Contacts of the helix formed by residues 21 - 37 (chain A) in PDB entry 3U81
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 ASP 21 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18A LYS* 3.1 45.0 + - + +
19A PRO 4.4 0.2 - - - +
20A GLY* 1.3 77.3 - - - +
22A PRO* 1.3 65.0 - - - +
23A GLN* 3.3 11.1 + - - +
24A SER* 2.8 47.9 + - - +
25A VAL* 3.2 9.0 + - - +
106A ALA* 4.2 1.4 + - - +
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Residues in contact with PRO 22 (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 GLY 3.4 11.9 - - - +
21A ASP* 1.3 85.7 - - - +
23A GLN* 1.3 63.6 + - - +
25A VAL* 3.1 8.7 + - + +
26A LEU* 3.0 28.3 + - - +
74A VAL* 3.9 16.2 - - + +
78A ARG* 3.6 28.5 - - + -
106A ALA* 3.9 10.1 - - + +
108A LEU* 3.7 24.2 - - + -
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Residues in contact with GLN 23 (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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21A ASP* 3.2 7.9 + - - +
22A PRO* 1.3 78.8 - - - +
24A SER* 1.3 57.9 + - - +
26A LEU* 3.3 14.2 + - - +
27A GLU* 2.9 67.7 + - - +
75A ARG* 5.2 7.7 - - - +
78A ARG* 3.3 35.7 + - - +
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Residues in contact with SER 24 (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 ALA* 3.7 5.8 - - - +
18A LYS* 2.9 35.8 + - - -
21A ASP* 2.8 36.2 + - - +
23A GLN* 1.3 76.4 - - - +
25A VAL* 1.3 56.3 + - - +
27A GLU* 3.8 8.8 - - - +
28A ALA* 2.9 30.3 + - - +
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Residues in contact with VAL 25 (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 VAL* 4.1 3.8 - - + +
17A ALA* 3.9 12.1 - - + -
18A LYS 4.5 0.7 - - - +
21A ASP 3.6 12.3 - - - +
22A PRO* 3.1 9.8 + - + +
24A SER* 1.3 74.7 + - - +
26A LEU* 1.3 66.3 + - - +
28A ALA* 3.3 3.5 + - - +
29A ILE* 3.0 29.4 + - + +
74A VAL* 4.4 14.4 - - + -
102A MET* 3.9 33.0 - - + +
105A PHE* 3.8 28.7 - - + -
106A ALA* 4.3 16.6 - - + +
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Residues in contact with LEU 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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22A PRO 3.0 16.8 + - - +
23A GLN* 3.6 15.3 - - - +
25A VAL* 1.3 76.1 - - - +
27A GLU* 1.3 63.9 + - + +
29A ILE* 3.3 2.2 + - + -
30A ASP* 3.0 29.7 + - - +
71A TYR* 3.5 57.1 - - + +
74A VAL* 3.8 9.2 - - + -
75A ARG* 3.8 33.7 - - - +
78A ARG* 3.8 36.1 - - - +
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Residues in contact with GLU 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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23A GLN* 2.9 51.0 + - - +
24A SER* 3.9 8.3 - - - +
26A LEU* 1.3 75.8 - - + +
28A ALA* 1.3 58.2 + - - +
30A ASP* 3.4 6.2 + - - +
31A THR* 2.8 37.2 + - - +
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Residues in contact with ALA 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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12A TYR* 3.3 34.5 - - + -
13A VAL* 4.3 8.1 - - + -
16A ASN* 4.8 1.8 - - + -
17A ALA* 4.0 21.1 - - + +
24A SER 2.9 18.5 + - - +
25A VAL 3.7 4.3 - - - +
26A LEU 3.2 0.2 - - - -
27A GLU* 1.3 74.3 - - - +
29A ILE* 1.3 65.4 + - - +
31A THR* 3.3 2.8 + - - -
32A TYR 3.0 18.9 + - - -
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Residues in contact with ILE 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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9A ILE* 3.9 22.2 - - + -
12A TYR* 5.4 0.2 - - - -
13A VAL* 3.5 17.9 - - + -
