Contacts of the helix formed by residues 61 - 71 (chain C) in PDB entry 2YYN
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 ASP 61 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41C PHE* 3.6 13.0 - - - +
43C ASP 3.8 15.5 - - - +
44C PRO* 3.3 30.6 - - + +
59C PRO 5.2 0.7 - - - -
60C MET* 1.3 83.7 + - - +
62C LEU* 1.3 65.6 + - - +
63C SER* 2.5 30.3 + - - -
64C THR* 2.8 30.5 + - - -
65C ILE* 3.3 22.5 + - - +
89C ILE* 3.7 10.8 - - - -
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Residues in contact with LEU 62 (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 LEU* 3.8 10.2 - - + +
32C LEU* 3.8 37.2 - - + -
33C TYR* 3.6 22.9 - - + +
38C SER* 4.0 26.9 - - - +
41C PHE* 2.9 29.1 + - + +
42C GLN* 4.0 8.3 - - + -
61C ASP* 1.3 69.2 - - - +
63C SER* 1.3 67.2 + - - +
65C ILE* 3.1 6.4 + - + +
66C LYS* 3.0 22.2 + - - +
86C PHE* 3.8 13.5 - - + -
89C ILE* 3.8 19.7 - - + -
110C LEU* 5.0 3.1 - - + -
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Residues in contact with SER 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C TYR* 3.3 12.9 + - - -
42C GLN 2.9 19.1 + - - -
43C ASP* 4.4 8.7 - - - -
44C PRO* 3.7 12.1 - - - +
61C ASP* 2.5 22.0 + - - -
62C LEU* 1.3 76.0 - - - +
64C THR* 1.3 56.5 + - - +
66C LYS* 3.3 7.5 + - - +
67C LYS* 2.9 46.0 + - - +
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Residues in contact with THR 64 (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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44C PRO* 4.4 4.5 - - - +
60C MET* 3.8 17.3 - - + -
61C ASP* 2.8 35.1 + - - -
62C LEU 3.1 0.4 - - - -
63C SER* 1.3 76.8 + - - +
65C ILE* 1.3 59.7 + - - +
67C LYS* 3.1 8.6 + - + +
68C ARG* 2.9 61.3 + - + +
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Residues in contact with ILE 65 (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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25C CYS* 4.3 9.0 - - - -
29C LEU* 4.1 13.7 - - + -
60C MET* 3.9 4.3 - - - -
61C ASP 3.3 10.1 + - - +
62C LEU* 3.1 8.0 + - + +
64C THR* 1.3 76.2 - - - +
66C LYS* 1.3 63.1 + - - +
68C ARG* 3.2 4.1 + - - +
69C LEU* 3.2 20.8 + - - +
76C TYR* 3.3 30.9 - - + +
82C PHE* 4.6 1.1 - - + -
85C ASP* 3.8 12.8 - - + +
86C PHE* 3.6 62.8 - - + +
89C ILE* 4.0 12.8 - - + -
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Residues in contact with LYS 66 (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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23B ARG* 5.3 9.2 - - - +
26B GLU* 5.5 11.1 - - - +
30B LEU* 6.0 2.8 - - - +
66B LYS* 5.8 4.2 - - - +
29C LEU* 3.8 26.2 - - + +
33C TYR* 3.5 40.0 - - - +
62C LEU 3.0 11.5 + - - +
63C SER* 3.5 10.3 - - - +
65C ILE* 1.3 78.0 - - - +
67C LYS* 1.3 64.4 + - + +
69C LEU* 3.2 12.8 + - - +
70C GLN* 3.4 34.7 + - - +
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Residues in contact with LYS 67 (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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63C SER* 2.9 35.3 + - - +
64C THR* 3.1 11.2 + - + +
66C LYS* 1.3 78.9 - - + +
68C ARG* 1.3 60.2 + - + +
69C LEU 3.2 0.2 + - - -
70C GLN* 3.3 10.7 + - - +
71C GLU* 3.0 38.7 + - + +
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Residues in contact with ARG 68 (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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60C MET* 3.6 24.0 - - - +
64C THR* 2.9 35.3 + - + +
65C ILE 3.6 0.2 - - - +
67C LYS* 1.3 77.8 - - + +
69C LEU* 1.3 60.0 + - - +
71C GLU* 4.0 28.8 + - - +
74C SER* 5.3 2.8 - - - -
75C MET* 3.9 46.0 + - + +
76C TYR* 3.6 41.5 - - + +
85C ASP* 3.1 22.4 + - - -
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Residues in contact with LEU 69 (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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17C LEU* 3.8 28.8 - - + +
22C LYS* 3.6 52.7 + - + +
25C CYS* 3.7 25.6 - - + -
26C GLU* 3.7 18.2 - - + +
29C LEU* 4.1 9.9 - - + -
65C ILE 3.2 10.4 + - - +
66C LYS* 3.6 10.1 - - + +
67C LYS 3.1 1.0 - - - -
68C ARG* 1.3 78.2 - - - +
70C GLN* 1.3 63.0 + - + +
71C GLU 3.5 2.4 - - - +
76C TYR* 4.3 12.1 - - + -
82C PHE* 5.1 0.7 - - + -
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Residues in contact with GLN 70 (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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22B LYS* 5.3 4.9 - - - +
26B GLU* 5.0 10.8 + - - +
70B GLN* 3.6 39.5 - - + +
22C LYS* 4.9 6.7 - - - +
26C GLU* 5.7 4.2 - - - +
66C LYS* 3.6 35.7 + - - +
67C LYS* 3.3 10.1 + - - +
69C LEU* 1.3 83.2 - - + +
71C GLU* 1.3 64.8 - - - +
72C ASP* 3.7 9.4 + - - +
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Residues in contact with GLU 71 (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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67C LYS* 3.0 30.8 + - + +
68C ARG* 4.0 25.4 - - - +
69C LEU 3.5 3.7 - - - +
70C GLN* 1.3 82.7 - - - +
72C ASP* 1.3 59.4 + - - +
73C TYR* 3.2 38.9 + - + +
74C SER* 4.0 12.0 + - - +
75C MET* 4.8 12.0 + - - +
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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