Contacts of the helix formed by residues 57 - 69 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A ALA* 3.6 23.1 - - + -
17A VAL 3.6 19.1 - - - -
18A ASP* 3.5 38.4 - - + -
37A TYR* 3.8 10.5 - + - -
53A VAL* 3.5 23.5 - - + +
54A TYR* 2.8 30.0 + + - -
56A PRO* 1.3 84.3 - - + +
58A LYS* 1.3 64.6 + - - +
59A GLU* 3.2 4.5 - - - -
60A GLU* 3.1 25.2 + - + +
61A LEU 3.2 8.3 + - - -
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Residues in contact with LYS 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A VAL* 4.4 0.4 - - - -
54A TYR 3.8 1.0 + - - -
55A GLU* 3.0 38.0 + - + +
56A PRO 3.6 0.4 - - - -
57A PHE* 1.3 77.5 - - - +
59A GLU* 1.3 87.6 + - + +
61A LEU* 3.1 6.5 + - - +
62A ILE* 3.0 31.6 + - + +
89A ALA* 3.9 28.3 - - + -
92A ALA* 3.8 27.1 - - + +
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Residues in contact with GLU 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A GLU* 4.4 0.9 - - - +
56A PRO* 3.2 24.8 - - - +
57A PHE* 3.8 2.1 - - - -
58A LYS* 1.3 107.5 + - + +
60A GLU* 1.3 57.4 + - - +
62A ILE* 3.8 7.6 - - - +
63A ALA* 2.8 31.4 + - - +
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Residues in contact with GLU 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A SER* 3.5 12.3 - - - +
14A VAL 5.1 0.2 - - - -
15A GLY 5.2 0.2 - - - -
16A ALA* 4.1 21.1 - - + -
17A VAL 6.0 0.2 - - - +
57A PHE* 3.1 21.3 + - + +
59A GLU* 1.3 75.8 + - - +
61A LEU* 1.3 66.2 + - - +
63A ALA* 3.7 7.0 - - - +
64A LYS* 2.6 62.8 + - - +
600A ZN 2.7 31.2 - - - -
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Residues in contact with LEU 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A VAL* 3.0 42.2 - - + +
15A GLY 5.4 0.4 - - - -
16A ALA* 5.5 0.8 - - - +
39A ALA* 4.4 6.5 - - + -
49A LEU* 4.7 5.4 - - + -
52A THR* 3.8 27.8 - - - -
53A VAL* 3.8 26.0 - - + -
57A PHE 3.2 8.0 + - - +
58A LYS* 3.1 12.0 + - - +
60A GLU* 1.3 78.2 - - - +
62A ILE* 1.3 59.3 + - + +
64A LYS* 2.9 6.6 + - - +
65A LEU* 2.8 41.7 + - + +
89A ALA* 4.5 4.7 - - + -
93A ILE* 4.4 13.9 - - + -
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Residues in contact with ILE 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A LYS* 3.0 24.5 + - + +
59A GLU* 4.0 6.7 - - - +
61A LEU* 1.3 78.2 - - - +
63A ALA* 1.3 64.5 + - - +
65A LEU* 3.1 9.3 + - + +
66A LYS* 2.9 53.7 + - + +
72A VAL* 5.2 2.0 - - + -
92A ALA* 4.4 26.0 - - + +
93A ILE* 4.1 21.1 - - + -
96A LEU* 4.9 16.2 - - + -
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Residues in contact with ALA 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A SER* 5.4 4.3 - - - +
59A GLU 2.8 25.4 + - - +
60A GLU* 3.7 11.2 - - - +
62A ILE* 1.3 75.6 - - - +
64A LYS* 1.3 62.8 + - + +
66A LYS* 3.5 8.7 + - - +
67A GLN* 3.3 27.6 + - - +
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Residues in contact with LYS 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A SER 3.4 23.1 - - - +
3A GLN 3.2 26.2 - - - +
4A PRO* 3.3 28.8 - - + +
13A TRP* 3.5 14.4 - - - -
14A VAL* 3.7 26.7 - - + +
15A GLY 3.2 27.7 + - - +
16A ALA* 4.7 2.0 - - - +
17A VAL 5.6 0.4 - - - +
60A GLU* 2.6 47.8 + - - +
61A LEU 2.9 5.4 + - - +
63A ALA* 1.3 74.7 - - + +
65A LEU* 1.3 68.9 + - - +
67A GLN* 3.1 11.0 + - - -
68A ILE* 3.6 5.4 + - - +
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Residues in contact with LEU 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A VAL* 4.3 9.8 - - + +
41A LEU* 3.5 36.3 - - + +
49A LEU* 3.9 19.1 - - + -
61A LEU* 2.8 29.2 + - + +
62A ILE* 3.6 13.0 - - + +
64A LYS* 1.3 76.7 - - - +
66A LYS* 1.3 57.4 + - - +
68A ILE* 2.9 25.9 + - - +
69A LYS 3.3 11.9 + - - +
72A VAL* 4.0 23.3 - - + -
74A LEU* 4.2 8.7 - - + -
93A ILE* 3.9 28.3 - - + -
96A LEU* 5.3 0.4 - - + -
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Residues in contact with LYS 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A ILE* 2.9 39.5 + - + +
63A ALA* 3.9 8.1 - - - +
65A LEU* 1.3 76.4 - - - +
67A GLN* 1.3 59.1 + - - +
68A ILE 3.4 0.2 + - - -
69A LYS 3.7 7.1 + - - -
70A ASP* 3.5 48.3 + - + +
72A VAL* 3.9 19.3 - - + +
96A LEU* 5.0 10.2 - - - +
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Residues in contact with GLN 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A SER* 3.1 24.3 + - - +
3A GLN* 4.1 22.6 - - - +
4A PRO* 3.8 15.3 - - + +
63A ALA* 3.3 15.8 + - - +
64A LYS 3.1 10.4 + - - +
65A LEU 3.1 0.2 + - - -
66A LYS* 1.3 78.4 - - - +
68A ILE* 1.3 64.5 + - - +
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Residues in contact with ILE 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A PRO* 4.4 14.1 - - + -
12A TYR* 3.4 44.6 - - + -
14A VAL* 4.7 3.1 - - + -
41A LEU* 3.6 31.2 - - + -
43A VAL* 4.0 16.8 - - + -
64A LYS 3.8 12.3 - - - +
65A LEU 2.9 8.3 + - - +
67A GLN* 1.3 84.2 - - - +
69A LYS* 1.3 66.6 + - + +
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Residues in contact with LYS 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A VAL* 6.5 0.7 - - + -
47A THR* 6.5 0.4 - - + -
65A LEU 3.3 9.7 + - - +
66A LYS* 3.6 6.6 - - - -
67A GLN 3.5 0.6 - - - -
68A ILE* 1.3 88.9 - - + +
70A ASP* 1.3 62.3 + - - +
71A PRO* 3.4 37.7 - - - +
72A VAL* 3.9 6.1 - - - -
73A LYS* 4.2 29.2 - - + +
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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