25A VAL* 3.0 21.7 + - + +
26A LEU* 3.7 6.1 - - + +
28A ALA* 1.3 75.8 - - - +
30A ASP* 1.3 58.2 + - - +
32A TYR* 3.8 2.7 - - - +
33A CYS* 2.9 40.2 + - - -
41A ASN 4.4 6.3 - - - +
69A CYS* 5.3 1.8 - - + +
71A TYR* 3.7 45.3 - - + +
74A VAL* 5.9 0.2 - - + -
102A MET* 4.0 26.9 - - + -
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Residues in contact with ASP 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 LEU* 3.0 18.4 + - - +
27A GLU* 3.9 5.7 - - - +
29A ILE* 1.3 75.7 - - - +
31A THR* 1.3 58.5 + - - +
33A CYS* 4.2 3.1 - - - +
34A THR* 2.7 35.3 + - - +
41A ASN 3.8 3.5 - - - +
42A VAL* 3.7 10.6 - - + +
43A GLY 2.8 27.5 + - - -
44A ASP* 3.5 20.4 + - + +
71A TYR* 2.6 33.8 + - - -
75A ARG* 4.6 1.0 + - - -
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Residues in contact with THR 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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12A TYR* 3.5 22.4 - - - +
27A GLU* 2.8 25.5 + - - +
28A ALA* 3.7 6.5 - - - -
30A ASP* 1.3 77.2 - - - +
32A TYR* 1.3 62.2 + - - +
34A THR* 3.7 4.8 - - - -
35A GLN* 3.1 23.0 + - + +
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Residues in contact with TYR 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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8A ARG* 3.4 45.3 - - + +
9A ILE* 4.0 22.2 - - + -
11A ARG* 5.6 1.2 + - - -
12A TYR* 3.4 41.2 - + + -
28A ALA 3.0 16.4 + - - +
29A ILE* 3.8 3.8 - - - +
31A THR* 1.3 79.8 - - - +
33A CYS* 1.3 58.9 + - - +
35A GLN* 3.1 11.7 + - + +
36A LYS* 3.0 53.5 + - + +
38A TRP* 3.7 24.1 - + - -
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Residues in contact with CYS 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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9A ILE* 3.8 28.7 - - - -
29A ILE* 2.9 25.0 + - - +
30A ASP 4.2 0.4 - - - +
32A TYR* 1.3 79.0 - - - +
34A THR* 1.3 58.0 + - - +
36A LYS 3.4 0.5 + - - -
37A GLU 3.0 21.7 + - - -
38A TRP* 3.0 30.1 + - + +
41A ASN* 3.4 46.4 - - + +
42A VAL* 3.9 5.3 - - + +
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Residues in contact with THR 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 ASP* 2.7 22.8 + - - +
31A THR* 3.7 6.1 - - - -
33A CYS* 1.3 73.4 - - - +
35A GLN* 1.3 67.5 + - - +
37A GLU* 3.0 7.6 + - - +
42A VAL* 3.6 24.7 - - - +
199A GLU* 4.1 14.0 + - - +
200A TYR* 2.8 34.5 + - - +
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Residues in contact with GLN 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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31A THR* 3.1 14.9 + - + +
32A TYR* 3.1 15.9 + - + +
34A THR* 1.3 79.4 - - - +
36A LYS* 1.3 80.5 + - - +
37A GLU* 3.4 9.2 + - - +
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Residues in contact with LYS 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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8A ARG* 3.7 18.3 - - - +
32A TYR* 3.0 45.8 + - + +
33A CYS 4.0 0.7 - - - +
34A THR 3.2 0.4 - - - -
35A GLN* 1.3 90.9 - - - +
37A GLU* 1.3 70.3 + - - +
38A TRP* 3.4 53.4 + - + +
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Residues in contact with GLU 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 CYS 3.0 3.4 + - - -
34A THR 3.0 5.2 + - - +
35A GLN 3.8 8.2 - - - +
36A LYS* 1.3 83.2 - - - +
38A TRP* 1.3 62.4 + - - +
39A ALA* 3.3 7.4 + - - +
200A TYR* 3.5 56.8 + - + +
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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