Contacts of the helix formed by residues 43 - 57 (chain A) in PDB entry 1A0A
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 ALA 43 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20A LEU* 4.3 1.4 - - - +
41A SER* 2.7 15.0 + - - +
42A LYS* 1.3 77.1 - - - +
44A THR* 1.3 58.1 + - + +
45A THR 3.1 5.5 + - - -
46A VAL* 3.2 18.8 + - - +
47A GLU* 2.7 20.4 - - - +
12B ARG 5.7 1.6 - - - +
15B ARG* 5.3 6.7 - - - +
16B LEU* 3.1 41.1 - - + +
7D C 5.9 0.9 - - + -
8D C 5.5 3.6 - - - +
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Residues in contact with THR 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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32A LYS* 5.5 1.0 + - - -
38A ALA* 3.9 19.6 - - + +
39A ALA* 2.7 17.1 + - + +
41A SER* 2.7 46.6 + - - +
43A ALA* 1.3 79.6 - - - +
45A THR* 1.3 55.7 + - - +
47A GLU* 2.9 39.7 - - - +
48A ALA* 3.9 1.9 + - - +
15B ARG* 3.8 28.7 - - - +
7D C 4.2 7.0 - - - +
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Residues in contact with THR 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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20A LEU* 3.6 16.8 + - - +
23A LEU* 5.2 1.7 - - - +
24A ALA* 5.7 4.5 - - - +
27A ILE* 5.2 8.7 - - + +
32A LYS* 4.2 16.2 - - - +
39A ALA 4.5 3.6 - - - +
40A PRO* 4.8 3.8 - - + -
41A SER 3.3 25.7 + - - +
43A ALA 3.1 0.4 - - - -
44A THR* 1.3 81.9 - - - +
46A VAL* 1.3 69.6 + - - +
47A GLU 2.7 1.8 - - - -
48A ALA* 2.8 21.2 + - - +
49A ALA* 3.0 13.7 + - - +
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Residues in contact with VAL 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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20A LEU* 3.1 44.4 - - + -
23A LEU* 4.2 16.4 - - + -
43A ALA 3.2 8.9 + - - +
45A THR* 1.3 80.3 + - - +
47A GLU* 1.3 66.4 + - - +
49A ALA* 3.5 8.5 + - - +
50A CYS* 3.8 8.7 + - - +
16B LEU* 3.9 14.6 - - + -
19B ALA* 3.9 5.1 - - + +
20B LEU* 3.1 46.7 - - + +
23B LEU* 4.2 7.9 - - + +
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Residues in contact with GLU 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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38A ALA* 4.2 8.1 - - - +
43A ALA 2.7 22.1 + - - +
44A THR* 2.9 43.1 + - - +
46A VAL* 1.3 83.2 - - - +
48A ALA* 1.3 54.7 + - - +
50A CYS* 3.0 24.4 - - - +
51A ARG* 3.7 6.1 + - - +
15B ARG* 3.5 32.1 + - + +
19B ALA* 4.2 19.7 - - + +
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Residues in contact with ALA 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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27A ILE* 4.3 13.2 - - + -
32A LYS* 4.0 27.8 - - + +
35A ASN* 4.6 9.0 - - - +
44A THR 4.7 0.9 - - - +
45A THR* 2.8 14.2 + - - +
47A GLU* 1.3 74.9 - - - +
49A ALA* 1.3 52.0 + - - +
50A CYS 2.7 6.4 + - - -
51A ARG* 2.6 40.6 + - + +
52A TYR* 3.2 6.3 + - - +
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Residues in contact with ALA 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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23A LEU* 3.4 51.1 - - + +
27A ILE* 5.3 6.1 - - + +
45A THR 3.0 13.1 + - - +
46A VAL 3.5 2.4 + - - +
48A ALA* 1.3 70.0 - - - +
50A CYS* 1.3 57.2 + - - +
52A TYR* 4.1 10.2 - - + +
53A ILE* 3.0 37.4 + - + +
23B LEU* 3.9 9.2 - - + -
53B ILE* 5.1 2.0 - - + -
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Residues in contact with CYS 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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46A VAL 4.1 1.6 - - - +
