Contacts of the helix formed by residues 25 - 42 (chain A) in PDB entry 1AU0
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 25 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A GLN* 3.5 10.5 - - - +
24A SER* 1.3 72.7 - - - +
26A TRP* 1.3 56.1 + - - +
28A PHE* 3.3 3.8 + - - +
29A SER* 3.0 30.3 + - - -
162A HIS* 3.1 32.5 - - + -
163A ALA* 3.4 19.2 - - - +
183A SER* 3.9 10.6 + - - +
300A SDK 1.8 81.1 + - - +
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Residues in contact with TRP 26 (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 GLY 3.4 16.8 + - - -
24A SER* 3.9 3.9 - - - +
25A CYS* 1.3 82.2 - - - +
27A ALA* 1.3 65.0 + - + +
29A SER* 3.8 0.9 - - - -
30A SER* 2.7 37.6 + - - -
53A LEU* 3.7 24.7 - - + -
54A VAL* 4.3 14.4 - - + -
57A VAL* 4.0 4.7 - - + -
60A ASN* 2.9 42.0 - - + -
62A GLY 3.2 28.3 + - - -
65A GLY 3.4 3.8 - - - -
66A GLY* 3.2 32.3 - - - +
67A TYR 3.8 9.6 - - - -
68A MET* 3.8 6.1 - - - +
71A ALA* 3.6 25.1 - - + -
163A ALA* 3.5 19.1 - - + -
300A SDK 3.7 7.9 - - + -
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Residues in contact with ALA 27 (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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24A SER* 2.9 12.8 + - - +
26A TRP* 1.3 90.9 - - + +
28A PHE* 1.3 65.0 + - - +
30A SER 3.4 0.5 + - - -
31A VAL* 3.0 25.6 + - - +
50A PRO* 3.6 29.6 - - + +
53A LEU* 3.6 17.8 - - + +
54A VAL* 3.8 15.9 - - + -
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Residues in contact with PHE 28 (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 LYS* 3.3 41.7 - - + -
18A ASN 4.1 2.0 - - - -
19A GLN* 3.8 19.7 - - + -
24A SER* 3.1 46.4 + - - -
25A CYS* 3.8 6.1 - - - +
27A ALA* 1.3 78.2 - - - +
29A SER* 1.3 56.2 + - - +
31A VAL* 3.3 5.5 + - + +
32A GLY* 2.8 27.2 + - - -
50A PRO* 3.8 28.0 - - + -
89A TYR* 3.6 36.8 - + + -
183A SER* 4.1 19.7 - - - -
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Residues in contact with SER 29 (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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25A CYS 3.0 17.5 + - - -
26A TRP 3.8 4.3 - - - -
28A PHE* 1.3 75.9 - - - +
30A SER* 1.3 64.4 + - - +
32A GLY* 2.9 11.4 + - - -
33A ALA 3.2 8.5 + - - -
68A MET* 3.8 4.0 - - - +
132A SER* 3.2 23.1 + - - -
133A VAL 4.2 0.9 + - - -
163A ALA* 4.0 12.3 - - - -
164A VAL* 2.6 34.7 + - - +
165A LEU* 3.6 9.3 - - - +
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Residues in contact with SER 30 (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 TRP 2.7 21.6 + - - -
27A ALA 3.7 3.8 - - - -
29A SER* 1.3 76.4 + - - +
31A VAL* 1.3 63.9 + - - +
33A ALA* 3.1 15.6 + - - +
34A LEU* 3.1 18.0 + - - +
53A LEU* 3.9 15.3 - - - -
68A MET* 3.2 25.7 - - - +
71A ALA* 3.6 12.7 - - - +
72A PHE* 3.9 14.5 - - - -
132A SER* 3.9 7.9 - - - -
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Residues in contact with VAL 31 (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 LYS* 5.9 1.1 - - - +
27A ALA 3.0 11.4 + - - +
28A PHE* 3.7 5.4 - - + +
30A SER* 1.3 79.1 - - - +
32A GLY* 1.3 58.6 + - - +
34A LEU* 3.1 7.9 + - + +
35A GLU* 2.9 53.0 + - - +
48A LEU* 3.7 19.3 - - + +
49A SER 3.7 22.0 - - - +
50A PRO* 4.1 9.0 - - + -
53A LEU* 3.7 23.3 - - + -
81A ILE* 3.8 14.4 - - + -
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Residues in contact with GLY 32 (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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12A TYR 5.0 1.4 - - - +
13A VAL* 6.1 0.2 - - - +
28A PHE 2.8 15.0 + - - -
29A SER 2.9 5.3 + - - -
31A VAL* 1.3 78.7 - - - +
33A ALA* 1.3 59.7 + - - +
35A GLU* 3.5 15.5 + - - +
36A GLY* 3.2 17.2 + - - -
130A PRO* 4.2 3.1 - - - +
165A LEU* 3.5 26.7 - - - +
181A LYS* 5.5 3.8 - - - -
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Residues in contact with ALA 33 (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 SER 3.2 3.4 + - - -
30A SER 3.1 6.5 + - - +
32A GLY* 1.3 74.5 - - - +
34A LEU* 1.3 65.1 + - - +
36A GLY* 3.3 1.8 + - - +
37A GLN* 3.2 28.1 + - - +
72A PHE* 4.5 0.7 - - + -
130A PRO* 3.6 24.9 - - - +
131A VAL* 4.9 0.2 - - - -
132A SER* 3.3 26.2 - - - +
165A LEU* 3.6 3.5 - - + +
213A PRO* 3.6 23.1 - - + -
