 + - - +
27F ASP* 3.7 16.9 + - + +
35F LYS* 3.3 11.6 - - - +
36F ARG* 2.9 100.3 + - + +
38F ASP* 4.3 23.1 - - + -
51F GLY 5.4 2.0 - - - +
52F VAL* 3.7 29.8 - - + +
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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