Contacts of the helix formed by residues 39 - 50 (chain A) in PDB entry 4A12
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 SER 39 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A SER* 4.2 0.9 - - - -
38A VAL* 1.3 76.0 - - - +
40A ILE* 1.3 62.1 + - - +
41A GLN* 2.6 31.4 + - - -
42A THR* 3.2 9.8 + - - -
43A ILE* 3.2 20.4 + - - +
7G T 2.7 53.5 + - - +
8G A 5.0 0.9 + - - -
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Residues in contact with ILE 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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29A ASP* 3.8 10.5 - - + +
30A HIS* 3.6 41.7 - - + +
33A SER* 4.1 12.0 - - - +
38A VAL 4.0 0.4 + - - -
39A SER* 1.3 75.2 + - - +
41A GLN* 1.4 77.7 + - - +
43A ILE* 3.2 4.4 + - - +
44A ARG* 2.9 74.5 + - - +
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Residues in contact with GLN 41 (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 SER* 2.6 30.2 + - - +
40A ILE* 1.4 88.1 - - - +
42A THR* 1.4 58.8 + - - +
44A ARG* 3.5 12.2 + - - +
45A LEU* 3.0 30.7 + - - +
31F C 6.2 0.2 - - - +
32F T 5.5 1.1 - - - +
7G T 3.8 25.0 - - + +
8G A 3.5 35.3 + - - +
9G A 3.5 29.9 + - - +
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Residues in contact with THR 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ARG* 4.0 17.3 - - - +
38A VAL* 3.2 29.6 - - + -
39A SER* 3.2 6.4 + - - -
41A GLN* 1.4 73.8 - - - +
43A ILE* 1.4 51.7 + - - +
45A LEU* 2.9 12.7 + - + +
46A ASP* 2.8 46.9 + - - +
6G T 3.5 28.0 - - + +
7G T 2.7 26.7 + - + +
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Residues in contact with ILE 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A ILE* 3.8 24.9 - - + +
29A ASP* 3.7 38.8 - - + +
32A LEU* 3.7 40.4 - - + +
33A SER* 3.9 19.7 - - - +
36A PHE* 4.6 6.1 - - + -
38A VAL* 4.9 7.0 - - + -
39A SER 3.2 14.7 + - - +
40A ILE 3.4 7.4 - - - +
42A THR* 1.4 72.4 - - - +
44A ARG* 1.3 57.0 + - - +
46A ASP* 3.2 8.7 + - - +
47A ARG* 3.0 32.7 + - + +
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Residues in contact with ARG 44 (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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29A ASP* 3.0 18.5 + - - +
40A ILE* 2.9 62.0 + - - +
41A GLN* 3.6 10.9 - - - +
43A ILE* 1.3 75.5 - - - +
45A LEU* 1.4 54.4 + - - +
47A ARG* 3.5 9.5 + - - +
48A THR* 2.7 33.7 + - - -
28F A 4.3 5.9 - - - +
29F G 3.1 42.8 + - - -
30F T 3.2 52.1 + - + +
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Residues in contact with LEU 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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14A ARG* 4.2 10.8 + - - +
41A GLN 3.0 11.1 + - - +
42A THR* 2.9 12.6 + - + +
44A ARG* 1.4 73.7 - - + +
46A ASP* 1.4 65.3 + - - +
48A THR* 3.4 11.8 + - + +
49A TYR* 3.1 23.4 + - - +
32F T 6.2 4.0 - - + -
6G T 4.2 19.1 - - + -
7G T 3.9 29.8 - - + +
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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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13A ARG* 2.6 36.7 + - - -
14A ARG* 2.9 32.5 + - + +
17A ILE* 3.5 24.4 - - + +
42A THR* 2.8 33.6 + - - +
43A ILE* 3.2 8.6 + - - +
45A LEU* 1.4 69.0 - - - +
47A ARG* 1.4 59.2 + - - +
49A TYR* 3.3 3.8 + - - +
50A LEU* 2.9 38.2 + - + +
6G T 5.3 0.5 + - - -
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Residues in contact with ARG 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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17A ILE* 5.0 2.9 - - + -
21A ILE* 3.9 21.8 - - + -
29A ASP* 2.8 41.3 + - - -
43A ILE* 3.0 18.7 + - + +
44A ARG* 3.5 10.8 + - - +
46A ASP* 1.4 74.3 - - - +
48A THR* 1.4 57.5 + - - +
50A LEU* 3.4 4.6 + - - +
51A ASN 2.9 8.3 + - - -
52A ILE* 2.8 62.9 + - + +
53A PRO* 4.3 0.2 - - - +
54A GLU* 3.5 16.5 - - - +
58A ARG* 3.5 23.1 - - - +
29F G 3.5 5.9 - - - -
30F T 2.9 42.8 + - - -
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Residues in contact with THR 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 ARG 2.7 22.2 + - - -
45A LEU* 3.5 14.7 - - + +
46A ASP 3.2 0.4 - - - -
47A ARG* 1.4 78.2 + - - +
49A TYR* 1.3 61.0 + - - +
51A ASN* 3.2 23.4 + - - +
52A ILE 5.1 0.9 - - - -
30F T 5.5 3.1 + - - -
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Residues in contact with TYR 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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10A LYS* 5.7 2.9 - - - -
11A ASP* 5.9 2.7 - - - -
14A ARG* 3.4 39.3 - - - +
45A LEU 3.1 15.5 + - - +
46A ASP 3.3 4.2 + - - +
48A THR* 1.3 76.4 - - - +
50A LEU* 1.4 63.3 + - + +
51A ASN* 3.2 12.7 + - - -
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Residues in contact with LEU 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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14A ARG* 3.4 49.6 - - + +
15A GLU* 5.0 1.3 - - - +
17A ILE* 4.2 10.3 - - + -
18A ARG* 2.8 45.5 + - + +
46A ASP 2.9 26.0 + - - +
47A ARG 4.0 0.4 - - - +
49A TYR* 1.4 78.0 - - + +
51A ASN* 1.4 66.4 + - - +
52A ILE* 3.2 30.9 + - + +
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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