Contacts of the strand formed by residues 40 - 47 (chain C) in PDB entry 1YCY
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 40 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36C PHE* 3.4 1.2 - - - -
37C ASP* 2.9 46.7 + - - +
39C GLU* 1.3 81.8 - - + +
41C ILE* 1.3 65.5 + - - +
58C LEU* 4.0 22.0 - - + -
59C ILE 3.1 10.5 - - - +
60C GLY* 3.4 23.3 - - - +
61C LEU* 4.2 2.0 - - - +
6D LEU* 4.0 5.8 - - + -
7D LEU* 4.0 39.3 - - + +
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Residues in contact with ILE 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C LEU* 4.3 10.3 - - + -
21C VAL* 4.4 9.9 - - + -
33C LEU* 4.2 8.3 - - + -
35C ASP 3.5 8.5 - - - +
36C PHE* 3.7 15.5 - - + +
40C VAL* 1.3 79.2 - - - +
42C LEU* 1.3 59.7 + - - +
43C LEU* 3.3 27.1 - - + -
57C MSE 3.6 0.9 - - - +
58C LEU* 3.4 5.0 - - - +
59C ILE* 2.6 60.0 + - + +
61C LEU* 3.4 24.9 - - + -
64C ILE* 4.0 12.1 - - + -
67C ILE* 4.7 13.0 - - + -
6D LEU* 5.7 0.4 - - - -
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Residues in contact with LEU 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C LEU* 3.7 0.7 - - - +
34C GLU* 2.9 38.9 + - + -
35C ASP* 2.7 30.7 + - + +
41C ILE* 1.3 74.2 - - - +
43C LEU* 1.3 65.4 + - - +
56C GLN* 3.9 30.1 - - + +
57C MSE 3.3 28.7 - - - +
58C LEU* 4.3 11.4 - - + +
6D LEU* 4.8 5.8 - - + +
10D VAL* 4.0 21.5 - - + -
13D GLU* 6.0 0.2 - - - +
14D TRP* 4.0 9.9 - - + -
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Residues in contact with LEU 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C VAL* 4.5 4.7 - - + -
21C VAL* 3.9 22.9 - - + -
29C PHE* 5.1 3.1 - - + +
30C THR* 4.6 3.8 - - - +
31C GLY 3.9 32.1 - - - +
32C THR 3.4 2.5 - - - +
33C LEU* 3.6 15.7 - - + -
41C ILE* 3.3 32.1 - - + -
42C LEU* 1.3 79.0 - - - +
44C LYS* 1.3 59.5 - - - +
46C VAL* 3.7 18.7 - - + +
56C GLN* 3.2 6.6 - - - +
57C MSE 2.7 46.4 + - + +
59C ILE* 4.1 10.1 - - + -
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Residues in contact with LYS 44 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31C GLY 3.7 0.5 - - - -
32C THR* 2.7 52.6 + - + +
34C GLU* 4.1 17.5 - - + +
42C LEU 4.2 0.4 + - - -
43C LEU* 1.3 70.6 - - - +
45C ASP* 1.3 89.1 + - - +
46C VAL 3.4 2.4 + - - -
55C LYS 3.7 7.2 - - - +
56C GLN* 4.2 12.1 - - + +
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Residues in contact with ASP 45 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C LYS* 5.2 0.7 + - - -
31C GLY* 3.8 6.8 - - - -
32C THR* 5.0 5.8 + - - +
44C LYS* 1.3 94.8 - - + +
46C VAL* 1.3 66.2 + - - +
47C VAL* 3.5 13.7 - - + +
52C ASN* 5.7 1.1 - - - +
54C GLY 4.4 2.2 - - - -
55C LYS* 2.9 21.7 + - - +
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Residues in contact with VAL 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C PHE* 4.0 21.5 - - + -
30C THR 3.5 11.0 - - - +
31C GLY* 4.3 0.9 - - - -
43C LEU* 3.7 30.3 - - + +
44C LYS 4.5 0.4 - - - +
45C ASP* 1.3 78.2 - - - +
47C VAL* 1.3 64.2 + - - +
52C ASN* 3.9 4.3 - - - +
53C ARG* 3.0 37.9 + - + +
54C GLY 3.5 19.0 + - - +
56C GLN 5.1 0.4 - - - +
57C MSE 3.6 38.8 - - + +
68D MSE 5.2 2.0 - - - -
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Residues in contact with VAL 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C LYS* 4.4 12.8 - - - +
29C PHE* 3.7 8.7 - - - -
30C THR* 2.7 49.6 + - + +
45C ASP* 3.5 12.3 - - + +
46C VAL* 1.3 82.7 - - - +
48C ASP* 1.3 84.8 + - - +
51C GLY* 3.7 11.4 - - - +
52C ASN* 4.2 13.7 - - - +
53C ARG* 4.2 2.5 - - - +
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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