Contacts of the helix formed by residues 16 - 29 (chain A) in PDB entry 3U7U
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 16 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A LEU* 3.3 4.2 - - + +
15A SER* 1.4 75.2 - - - +
17A LEU* 1.3 58.2 + - - +
18A GLU* 3.1 21.9 + - - +
19A GLN* 3.1 34.3 + - + +
20A GLN* 2.8 27.4 + - - +
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Residues in contact with LEU 17 (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 SER* 5.8 0.2 - - - +
14A LEU 4.2 9.9 - - - +
15A SER 3.2 12.4 + - - +
16A ASP* 1.3 70.3 + - - +
18A GLU* 1.4 58.5 + - - +
20A GLN* 3.5 6.7 + - + +
21A TYR* 3.1 25.3 + - - +
42A SER* 3.8 33.3 - - - +
43A ILE* 5.9 0.9 - - - +
44A GLU* 3.5 43.1 - - + +
68A GLN* 5.9 2.2 - - - +
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Residues in contact with GLU 18 (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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16A ASP* 3.1 11.5 + - - +
17A LEU* 1.4 75.7 - - - +
19A GLN* 1.4 55.0 + - - +
21A TYR* 3.2 6.8 + - - +
22A ARG* 2.7 67.8 + - - +
44A GLU* 4.3 0.2 + - - -
47A ARG* 3.4 42.9 + - - +
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Residues in contact with GLN 19 (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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14A LEU* 3.4 20.1 - - + +
16A ASP* 3.1 37.1 + - + +
18A GLU* 1.4 77.5 - - - +
20A GLN* 1.3 57.3 + - - +
22A ARG* 3.5 44.1 + - - +
23A ALA* 3.0 29.5 + - - +
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Residues in contact with GLN 20 (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 ASN* 5.9 2.2 + - - +
12A SER 4.9 0.8 + - - -
13A SER* 3.4 24.1 - - - +
14A LEU* 3.1 34.1 + - + +
16A ASP 2.8 13.6 + - - +
17A LEU* 3.5 13.2 - - + +
18A GLU 3.2 0.2 - - - -
19A GLN* 1.3 75.5 - - - +
21A TYR* 1.4 62.0 + - - +
23A ALA* 3.3 8.2 + - - +
24A LEU* 3.1 23.1 + - - +
39A GLU 5.8 1.0 + - - -
41A THR* 2.8 38.3 + - - +
42A SER* 4.0 13.9 - - - +
43A ILE* 4.7 5.3 - - + +
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Residues in contact with TYR 21 (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 LEU 3.1 14.9 + - - +
18A GLU* 3.2 13.4 + - - +
20A GLN* 1.4 73.3 - - - +
22A ARG* 1.3 72.2 + - + +
24A LEU* 3.1 11.1 + - + +
25A ARG* 3.1 52.3 + - - +
43A ILE* 4.5 16.8 - - + +
47A ARG* 3.6 55.9 - - + +
48A ASP* 2.6 40.8 + - - +
49A LEU* 4.0 10.3 - - + -
51A PHE* 4.2 5.8 - + - -
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Residues in contact with ARG 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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18A GLU* 2.7 51.0 + - - +
19A GLN* 3.5 38.7 + - - +
21A TYR* 1.3 78.8 - - + +
23A ALA* 1.4 56.2 + - - +
25A ARG* 3.5 8.9 + - + +
26A LYS* 2.9 28.0 + - - +
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Residues in contact with ALA 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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14A LEU* 4.3 13.5 - - + -
19A GLN 3.0 19.0 + - - +
20A GLN* 3.4 9.2 - - - +
21A TYR 3.2 0.2 - - - -
22A ARG* 1.4 73.1 - - - +
24A LEU* 1.4 55.4 + - - +
26A LYS* 3.1 10.7 + - + +
27A TYR* 2.9 52.6 + - + -
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Residues in contact with LEU 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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20A GLN* 3.1 15.1 + - - +
21A TYR* 3.1 11.2 + - + +
23A ALA* 1.4 73.6 - - - +
25A ARG* 1.3 62.5 + - - +
27A TYR* 4.9 0.9 - - - -
28A TYR* 3.1 47.3 + - + +
39A GLU 3.3 26.7 - - - +
40A ILE* 3.9 24.0 - - + -
43A ILE* 3.8 21.3 - - + -
49A LEU* 3.8 20.2 - - + -
51A PHE* 3.7 23.5 - - + -
52A LEU* 5.0 3.8 - - + -
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Residues in contact with ARG 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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21A TYR* 3.1 41.2 + - + +
22A ARG* 3.6 12.8 - - - +
24A LEU* 1.3 76.0 - - - +
26A LYS* 1.4 62.1 + - - +
29A GLU* 2.7 70.9 + - - +
48A ASP* 2.8 30.1 + - - +
50A SER* 4.5 2.0 + - - -
51A PHE* 3.7 37.2 - - + +
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Residues in contact with LYS 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 ARG 2.9 15.6 + - - +
23A ALA* 3.4 12.3 - - + +
25A ARG* 1.4 75.5 - - - +
27A TYR* 1.3 94.8 + - + +
28A TYR 3.6 0.2 + - - -
29A GLU* 4.4 5.6 + - - +
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Residues in contact with TYR 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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4A CYS* 3.9 19.2 - - - +
5A ALA* 6.1 2.7 - - + -
6A GLY* 4.5 11.8 + - - -
7A THR* 3.7 37.6 - - + +
23A ALA* 2.9 40.0 + - + +
24A LEU* 3.9 3.1 - - - +
26A LYS* 1.3 108.4 + - + +
28A TYR* 1.3 79.2 + - + +
29A GLU 3.9 0.6 - - - +
31A CYS* 4.9 0.2 - - - +
405A SER* 5.9 3.8 - - - -
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Residues in contact with TYR 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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4A CYS* 4.3 2.2 - - - -
6A GLY* 3.7 16.8 - - - -
7A THR* 3.2 19.5 + - + -
24A LEU* 3.1 37.2 + - + +
27A TYR* 1.3 89.9 - + + +
29A GLU* 1.3 66.6 + - - +
30A ASN 3.5 0.3 + - - -
31A CYS* 3.5 18.9 + - + +
34A VAL* 3.7 22.7 - - + -
37A ASN 2.6 29.2 + - - -
38A LEU* 3.8 23.8 - - + -
39A GLU 3.2 27.6 + - - -
51A PHE* 4.3 12.2 - - + +
52A LEU* 4.5 8.9 - - + +
54A SER* 3.6 8.3 + - - -
55A VAL* 4.7 4.9 - - + +
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Residues in contact with GLU 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 ARG* 2.7 60.2 + - - +
26A LYS* 4.4 5.1 + - - +
27A TYR 3.9 0.7 - - - +
28A TYR* 1.3 77.9 - - - +
30A ASN* 1.4 81.8 + - - +
31A CYS* 3.2 6.2 + - - +
51A PHE* 3.8 25.8 - - + +
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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