Contacts of the helix formed by residues 44 - 53 (chain A) in PDB entry 1A4Y
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 CYS 44 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39A LEU* 5.6 0.4 - - - -
40A THR 3.2 17.0 + - - -
41A GLU* 3.4 19.1 - - - +
42A ALA 3.2 0.4 - - - -
43A ARG* 1.3 76.7 - - - +
45A LYS* 1.3 56.9 + - - +
46A ASP 3.4 0.2 - - - -
47A ILE* 3.7 14.8 - - - +
48A SER* 3.0 27.9 + - - -
67A LEU* 3.7 28.5 - - - -
71A GLY* 3.7 27.4 - - - +
74A CYS* 3.4 10.7 - - + -
75A VAL* 3.9 12.4 - - + +
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Residues in contact with LYS 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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41A GLU* 3.3 38.1 + - - +
42A ALA* 3.6 20.3 + - - +
43A ARG 3.0 1.0 - - - -
44A CYS* 1.3 77.5 - - - +
46A ASP* 1.3 63.5 + - - +
48A SER* 3.5 3.1 + - - -
49A SER* 3.0 34.5 + - - +
74A CYS* 3.8 18.2 - - - -
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Residues in contact with ASP 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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19A TRP* 2.7 26.8 + - + -
23A LEU* 3.5 32.1 - - + +
42A ALA 4.5 2.8 - - - +
43A ARG* 3.0 17.6 + - - +
45A LYS* 1.3 79.0 - - - +
47A ILE* 1.3 66.6 + - - +
49A SER* 3.3 6.3 + - - -
50A ALA* 2.8 26.9 + - - +
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Residues in contact with ILE 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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19A TRP* 3.8 18.6 - - + -
26A LEU* 4.4 15.7 - - + -
34A LEU* 4.8 4.0 - - + -
39A LEU* 4.1 26.5 - - + -
43A ARG 3.0 14.3 + - - +
44A CYS* 3.7 21.5 - - - +
46A ASP* 1.3 77.1 - - - +
48A SER* 1.3 54.0 + - - +
50A ALA* 3.6 0.7 - - - +
51A LEU* 2.7 64.4 + - + +
60A LEU* 5.3 1.6 - - + -
62A LEU* 4.5 20.0 - - + -
67A LEU* 6.0 0.2 - - + -
75A VAL* 3.7 13.9 - - + -
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Residues in contact with SER 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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44A CYS 3.0 20.1 + - - -
45A LYS* 3.6 8.1 - - - -
47A ILE* 1.3 77.2 - - - +
49A SER* 1.3 60.3 + - - +
51A LEU* 3.5 2.8 + - - +
52A ARG* 3.0 40.6 + - - +
74A CYS* 2.8 28.7 + - - -
75A VAL* 4.3 4.5 - - - +
77A GLN* 4.0 1.9 - - - +
78A GLY* 3.2 21.5 + - - -
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Residues in contact with SER 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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45A LYS* 3.0 19.4 + - - +
46A ASP* 3.3 5.1 + - - -
48A SER* 1.3 75.4 - - - +
50A ALA* 1.3 61.9 + - - +
52A ARG* 3.4 28.7 + - - +
53A VAL* 3.8 11.8 + - - +
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Residues in contact with ALA 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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23A LEU* 4.0 15.0 - - + +
26A LEU* 3.9 27.6 - - + -
27A GLN* 3.9 16.3 - - + +
46A ASP 2.8 21.5 + - - +
47A ILE 3.7 2.9 - - - +
49A SER* 1.3 70.4 - - - +
51A LEU* 1.3 64.6 + - - +
53A VAL* 3.2 26.0 + - - +
54A ASN* 3.4 8.5 + - - +
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Residues in contact with LEU 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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26A LEU* 4.0 22.4 - - + +
32A VAL* 5.2 5.2 - - + -
47A ILE* 2.7 47.0 + - + +
48A SER* 3.9 4.9 - - - +
50A ALA* 1.3 73.1 - - - +
52A ARG* 1.3 62.2 + - - +
54A ASN* 3.3 20.5 + - - +
57A LEU* 3.7 31.5 - - + +
60A LEU* 3.4 35.2 - - + -
75A VAL* 4.0 9.6 - - + +
78A GLY 3.8 11.4 - - - +
79A LEU* 4.1 9.6 - - + +
81A THR* 5.5 0.3 + - - -
84A CYS* 6.1 1.2 - - - -
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Residues in contact with ARG 52 (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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48A SER* 3.0 34.0 + - - +
49A SER* 3.4 19.9 + - - +
50A ALA 3.2 0.2 - - - -
51A LEU* 1.3 78.2 - - - +
53A VAL* 1.3 62.2 + - + +
54A ASN 3.3 2.6 + - - +
77A GLN* 3.1 45.8 + - - +
78A GLY* 3.4 19.1 - - - +
81A THR* 4.4 22.5 + - + +
83A SER* 4.4 12.5 + - - -
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Residues in contact with VAL 53 (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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27A GLN* 3.5 32.9 - - + +
49A SER 3.8 9.4 + - - +
50A ALA* 3.2 17.5 - - - +
52A ARG* 1.3 79.9 - - + +
54A ASN* 1.3 57.5 + - - +
55A PRO* 3.0 13.7 - - - +
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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