Contacts of the strand formed by residues 40 - 47 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36D PHE* 3.3 2.1 - - - -
37D ASP* 2.8 55.4 + - - +
39D GLU* 1.3 84.7 - - + +
41D ILE* 1.3 69.5 + - - +
58D LEU* 4.3 23.1 - - + -
59D ILE 3.4 18.6 - - - +
60D GLY* 3.8 7.6 - - - +
61D LEU* 4.4 2.0 - - - +
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Residues in contact with ILE 41 (chain D).
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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11D LEU* 4.6 9.2 - - + -
19D VAL* 5.8 0.4 - - + -
21D VAL* 4.4 20.6 - - + -
33D LEU* 3.8 16.2 - - + -
35D ASP 3.5 5.6 - - - +
36D PHE* 3.7 13.9 - - + +
40D VAL* 1.3 82.3 - - - +
42D LEU* 1.3 61.0 + - - +
43D LEU* 3.8 22.2 - - + -
57D MSE 3.7 1.0 - - - +
58D LEU* 3.7 4.0 - - - +
59D ILE* 2.9 47.5 + - + +
61D LEU* 3.6 22.2 - - + -
64D ILE* 5.1 4.9 - - + -
67D ILE* 4.7 15.3 - - + -
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Residues in contact with LEU 42 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33D LEU* 3.6 1.4 - - - +
34D GLU* 3.0 46.5 + - + +
35D ASP* 2.7 27.6 + - + +
41D ILE* 1.3 74.9 - - - +
43D LEU* 1.3 72.8 + - - +
56D GLN* 3.3 39.9 - - + +
57D MSE 3.3 15.3 - - - +
58D LEU* 4.2 18.8 - - + -
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Residues in contact with LEU 43 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D VAL* 4.8 2.2 - - + -
21D VAL* 4.1 21.1 - - + -
29D PHE 5.2 2.0 - - - +
30D THR* 4.4 3.6 - - - -
31D GLY 4.0 27.4 - - - +
32D THR 3.2 10.8 - - - +
33D LEU* 4.1 10.1 - - + -
34D GLU* 4.6 0.7 - - - -
41D ILE* 3.8 28.9 - - + -
42D LEU* 1.3 87.6 - - - +
44D LYS* 1.3 59.1 + - - +
46D VAL* 3.7 20.2 - - + -
56D GLN* 3.1 27.9 - - - +
57D MSE 3.0 18.9 + - + +
59D ILE* 4.2 13.7 - - + -
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Residues in contact with LYS 44 (chain D).
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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31D GLY* 3.6 2.8 - - - -
32D THR* 2.7 38.2 + - + +
34D GLU* 3.7 25.0 - - + +
43D LEU* 1.3 73.7 - - - +
45D ASP* 1.3 79.2 + - - +
46D VAL* 3.2 3.2 + - - +
55D LYS 3.4 7.4 - - - +
56D GLN* 4.6 1.1 - - + +
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Residues in contact with ASP 45 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31D GLY* 3.9 7.4 - - - -
32D THR* 4.6 11.8 + - - +
44D LYS* 1.3 81.8 - - + +
46D VAL* 1.3 63.7 + - - +
47D VAL* 3.5 5.7 + - - +
52D ASN* 6.3 0.4 - - - -
54D GLY 4.4 1.6 - - - -
55D LYS* 3.0 13.6 + - - +
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Residues in contact with VAL 46 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29D PHE* 4.0 30.3 - - + -
30D THR 3.3 14.1 - - - +
43D LEU* 3.7 36.1 - - + +
44D LYS 3.9 4.5 - - - +
45D ASP* 1.3 75.7 - - - +
47D VAL* 1.3 55.3 + - - +
52D ASN* 3.6 4.4 - - - +
53D ARG* 2.7 38.5 + - + -
54D GLY* 3.2 22.5 + - - +
57D MSE 3.9 24.0 - - + -
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Residues in contact with VAL 47 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29D PHE* 4.1 5.9 - - - -
30D THR* 2.8 44.3 + - + +
45D ASP 3.5 5.1 + - - +
46D VAL* 1.3 74.1 - - - +
48D ASP* 1.3 65.2 + - - +
51D GLY 3.3 15.9 - - - +
52D ASN* 4.1 3.1 - - + +
53D ARG* 4.2 4.5 - - - +
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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