Contacts of the strand formed by residues 52 - 60 (chain B) 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 ASN 52 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46B VAL 4.0 5.8 - - - +
47B VAL* 4.2 7.8 - - - +
51B GLY* 1.3 78.3 - - - -
53B ARG* 1.3 78.3 + - - +
54B GLY 4.8 2.9 - - - +
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Residues in contact with ARG 53 (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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68A MSE 3.5 34.3 - - + +
70A LEU* 3.9 8.0 - - - +
29B PHE* 3.6 28.3 - - + -
46B VAL* 2.9 17.6 + - + +
48B ASP* 3.7 26.1 - - + +
50B ILE* 6.2 1.3 - - - -
51B GLY 4.3 3.4 - - - +
52B ASN* 1.3 90.3 + - - +
54B GLY* 1.3 59.2 + - - +
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Residues in contact with GLY 54 (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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68A MSE 4.0 7.5 - - - -
69A LEU 3.4 8.7 - - - -
70A LEU* 4.3 5.4 - - - -
45B ASP* 4.5 0.8 - - - -
46B VAL* 3.4 27.1 + - - +
52B ASN* 3.9 3.2 - - - +
53B ARG* 1.3 81.4 - - - +
55B LYS* 1.3 68.3 + - - +
56B GLN* 3.0 5.9 + - - +
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Residues in contact with LYS 55 (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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69A LEU* 2.8 26.4 + - + +
70A LEU* 4.4 9.6 - - - +
44B LYS* 3.8 1.9 - - - +
45B ASP* 3.2 26.7 + - - +
54B GLY* 1.3 69.8 - - - -
56B GLN* 1.3 68.2 + - + +
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Residues in contact with GLN 56 (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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10A VAL* 4.8 1.2 - - - +
13A GLU* 4.8 5.9 + - - +
14A TRP* 3.1 39.2 + - + -
68A MSE 3.2 12.1 - - - +
69A LEU* 3.1 29.0 + - + +
34B GLU* 2.5 37.3 + - - +
42B LEU* 3.8 13.4 - - + +
43B LEU 3.3 12.3 - - - +
44B LYS* 4.6 2.4 - - + +
46B VAL* 4.6 0.7 - - - -
54B GLY 3.0 4.0 + - - +
55B LYS* 1.3 88.4 - - + +
57B MSE 1.3 62.3 + - - +
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Residues in contact with MSE 57 (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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14A TRP* 4.0 0.7 - - - -
66A TRP* 4.1 30.3 - - + -
67A ILE 3.5 9.6 - - - +
68A MSE 4.2 9.0 - - + +
21B VAL* 5.7 3.6 - - + -
23B VAL* 6.1 2.2 - - + -
29B PHE* 4.1 30.5 - - + -
41B ILE 3.6 0.5 - - - +
42B LEU* 3.3 8.1 - - - -
43B LEU* 2.8 35.3 + - + +
46B VAL* 3.7 34.8 - - + -
56B GLN* 1.3 80.2 - - - +
58B LEU* 1.3 70.6 + - - +
59B ILE* 3.2 35.0 - - + +
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Residues in contact with LEU 58 (chain B).
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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6A LEU* 4.7 4.0 - - + +
7A LEU* 3.7 26.5 - - + +
10A VAL* 4.1 41.3 - - + -
11A LEU* 4.2 17.5 - - + -
14A TRP* 3.9 10.9 - - + -
66A TRP* 3.3 19.4 - - - +
67A ILE* 2.9 26.5 + - + +
40B VAL* 4.3 22.4 - - + -
41B ILE 3.4 10.5 - - - +
42B LEU* 4.5 9.4 - - + -
57B MSE 1.3 71.0 - - - +
59B ILE* 1.3 69.2 + - - +
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Residues in contact with ILE 59 (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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65A ASN 4.1 14.8 - - - +
66A TRP* 4.4 1.6 - - + +
21B VAL* 4.6 11.4 - - + -
23B VAL* 4.7 13.2 - - + -
40B VAL* 3.2 5.4 - - - -
41B ILE* 2.8 47.9 + - + +
43B LEU* 4.1 26.7 - - + -
57B MSE 3.2 40.8 - - + +
58B LEU* 1.3 83.9 - - - +
60B GLY* 1.3 73.0 + - - +
63B ASP* 5.8 0.4 - - + -
64B ILE* 4.0 14.9 - - + +
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Residues in contact with GLY 60 (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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65A ASN 4.1 7.9 + - - -
39B GLU 3.4 10.1 - - - -
40B VAL* 3.8 7.7 - - - +
59B ILE* 1.3 78.5 - - - +
61B LEU* 1.3 64.9 + - - -
62B GLU* 3.4 3.8 - - - -
63B ASP* 3.6 12.2 + - - +
64B ILE* 3.4 15.3 + - - +
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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