Contacts of the helix formed by residues 35 - 52 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28A PHE* 3.4 28.9 - - + -
34C GLY* 1.3 65.4 - - - -
36C GLU* 1.3 56.5 + - - +
37C ARG 2.9 3.1 - - - -
38C PHE* 2.7 28.4 + - - +
39C GLU* 3.1 28.2 + - - +
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Residues in contact with GLU 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C GLY 5.2 0.2 - - - -
35C ARG* 1.3 78.4 - - - +
37C ARG* 1.3 59.3 + - + +
39C GLU* 3.6 22.1 - - - +
40C LYS* 2.9 35.8 + - + +
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Residues in contact with ARG 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32C ILE* 3.1 41.4 + - + +
33C ARG* 3.1 28.5 + - - +
34C GLY* 3.1 16.2 + - - +
35C ARG 2.9 1.0 + - - -
36C GLU* 1.3 81.8 - - + +
38C PHE* 1.3 60.2 + - - +
40C LYS* 3.3 14.8 - - + +
41C ILE* 3.2 9.8 - - - +
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Residues in contact with PHE 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A PHE* 3.3 42.4 - + + -
29A THR 3.8 21.1 - - - -
30A LEU* 3.6 33.7 - - + -
32C ILE* 3.5 25.9 - - + +
34C GLY 3.2 4.8 + - - -
35C ARG 2.7 13.0 + - - +
37C ARG* 1.3 71.5 - - - +
39C GLU* 1.3 53.2 + - - +
41C ILE* 2.8 25.5 + - - +
42C ARG* 3.1 38.0 + - - +
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Residues in contact with GLU 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C ARG* 3.1 28.1 + - - +
36C GLU* 3.6 26.1 - - - +
38C PHE* 1.3 78.6 - - - +
40C LYS* 1.3 55.1 + - - +
42C ARG* 2.7 41.6 + - + +
43C GLU* 3.2 14.4 + - - +
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Residues in contact with LYS 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A LYS* 6.1 0.8 - - - +
36C GLU* 2.9 23.0 + - + +
37C ARG* 3.3 10.3 - - - +
39C GLU* 1.3 75.5 - - - +
41C ILE* 1.3 63.4 + - + +
43C GLU* 3.5 19.0 + - + +
44C TYR* 2.9 26.3 + - + +
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Residues in contact with ILE 41 (chain C).
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* 3.1 33.7 - - + -
30C LEU* 6.2 0.2 - - + -
32C ILE* 3.2 39.9 - - + -
37C ARG* 3.2 5.2 - - - +
38C PHE 2.8 14.5 + - - +
40C LYS* 1.3 78.5 - - + +
42C ARG* 1.3 59.2 + - - +
44C TYR* 2.9 65.2 - - + +
45C ASN* 2.9 14.0 + - - -
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Residues in contact with ARG 42 (chain C).
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* 5.4 5.3 - - - +
38C PHE* 3.3 43.2 - - - +
39C GLU* 2.7 31.6 + - + +
41C ILE* 1.3 73.6 - - - +
43C GLU* 1.3 55.1 + - - +
45C ASN* 2.9 29.6 + - - +
46C GLU* 3.3 6.1 + - - +
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Residues in contact with GLU 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A LYS* 5.1 9.9 - - - +
39C GLU* 3.2 13.5 + - - +
40C LYS* 3.7 20.6 + - + +
42C ARG* 1.3 73.5 - - - +
44C TYR* 1.3 67.4 + - - +
45C ASN 3.0 1.6 - - - -
46C GLU* 2.9 34.3 + - - +
47C ALA* 3.2 6.9 + - - +
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Residues in contact with TYR 44 (chain C).
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* 4.9 0.2 - - - +
44A TYR* 3.2 46.2 + + - -
45A ASN* 3.4 25.3 + - - -
48A LEU* 3.0 37.3 - - + +
51A LYS* 6.0 1.3 - - - +
30C LEU* 4.0 18.3 - - + +
40C LYS 2.9 18.5 + - - +
41C ILE* 2.9 54.0 + - + +
43C GLU* 1.3 79.0 - - - +
45C ASN* 1.4 63.4 + - - +
47C ALA* 3.4 6.7 - - - +
48C LEU* 3.4 15.3 + - + +
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Residues in contact with ASN 45 (chain C).
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 14.6 - - - +
44A TYR* 3.5 29.8 + - - -
41C ILE* 2.9 30.1 + - - +
42C ARG* 2.9 16.5 + - - +
44C TYR* 1.4 89.2 - - - +
46C GLU* 1.3 65.3 + - - +
48C LEU* 2.9 28.3 - - - +
49C GLU* 3.2 5.9 + - - +
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Residues in contact with GLU 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A LYS* 6.3 0.9 - - - -
42C ARG 3.3 5.9 + - - +
43C GLU* 2.9 26.2 + - + +
45C ASN* 1.3 75.8 - - - +
47C ALA* 1.3 55.3 + - - +
49C GLU* 2.8 36.7 + - + +
50C LEU* 3.2 4.3 + - - +
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Residues in contact with ALA 47 (chain C).
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 3.4 11.4 - - - +
48A LEU* 3.3 28.3 - - + +
51A LYS* 3.2 42.2 - - + +
43C GLU 3.2 6.4 + - - +
44C TYR 3.4 4.3 - - - +
46C GLU* 1.3 81.2 - - - +
48C LEU* 1.3 62.2 + - - +
50C LEU* 2.9 21.6 - - - +
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Residues in contact with LEU 48 (chain C).
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* 3.0 61.2 - - + +
47A ALA* 3.4 25.8 - - + -
48A LEU* 4.3 1.5 - - + +
44C TYR* 3.4 4.8 + - + +
45C ASN* 2.9 26.1 + - - +
47C ALA* 1.3 78.6 - - - +
49C GLU* 1.3 62.2 + - - +
51C LYS* 2.9 21.9 + - + +
52C ASP* 3.3 10.3 + - + +
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Residues in contact with GLU 49 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45C ASN 3.2 3.7 + - - +
46C GLU* 2.8 21.6 + - + +
48C LEU* 1.3 78.0 - - - +
50C LEU* 1.3 63.8 + - - +
52C ASP* 2.8 13.7 + - + +
53C ALA* 2.7 38.1 + - - +
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Residues in contact with LEU 50 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A LEU* 3.1 26.7 - - + +
51A LYS* 3.3 41.1 - - + +
54A GLN 5.0 7.9 - - - -
46C GLU 3.2 3.2 + - - +
47C ALA* 2.9 20.1 + - - +
49C GLU* 1.3 77.7 - - - +
51C LYS* 1.3 56.3 + - - +
53C ALA* 3.0 6.2 + - - -
54C GLN* 2.9 64.3 + - + +
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Residues in contact with LYS 51 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A LYS* 5.9 2.6 - - - +
43A GLU* 5.3 8.2 + - - +
44A TYR* 6.1 0.8 - - - +
47A ALA* 3.2 39.9 - - + +
50A LEU* 3.3 24.5 - - + +
47C ALA 3.7 0.8 + - - -
48C LEU* 2.9 9.9 + - + +
50C LEU* 1.3 77.9 - - - +
52C ASP* 1.3 70.8 + - + +
54C GLN 2.9 21.0 - - - +
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Residues in contact with ASP 52 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48C LEU* 3.3 11.9 + - + +
49C GLU* 2.8 21.1 + - + +
51C LYS* 1.3 88.2 + - + +
53C ALA* 1.4 61.1 + - - +
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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