Contacts of the helix formed by residues 35 - 52 (chain A) in PDB entry 1A1U
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 ARG 35 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34A GLY* 1.3 68.1 - - - -
36A GLU* 1.3 57.5 + - - +
38A PHE* 2.7 28.6 + - - +
39A GLU* 3.2 27.2 + - - +
28C PHE* 3.4 28.2 - - + -
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Residues in contact with GLU 36 (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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35A ARG* 1.3 79.7 - - - +
37A ARG* 1.3 59.0 + - + +
39A GLU* 3.6 23.1 - - - +
40A LYS* 2.9 37.1 + - + +
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Residues in contact with ARG 37 (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 ILE* 3.1 42.4 + - + +
33A ARG* 3.1 29.3 + - - +
34A GLY* 3.0 16.2 + - - +
35A ARG 2.9 1.4 + - - -
36A GLU* 1.3 82.1 - - + +
38A PHE* 1.3 61.6 + - - +
40A LYS* 3.3 14.3 - - + +
41A ILE* 3.2 9.6 - - - +
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Residues in contact with PHE 38 (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 ILE* 3.5 25.7 - - + +
34A GLY 3.1 4.8 + - - -
35A ARG 2.7 12.9 + - - +
37A ARG* 1.3 69.0 - - - +
39A GLU* 1.3 59.3 + - - +
41A ILE* 2.8 24.9 + - - +
42A ARG* 3.1 37.4 + - - +
28C PHE* 3.4 37.0 - + + -
29C THR 3.7 22.0 - - - -
30C LEU* 3.6 33.7 - - + -
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Residues in contact with GLU 39 (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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35A ARG* 3.2 28.5 + - - +
36A GLU* 3.6 26.0 - - - +
38A PHE* 1.3 78.5 - - - +
40A LYS* 1.3 55.1 + - - +
42A ARG* 2.7 40.9 + - + +
43A GLU* 3.2 14.6 + - - +
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Residues in contact with LYS 40 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36A GLU* 2.9 22.4 + - + +
37A ARG* 3.3 10.8 - - + +
39A GLU* 1.3 75.4 + - - +
41A ILE* 1.3 64.3 + - + +
43A GLU* 3.5 19.6 + - + +
44A TYR* 2.9 25.7 + - + +
51C LYS* 5.9 2.6 - - - +
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Residues in contact with ILE 41 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30A LEU* 6.2 0.2 - - + -
32A ILE* 3.1 38.6 - - + -
37A ARG* 3.2 5.2 - - - +
38A PHE 2.8 10.3 + - - +
40A LYS* 1.3 80.8 - - + +
42A ARG* 1.3 59.4 + - - +
44A TYR* 2.9 52.3 - - + +
45A ASN* 2.9 27.2 + - - -
30C LEU* 3.1 33.4 - - + -
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Residues in contact with ARG 42 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38A PHE* 3.3 42.1 - - - +
39A GLU* 2.7 31.9 + - + +
41A ILE* 1.3 73.7 - - - +
43A GLU* 1.3 54.8 + - + +
45A ASN* 2.9 30.9 + - - +
46A GLU* 3.3 6.2 + - - +
30C LEU* 5.4 5.3 - - - +
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Residues in contact with GLU 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 GLU* 3.2 14.4 + - - +
40A LYS* 3.7 20.1 + - + +
42A ARG* 1.3 74.4 - - + +
44A TYR* 1.4 67.0 + - - +
45A ASN 3.0 1.6 - - - -
46A GLU* 2.8 34.7 + - - +
47A ALA* 3.2 6.8 + - - +
51C LYS* 5.3 7.4 - - - +
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Residues in contact with TYR 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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30A LEU* 4.1 18.1 - - + +
40A LYS* 2.9 18.1 + - + +
41A ILE* 2.9 57.2 + - + +
43A GLU* 1.4 79.3 - - - +
45A ASN* 1.4 63.1 + - - +
47A ALA* 3.4 6.8 - - - +
48A LEU* 3.4 15.5 + - + +
30C LEU* 4.9 0.2 - - - +
44C TYR* 3.2 43.9 + + - -
45C ASN* 3.5 25.4 + - - -
48C LEU* 3.0 37.7 - - + +
51C LYS* 6.1 1.3 - - - +
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Residues in contact with ASN 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 ILE* 2.9 31.1 + - - +
42A ARG* 2.9 15.8 + - - +
44A TYR* 1.4 89.3 - - - +
46A GLU* 1.3 61.4 + - - +
48A LEU* 2.9 31.4 - - - +
49A GLU* 3.2 5.7 + - - +
30C LEU* 4.1 13.5 - - - +
44C TYR* 3.4 30.4 + - - -
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Residues in contact with GLU 46 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42A ARG 3.3 6.4 + - - +
43A GLU* 2.8 26.0 + - - +
45A ASN* 1.3 76.4 - - - +
47A ALA* 1.3 54.4 + - - +
49A GLU* 2.7 36.9 + - + +
50A LEU* 3.2 4.9 + - - +
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Residues in contact with ALA 47 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43A GLU 3.2 5.3 + - - +
44A TYR* 3.4 13.7 - - - +
46A GLU* 1.3 80.1 - - - +
48A LEU* 1.3 62.3 + - - +
50A LEU* 2.9 21.9 - - - +
47C ALA 3.4 12.1 - - - +
48C LEU* 3.4 19.1 - - + +
51C LYS* 3.2 42.0 - - + +
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Residues in contact with LEU 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 TYR* 3.4 4.8 + - + +
45A ASN* 2.9 26.1 + - - +
47A ALA* 1.3 79.3 - - - +
49A GLU* 1.3 61.6 + - - +
51A LYS* 2.9 24.1 + - + +
52A ASP* 3.3 8.1 + - + +
44C TYR* 3.0 63.5 - - + +
47C ALA* 3.3 24.9 - - + -
48C LEU* 4.3 1.9 - - + +
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Residues in contact with GLU 49 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45A ASN 3.2 4.0 + - - +
46A GLU* 2.7 25.1 + - + +
48A LEU* 1.3 74.3 - - - +
50A LEU* 1.3 63.4 + - - +
52A ASP* 2.9 13.7 + - + +
53A ALA* 2.7 38.4 + - - +
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Residues in contact with LEU 50 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46A GLU 3.2 3.0 + - - +
47A ALA* 2.9 19.9 + - - +
49A GLU* 1.3 78.4 - - - +
51A LYS* 1.3 56.9 + - - +
53A ALA* 3.1 6.4 + - - -
54A GLN* 2.9 64.8 + - + +
50C LEU* 3.1 28.3 - - + +
51C LYS* 3.3 37.9 - - + +
54C GLN 5.1 7.9 - - - +
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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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47A ALA 3.8 0.2 + - - -
48A LEU* 2.9 12.2 + - + +
50A LEU* 1.3 75.7 - - - +
52A ASP* 1.3 72.1 + - + +
54A GLN 2.9 21.5 - - - +
40C LYS* 6.1 1.0 - - - +
43C GLU* 5.1 11.6 + - - +
44C TYR* 6.0 0.8 - - - +
46C GLU* 6.3 0.7 - - - -
47C ALA* 3.2 40.5 - - + +
50C LEU* 3.3 23.6 - - + +
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Residues in contact with ASP 52 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48A LEU* 3.3 11.3 + - + +
49A GLU* 2.9 17.8 + - + +
51A LYS* 1.3 90.2 + - + +
53A ALA* 1.4 60.2 + - - +
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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