47A GLU* 3.0 15.2 + - - +
49A ALA* 1.3 77.1 - - - +
51A ARG* 1.3 59.6 + - - +
53A ILE* 3.1 4.5 + - - -
54A ARG* 2.5 56.3 + - - +
19B ALA* 5.9 2.2 - - + -
22B GLU* 3.5 39.9 - - - -
23B LEU* 3.4 17.2 - - + +
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Residues in contact with ARG 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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31A TRP* 3.7 43.2 - - + -
34A GLN* 5.7 1.4 - - - +
35A ASN* 5.0 13.3 - - + +
47A GLU 4.5 3.8 - - - +
48A ALA* 2.6 24.5 + - + +
50A CYS* 1.3 74.3 - - + +
52A TYR* 1.3 62.6 + - - +
54A ARG* 3.7 6.6 + - - +
55A HIS* 3.0 23.6 + - - +
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Residues in contact with TYR 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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26A LEU 2.6 28.9 + - - -
27A ILE* 3.7 8.0 - - + -
28A PRO* 3.2 46.8 - - + +
31A TRP* 3.7 21.1 - + + +
48A ALA 3.2 8.7 + - - +
49A ALA* 4.1 8.7 - - - +
51A ARG* 1.3 77.0 - - - +
53A ILE* 1.3 50.9 + - + +
55A HIS* 2.8 10.4 + + + +
56A LEU* 2.6 67.9 + - + +
53B ILE* 4.1 9.4 - - + -
57B GLN* 2.5 29.4 + - - +
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Residues in contact with ILE 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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49A ALA* 3.0 25.8 + - + +
50A CYS* 3.1 6.0 + - - +
52A TYR* 1.3 77.5 - - + +
54A ARG* 1.3 76.0 + - + +
55A HIS 2.9 2.0 + - - -
56A LEU* 3.4 12.1 + - + +
57A GLN* 3.2 19.8 + - - +
23B LEU* 4.7 13.9 - - + +
26B LEU 5.1 4.3 - - - +
27B ILE* 5.8 4.0 - - + -
28B PRO* 4.9 7.2 - - + -
49B ALA* 3.6 9.6 - - - +
52B TYR* 4.3 26.5 - - + -
53B ILE* 3.1 48.7 - - + -
56B LEU* 6.0 1.1 - - + -
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Residues in contact with ARG 54 (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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50A CYS* 2.5 40.5 + - - +
51A ARG* 3.8 7.0 - - - +
53A ILE* 1.3 77.0 - - + +
55A HIS* 1.3 60.7 + - - +
57A GLN* 2.4 36.1 - - - +
58A GLN* 4.6 1.9 + - - +
22B GLU* 3.9 26.0 + - - -
26B LEU* 5.0 19.5 - - - +
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Residues in contact with HIS 55 (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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31A TRP* 4.6 17.1 + - + +
34A GLN* 5.1 6.2 + - - -
51A ARG 3.0 13.8 + - - +
52A TYR* 2.8 12.7 + + - +
54A ARG* 1.3 73.2 - - - +
56A LEU* 1.3 67.8 + - + +
57A GLN 2.5 19.8 + - - -
58A GLN* 3.0 23.4 + - - +
59A ASN* 5.0 13.4 + - - -
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Residues in contact with LEU 56 (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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52A TYR* 2.6 67.2 + - + +
53A ILE* 3.4 6.3 + - - +
55A HIS* 1.3 79.2 - - + +
57A GLN* 1.3 64.0 + - - +
59A ASN* 3.4 29.0 - - - +
53B ILE* 4.0 10.8 - - + -
56B LEU* 4.4 25.4 - - + +
57B GLN* 3.3 26.7 - - - +
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Residues in contact with GLN 57 (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 ILE* 3.2 13.4 - - - +
54A ARG* 2.4 42.7 - - - +
55A HIS 2.5 9.1 + - - -
56A LEU* 1.3 72.3 - - - +
58A GLN* 1.3 58.2 + - + +
59A ASN* 2.7 15.9 + - - +
26B LEU* 4.8 2.8 + - - +
28B PRO* 3.1 31.3 - - - +
52B TYR* 3.2 23.3 + - + +
56B LEU* 5.1 6.3 - - - +
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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