Contacts of the helix formed by residues 57 - 67 (chain C) in PDB entry 1YCH
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 PHE 57 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16C ALA* 3.7 28.0 - - + -
17C VAL 3.6 18.2 - - - -
18C ASP* 3.5 39.0 - - + -
37C TYR* 3.8 16.2 - + + -
53C VAL* 3.5 11.9 - - + +
54C TYR* 2.7 29.0 + + - +
56C PRO* 1.3 84.8 - - + +
58C LYS* 1.3 65.8 + - - +
59C GLU* 3.2 3.6 - - - -
60C GLU* 3.1 24.9 + - + +
61C LEU 3.3 8.3 + - - -
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Residues in contact with LYS 58 (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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53C VAL* 4.2 8.3 - - - -
54C TYR 3.8 1.8 + - - -
55C GLU* 3.0 39.5 + - + +
57C PHE* 1.3 77.2 - - - +
59C GLU* 1.3 87.2 + - + +
61C LEU* 3.1 5.0 + - - +
62C ILE* 3.0 31.3 + - + +
89C ALA* 3.8 21.1 - - + -
92C ALA* 3.8 26.6 - - + +
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Residues in contact with GLU 59 (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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56C PRO* 3.6 15.7 - - - +
57C PHE* 3.9 1.0 - - - -
58C LYS* 1.3 104.6 + - + +
60C GLU* 1.3 57.8 + - + +
62C ILE* 4.0 7.6 - - + +
63C ALA* 2.8 31.1 + - - +
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Residues in contact with GLU 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2C SER* 3.6 11.0 - - - -
15C GLY 5.2 0.4 - - - -
16C ALA* 4.0 22.0 - - + -
57C PHE* 3.1 20.8 + - + +
59C GLU* 1.3 77.9 + - + +
61C LEU* 1.3 65.5 + - - +
63C ALA* 3.6 6.7 - - - +
64C LYS* 2.5 62.4 + - - +
620C ZN 2.7 29.2 - - - -
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Residues in contact with LEU 61 (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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14C VAL* 3.1 47.6 - - + +
15C GLY 5.4 0.6 + - - -
16C ALA* 5.4 0.6 - - - +
39C ALA* 4.0 12.1 - - + -
49C LEU* 4.4 6.3 - - + -
52C THR* 3.9 29.2 - - - -
53C VAL* 4.2 16.8 - - + -
57C PHE 3.3 7.1 + - - +
58C LYS 3.1 8.8 + - - +
60C GLU* 1.3 77.2 - - - +
62C ILE* 1.3 58.5 + - + +
64C LYS* 3.0 5.7 + - - +
65C LEU* 2.8 42.6 + - + +
89C ALA* 4.4 4.9 - - + -
93C ILE* 3.9 24.5 - - + -
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Residues in contact with ILE 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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58C LYS* 3.0 22.1 + - + +
59C GLU* 4.0 6.7 - - + +
61C LEU* 1.3 74.6 - - + +
63C ALA* 1.3 63.1 + - - +
65C LEU* 3.2 9.2 + - - +
66C LYS* 2.9 46.6 + - - +
72C VAL* 5.4 0.4 - - + -
89C ALA* 6.4 0.2 - - + -
92C ALA* 4.3 25.6 - - + +
93C ILE* 4.1 21.5 - - + -
96C LEU* 4.2 24.7 - - + -
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Residues in contact with ALA 63 (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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2C SER* 5.4 4.9 - - - +
59C GLU 2.8 23.5 + - - +
60C GLU* 3.6 13.7 - - - +
61C LEU 3.2 0.2 - - - -
62C ILE* 1.3 74.6 - - - +
64C LYS* 1.3 62.6 + - + +
66C LYS* 3.6 9.8 + - - +
67C GLN* 3.0 29.9 + - - +
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Residues in contact with LYS 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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2C SER 3.1 29.3 - - - +
3C GLN 3.2 29.4 - - - +
4C PRO* 3.3 27.5 - - + +
13C TRP* 3.7 13.1 - - + -
14C VAL* 4.1 20.2 - - + +
15C GLY 3.1 25.9 + - - +
16C ALA* 4.7 1.8 - - - +
60C GLU* 2.5 49.3 + - - +
61C LEU 3.0 3.1 + - - +
63C ALA* 1.3 76.7 - - + +
65C LEU* 1.3 65.7 + - - +
67C GLN* 3.2 13.2 + - - +
68C ILE* 3.6 6.1 + - - +
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Residues in contact with LEU 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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14C VAL* 4.2 8.3 - - + -
41C LEU* 3.7 36.9 - - + +
49C LEU* 4.2 19.7 - - + -
61C LEU* 2.8 28.4 + - + +
62C ILE* 3.2 11.9 + - + +
64C LYS* 1.3 75.0 - - - +
66C LYS* 1.3 58.6 + - - +
68C ILE* 2.9 26.1 + - - +
69C LYS* 3.3 10.7 + - - +
72C VAL* 3.8 28.7 - - + -
74C LEU* 4.5 5.8 - - + -
93C ILE* 3.9 28.0 - - + -
96C LEU* 4.9 0.2 - - + -
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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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62C ILE* 2.9 35.0 + - - +
63C ALA* 3.7 9.8 - - - +
64C LYS 3.2 0.2 - - - -
65C LEU* 1.3 78.8 - - - +
67C GLN* 1.3 61.2 + - + +
68C ILE 3.3 0.7 + - - -
69C LYS 3.5 20.1 + - - -
70C ASP* 3.5 40.6 + - + +
72C VAL* 4.1 13.2 - - + +
96C LEU* 6.2 3.4 - - - -
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Residues in contact with GLN 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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2C SER* 2.8 23.4 + - - +
3C GLN* 2.3 44.8 + - - +
4C PRO* 4.0 10.8 - - + -
63C ALA* 3.0 21.7 + - - +
64C LYS* 3.2 10.8 + - - +
65C LEU 3.1 1.4 + - - -
66C LYS* 1.3 78.4 - - + +
68C ILE* 1.3 63.4 + - - +
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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