Contacts of the helix formed by residues 39 - 51 (chain A) in PDB entry 1Y8M
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 ILE 39 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37A ALA 5.5 0.7 - - - +
38A THR* 1.3 70.4 - - - +
40A GLN* 1.3 64.3 + - + +
41A SER 2.9 2.1 + - - -
42A ARG* 3.0 6.4 + - - +
43A PHE* 2.7 31.2 + - + +
68A ILE* 3.3 33.9 - - + -
71A GLU* 5.5 7.4 - - + +
72A ALA* 3.7 27.4 - - + +
75A ARG* 3.6 33.4 - - - +
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Residues in contact with GLN 40 (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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38A THR* 4.2 9.7 + - - +
39A ILE* 1.3 80.5 - - + +
41A SER* 1.3 60.2 + - - +
43A PHE* 3.9 8.6 - - - +
44A ASN* 3.4 21.3 + - - +
75A ARG* 5.3 17.2 + - - +
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Residues in contact with SER 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A LEU* 5.8 1.4 - - - +
28A GLN* 4.7 15.9 + - - +
29A VAL* 3.4 30.4 - - - +
32A GLU* 4.9 3.5 + - - +
37A ALA* 3.9 11.1 - - - +
38A THR* 2.4 33.3 + - - -
39A ILE 3.0 0.8 - - - -
40A GLN* 1.3 78.7 - - - +
42A ARG* 1.3 64.8 + - - +
44A ASN* 3.6 4.2 + - - +
45A TYR 3.3 14.2 + - - -
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Residues in contact with ARG 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A VAL* 4.1 23.6 - - - +
34A GLY 4.6 8.7 + - - -
35A PRO* 5.0 11.9 - - - +
37A ALA* 5.2 3.1 - - - +
38A THR 3.4 7.7 + - - +
39A ILE* 3.0 8.3 + - - +
41A SER* 1.3 76.2 - - - +
43A PHE* 1.3 68.0 + - - +
45A TYR* 2.9 49.2 + - - +
46A ALA* 3.1 13.5 + - - +
60A LEU* 6.0 1.6 - - - +
64A ILE* 3.5 36.0 - - + +
68A ILE* 4.1 13.0 - - + -
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Residues in contact with PHE 43 (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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39A ILE* 2.7 24.5 + - + +
40A GLN* 3.9 10.5 - - - +
42A ARG* 1.3 74.4 - - - +
44A ASN* 1.3 67.2 + - + +
46A ALA* 3.3 6.4 + - - +
47A TRP* 3.3 16.0 + - + +
65A LEU* 3.8 24.1 - - + +
68A ILE* 3.7 19.6 - - + +
75A ARG* 5.7 7.2 - - + -
78A GLU* 4.0 26.9 - - + -
79A CYS* 4.4 9.9 - - - -
82A TYR* 3.3 51.6 - + - -
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Residues in contact with ASN 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A LEU* 3.1 40.9 - - + +
40A GLN 3.4 14.0 + - - +
41A SER* 4.0 4.3 - - - +
42A ARG 3.2 0.8 - - - -
43A PHE* 1.3 82.5 - - + +
45A TYR* 1.3 67.1 + - - +
47A TRP* 2.9 30.1 + - - +
48A GLY* 3.2 7.8 + - - -
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Residues in contact with TYR 45 (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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22A LEU* 4.7 12.8 - - + +
25A LEU* 4.8 17.4 - - + +
26A ARG* 3.1 57.8 + - + -
29A VAL* 4.4 12.1 - - + -
41A SER 3.3 11.3 + - - +
42A ARG* 2.9 45.7 + - - +
44A ASN* 1.3 80.5 - - - +
46A ALA* 1.3 61.0 + - - +
48A GLY* 3.7 1.0 + - - -
49A LEU* 3.2 48.1 + - + +
60A LEU* 4.7 9.2 - - + +
64A ILE* 3.8 7.2 - - + -
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Residues in contact with ALA 46 (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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42A ARG 3.1 4.8 + - - -
43A PHE* 3.7 9.0 - - - +
44A ASN 3.1 0.2 - - - -
45A TYR* 1.3 77.2 - - - +
47A TRP* 1.3 66.4 + - - +
49A LEU* 3.4 11.4 + - - +
50A ILE* 3.2 28.0 + - - +
61A GLY* 3.9 19.2 - - - +
64A ILE* 3.7 28.0 - - + -
65A LEU* 4.1 13.9 - - + -
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Residues in contact with TRP 47 (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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8A PRO* 4.4 23.6 - - + -
9A THR 5.1 2.0 - - - -
12A ASP* 4.5 9.0 - - + -
13A ALA* 5.0 7.4 - - + -
17A LEU* 5.5 2.0 - - + -
43A PHE* 3.3 10.8 + - + +
44A ASN* 2.9 26.1 + - - +
46A ALA* 1.3 79.6 - - - +
48A GLY* 1.3 64.0 + - - +
50A ILE* 3.1 27.0 + - + +
51A LYS* 3.0 57.1 + - + +
82A TYR* 3.2 48.2 - + + -
85A ILE* 4.7 27.1 - - + -
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Residues in contact with GLY 48 (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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17A LEU* 3.4 30.7 - - - +
22A LEU* 4.5 13.3 - - - +
25A LEU* 5.2 3.8 - - - -
44A ASN* 3.2 9.2 + - - -
45A TYR 3.7 2.0 + - - -
47A TRP* 1.3 82.9 - - - +
49A LEU* 1.3 61.9 + - - +
51A LYS* 3.1 13.5 + - - +
52A SER* 3.4 10.2 + - - -
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Residues in contact with LEU 49 (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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22A LEU* 4.7 15.7 - - + +
26A ARG* 5.2 2.9 - - - +
45A TYR* 3.2 59.1 + - + +
46A ALA* 3.7 11.7 - - - +
47A TRP 3.2 0.6 - - - -
48A GLY* 1.3 77.7 - - - +
50A ILE* 1.3 51.8 + - - +
52A SER* 3.4 3.8 - - - -
57A ASP* 3.0 52.1 - - + +
58A GLU* 2.4 26.9 - - - +
60A LEU* 3.8 25.4 - - + -
61A GLY 4.5 2.2 - - - +
64A ILE* 4.2 2.7 - - + -
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Residues in contact with ILE 50 (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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13A ALA* 5.5 1.6 - - + -
46A ALA 3.2 17.4 + - - +
47A TRP* 3.1 25.0 + - + +
48A GLY 3.1 0.6 - - - -
49A LEU* 1.3 76.2 - - - +
51A LYS* 1.3 55.7 + - + +
52A SER 3.1 5.4 + - - -
58A GLU* 3.4 21.4 - - + +
61A GLY* 4.6 9.9 - - - -
62A VAL 5.3 0.2 - - - +
65A LEU* 3.7 28.5 - - + -
82A TYR* 4.4 5.8 - - + +
85A ILE* 4.5 8.7 - - + -
86A GLY* 4.0 31.0 - - - +
89A LYS* 2.6 47.3 + - + +
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Residues in contact with LYS 51 (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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12A ASP* 2.7 31.9 + - - +
13A ALA* 4.0 16.2 - - - +
15A GLU* 2.9 36.3 - - - +
16A PRO* 4.3 13.6 - - + +
17A LEU* 4.0 29.2 - - + -
47A TRP* 3.0 61.3 - - + +
48A GLY 3.1 7.2 + - - +
50A ILE* 1.3 72.7 - - + +
52A SER* 1.3 68.4 + - - +
53A THR* 3.5 4.5 + - - +
89A LYS* 3.9 7.1 + - - +
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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