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Residues in contact with LEU 34 (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 SER* 3.1 18.7 + - - +
31A VAL* 3.1 13.4 + - + +
33A ALA* 1.3 77.2 - - - +
35A GLU* 1.3 61.8 + - - +
37A GLN* 3.6 3.0 + - + +
38A LEU* 3.1 22.5 + - - +
48A LEU* 3.6 17.7 - - + +
53A LEU* 5.3 2.5 - - + -
71A ALA 5.7 0.9 - - - +
72A PHE* 4.7 9.2 - - + -
75A VAL* 4.1 17.9 - - + -
81A ILE* 4.0 28.5 - - + -
105A ALA* 5.4 3.6 - - + -
106A LYS 4.9 5.4 - - - +
107A CYS* 4.2 20.2 - - + -
213A PRO* 4.1 24.2 - - + -
215A MET* 4.6 8.5 - - - +
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Residues in contact with GLU 35 (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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12A TYR 4.2 4.0 - - - +
13A VAL* 5.5 0.9 - - - +
14A THR* 2.7 35.8 + - - +
17A LYS* 4.8 2.1 + - - -
31A VAL* 2.9 40.7 + - - +
32A GLY* 3.8 12.3 - - - +
33A ALA 3.2 0.4 - - - -
34A LEU* 1.3 73.7 - - - +
36A GLY* 1.3 66.1 + - - +
38A LEU* 3.2 7.8 + - - +
39A LYS 3.1 18.9 + - - -
45A LEU* 3.8 18.6 - - + +
46A LEU 3.6 17.5 - - - +
47A ASN* 4.0 4.5 + - - -
48A LEU* 3.1 28.3 + - + +
181A LYS* 4.5 2.1 + - - -
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Residues in contact with GLY 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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12A TYR* 3.3 41.4 + - - -
32A GLY 3.2 12.1 + - - -
33A ALA 3.3 3.9 + - - -
35A GLU* 1.3 79.8 - - - +
37A GLN* 1.3 64.4 + - - +
39A LYS* 3.5 0.9 + - - +
40A LYS 3.1 15.6 + - - -
130A PRO* 4.3 10.8 - - - -
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Residues in contact with GLN 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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33A ALA 3.2 17.1 + - - +
34A LEU* 4.0 5.2 - - + +
36A GLY* 1.3 75.6 - - - +
38A LEU* 1.3 66.7 + - - +
40A LYS* 3.0 22.3 + - - +
41A LYS* 2.9 39.0 + - + +
128A VAL* 2.7 50.8 + - + +
129A GLY* 4.3 6.1 - - - +
130A PRO 4.9 4.4 + - - +
212A PHE* 5.8 0.2 - - - +
213A PRO* 4.1 24.8 - - + +
215A MET* 4.2 22.3 + - + +
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Residues in contact with LEU 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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34A LEU 3.1 15.5 + - - +
35A GLU* 3.2 11.9 + - - +
37A GLN* 1.3 76.9 - - - +
39A LYS* 1.3 63.5 + - - +
42A THR* 2.8 48.1 + - + +
44A LYS 3.9 9.0 - - - +
46A LEU* 3.9 37.9 - - + +
48A LEU* 5.0 9.2 - - + -
104A ALA 3.6 24.5 - - - +
105A ALA* 4.0 13.0 - - + -
215A MET* 3.8 19.4 - - + -
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Residues in contact with LYS 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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10A LYS 3.7 15.9 - - - -
11A GLY* 3.4 33.4 - - - +
12A TYR* 3.9 18.4 - - + -
35A GLU 3.1 8.7 + - - +
36A GLY 3.6 9.2 - - - +
38A LEU* 1.3 77.8 - - - +
40A LYS* 1.3 65.7 + - - +
43A GLY* 2.7 53.2 + - - +
44A LYS* 3.9 10.8 + - - +
45A LEU* 4.0 14.0 - - + +
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Residues in contact with LYS 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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7A TYR* 5.8 1.8 + - - -
12A TYR* 3.9 26.6 + - + +
36A GLY 3.1 13.6 + - - +
37A GLN* 3.0 30.2 + - - +
39A LYS* 1.3 78.8 - - - +
41A LYS* 1.3 84.0 + - + +
43A GLY* 4.3 1.4 + - - -
127A ARG 3.6 21.2 + - - -
128A VAL* 3.9 17.9 + - - +
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Residues in contact with LYS 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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37A GLN* 2.9 31.9 + - - +
38A LEU 3.9 0.9 - - - +
40A LYS* 1.3 107.4 - - - +
42A THR* 1.3 64.5 + - + +
43A GLY 3.5 0.3 + - - -
215A MET* 3.7 49.4 + - + +
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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
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38A LEU* 2.8 38.6 + - + +
41A LYS* 1.3 76.9 - - + +
43A GLY* 1.3 60.1 + - - +
44A LYS* 3.2 41.9 + - - +
215A MET* 5.1 3.4 - - + -
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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