Contacts of the helix formed by residues 57 - 67 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16D ALA* 3.5 29.4 - - + -
17D VAL 3.3 22.2 - - - -
18D ASP* 3.4 39.5 - - + -
37D TYR* 4.0 15.0 - + - -
53D VAL* 3.7 16.9 - - + +
54D TYR* 2.8 19.7 + + - -
56D PRO* 1.3 87.4 - - + +
58D LYS* 1.3 66.4 + - - +
59D GLU* 3.2 4.7 - - - -
60D GLU* 3.0 25.3 + - + +
61D LEU 3.3 7.4 + - - -
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Residues in contact with LYS 58 (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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53D VAL* 4.5 0.2 - - - -
54D TYR 3.8 1.0 + - - -
55D GLU* 3.1 39.2 + - + +
56D PRO 3.5 0.4 - - - -
57D PHE* 1.3 78.4 - - - +
59D GLU* 1.3 90.3 + - + +
61D LEU* 3.0 14.5 + - - +
62D ILE* 3.0 25.2 + - + +
89D ALA* 3.8 26.7 - - + -
92D ALA* 3.8 26.7 - - + +
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Residues in contact with GLU 59 (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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56D PRO 3.7 18.0 - - - +
57D PHE* 4.0 1.2 - - - -
58D LYS* 1.3 104.5 - - + +
60D GLU* 1.3 57.5 + - + +
62D ILE* 3.9 7.5 - - + +
63D ALA* 2.8 32.3 + - - +
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Residues in contact with GLU 60 (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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2D SER* 3.7 13.1 + - - -
15D GLY 5.2 0.2 - - - -
16D ALA* 4.1 19.7 - - + -
57D PHE* 3.0 20.8 + - + +
59D GLU* 1.3 77.1 - - + +
61D LEU* 1.3 65.7 + - - +
63D ALA* 3.7 5.9 - - - +
64D LYS* 2.7 63.5 + - - +
630D ZN 2.7 31.6 - - - -
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Residues in contact with LEU 61 (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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14D VAL* 3.1 44.6 - - + +
15D GLY 5.5 0.4 - - - -
16D ALA* 5.4 0.6 - - - +
39D ALA* 4.3 8.5 - - + -
49D LEU* 4.5 6.1 - - + -
52D THR* 3.8 36.8 - - + -
53D VAL* 4.2 11.7 - - + +
57D PHE 3.3 5.9 + - - +
58D LYS* 3.0 12.6 + - - +
60D GLU* 1.3 78.0 - - - +
62D ILE* 1.3 59.0 + - - +
64D LYS* 3.0 5.4 + - - +
65D LEU* 2.9 40.6 + - + +
89D ALA* 4.3 5.8 - - + -
93D ILE* 4.0 20.9 - - + -
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Residues in contact with ILE 62 (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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58D LYS* 3.1 23.8 - - + +
59D GLU* 3.9 7.4 - - + +
61D LEU* 1.3 75.9 - - + +
63D ALA* 1.3 63.8 + - - +
65D LEU* 3.1 10.3 + - + +
66D LYS* 2.9 52.6 + - + +
72D VAL* 5.2 2.9 - - + -
92D ALA* 4.4 22.9 - - + +
93D ILE* 4.0 24.2 - - + -
96D LEU* 5.0 12.6 - - + -
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Residues in contact with ALA 63 (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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2D SER* 5.4 5.8 - - - +
59D GLU 2.8 25.7 + - - +
60D GLU* 3.7 10.5 - - - +
62D ILE* 1.3 74.3 - - - +
64D LYS* 1.3 61.7 + - + +
66D LYS* 3.5 9.1 + - - +
67D GLN* 2.9 31.3 + - - +
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Residues in contact with LYS 64 (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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2D SER 3.2 23.1 - - - +
3D GLN 3.4 31.4 - - - +
4D PRO* 3.3 30.6 - - + +
13D TRP* 3.7 13.0 - - - +
14D VAL* 4.1 19.5 + - + +
15D GLY 2.7 30.3 + - - +
16D ALA* 4.5 1.6 - - - +
60D GLU* 2.7 44.5 + - - +
61D LEU 3.0 5.3 + - - +
63D ALA* 1.3 76.2 - - + +
65D LEU* 1.3 66.3 + - - +
67D GLN* 3.1 10.9 + - - -
68D ILE* 3.5 6.0 - - - +
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Residues in contact with LEU 65 (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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14D VAL* 4.3 10.3 - - + +
41D LEU* 3.9 32.6 - - + +
49D LEU* 4.1 19.3 - - + -
61D LEU* 2.9 21.9 + - + +
62D ILE* 3.5 10.5 - - + +
64D LYS* 1.3 75.3 - - - +
66D LYS* 1.3 58.9 + - - +
68D ILE* 2.8 26.1 + - - +
69D LYS* 3.3 12.1 + - - +
72D VAL* 3.9 30.7 - - + -
74D LEU* 4.2 11.7 - - + -
93D ILE* 4.0 26.9 - - + -
96D LEU* 5.8 0.2 - - + -
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Residues in contact with LYS 66 (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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62D ILE* 2.9 39.7 + - + +
63D ALA* 3.8 8.5 - - - +
65D LEU* 1.3 76.5 - - - +
67D GLN* 1.3 61.2 + - + +
68D ILE 3.2 0.9 + - - -
69D LYS 3.7 6.7 + - - -
70D ASP* 3.3 53.7 + - - +
71D PRO* 6.1 0.4 - - - -
72D VAL* 3.9 16.4 - - + +
96D LEU* 4.4 18.0 - - - +
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Residues in contact with GLN 67 (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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2D SER* 2.9 29.3 + - - +
3D GLN* 2.2 43.5 + - - +
4D PRO* 3.8 8.3 - - + +
63D ALA* 2.9 21.4 - - - +
64D LYS 3.6 8.1 - - - +
65D LEU 3.1 1.4 + - - -
66D LYS* 1.3 77.6 - - + +
68D ILE* 1.3 65.6 + - - +
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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