Contacts of the helix formed by residues 20 - 38 (chain A) in PDB entry 3PS8
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 GLU 20 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A ALA* 3.9 8.2 - - - +
17A SER* 3.1 35.9 + - - +
18A VAL 3.1 1.2 - - - -
19A GLU* 1.4 77.1 - - + +
21A GLU* 1.3 66.5 + - - +
22A GLY 3.0 4.0 + - - +
23A VAL* 3.0 18.9 + - + +
24A ARG* 3.0 11.4 + - - +
54A LYS* 3.2 30.7 + - - -
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Residues in contact with GLU 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A GLU 3.6 4.8 + - - -
20A GLU* 1.3 71.6 - - - +
22A GLY* 1.3 56.2 + - - +
24A ARG* 3.4 29.0 + - - +
25A ARG* 2.9 57.4 + - - +
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Residues in contact with GLY 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A GLU* 3.0 2.8 + - - +
21A GLU* 1.3 76.1 - - - +
23A VAL* 1.3 60.9 + - - +
25A ARG* 3.4 12.4 + - - +
26A ALA* 3.0 29.5 + - - +
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Residues in contact with VAL 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ALA* 3.7 24.0 - - + -
17A SER 3.5 26.9 - - - +
18A VAL* 3.8 16.4 - - + -
20A GLU* 3.0 10.4 + - + +
22A GLY* 1.3 73.9 - - - +
24A ARG* 1.3 60.0 + - - +
26A ALA* 3.2 6.0 + - - +
27A LEU* 3.0 30.7 + - + +
52A ALA* 3.8 23.3 - - + -
53A ARG 5.9 0.9 - - - +
54A LYS* 5.1 9.9 - - + -
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Residues in contact with ARG 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A VAL* 3.6 26.1 + - + +
19A GLU* 5.0 8.2 + - - +
20A GLU 3.0 11.7 + - - +
21A GLU* 3.4 38.0 + - - +
23A VAL* 1.3 75.7 - - - +
25A ARG* 1.3 72.4 + - - +
27A LEU* 3.5 7.9 + - + +
28A ASP* 3.0 46.9 + - - +
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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 GLU* 2.9 46.0 + - - +
22A GLY* 3.9 10.6 + - - +
23A VAL 3.3 0.2 - - - -
24A ARG* 1.3 87.1 - - - +
26A ALA* 1.3 62.6 + - - +
28A ASP* 3.5 5.9 + - - +
29A PHE* 3.1 24.0 + - - +
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Residues in contact with ALA 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 GLY 3.0 18.2 + - - +
23A VAL* 3.7 6.5 - - - +
25A ARG* 1.3 76.1 - - - +
27A LEU* 1.3 59.3 + - - +
29A PHE* 3.3 10.9 + - + +
30A ALA* 2.8 31.5 + - - +
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Residues in contact with LEU 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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18A VAL* 4.3 17.7 - - + -
23A VAL* 3.0 18.8 + - + +
24A ARG* 3.8 7.9 - - + +
26A ALA* 1.3 73.6 - - - +
28A ASP* 1.3 72.9 + - - +
30A ALA* 3.1 6.3 + - + +
31A VAL* 3.0 47.4 + - + +
46A ALA* 4.7 13.2 - - + -
49A VAL* 3.7 31.9 - - + -
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Residues in contact with ASP 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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24A ARG* 3.0 38.3 + - - +
25A ARG* 4.0 5.5 - - - +
27A LEU* 1.3 82.5 - - - +
29A PHE* 1.3 57.1 + - - +
31A VAL* 3.6 5.1 + - - +
32A GLY* 2.8 26.0 + - - -
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Residues in contact with PHE 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 3.1 18.3 + - - +
26A ALA* 3.4 9.9 - - - +
27A LEU 3.1 0.4 - - - -
28A ASP* 1.3 75.7 - - - +
30A ALA* 1.3 69.8 + - + +
32A GLY* 3.1 3.5 + - - -
33A GLU* 2.9 60.9 + - + +
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Residues in contact with ALA 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 ALA 2.8 19.1 + - - +
27A LEU* 3.1 6.9 + - + +
29A PHE* 1.3 80.6 - - + +
31A VAL* 1.3 56.3 + - + +
33A GLU* 3.2 6.5 + - - +
34A TYR* 2.8 35.0 + - - +
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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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27A LEU* 3.0 38.7 + - + +
28A ASP* 4.0 3.6 - - - +
30A ALA* 1.3 76.6 - - + +
32A GLY* 1.3 64.6 + - - +
34A TYR* 3.7 9.4 - - + +
35A ASN* 3.0 44.8 + - - +
43A HIS* 5.3 2.7 - - + -
44A SER 4.0 9.9 - - - +
45A ARG* 4.3 12.1 - - + -
46A ALA* 4.8 13.7 - - + +
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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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28A ASP 2.8 17.4 + - - -
29A PHE* 3.1 5.4 + - - -
31A VAL* 1.3 77.1 - - - +
33A GLU* 1.3 59.1 + - - +
35A ASN* 3.4 7.3 + - - +
36A LYS* 3.1 31.1 + - - +
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Residues in contact with GLU 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 PHE* 2.9 56.5 + - + +
30A ALA* 3.2 6.9 + - - +
32A GLY* 1.3 73.4 - - - +
34A TYR* 1.3 66.2 + - - +
36A LYS* 3.1 33.7 + - - +
37A ALA* 3.0 27.6 + - - +
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Residues in contact with TYR 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 ALA 2.8 17.1 + - - +
31A VAL* 3.7 11.9 - - + +
33A GLU* 1.3 77.6 - - - +
35A ASN* 1.3 60.9 + - - +
37A ALA* 3.5 5.7 + - - +
38A SER* 3.1 36.5 + - - -
44A SER* 4.0 26.7 - - - -
124A ACT 3.1 27.3 + - + +
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Residues in contact with ASN 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 VAL* 3.0 28.0 + - - +
32A GLY* 3.5 7.7 - - - +
34A TYR* 1.3 80.2 - - - +
36A LYS* 1.3 61.3 + - - +
38A SER* 3.4 20.8 + - - +
40A ASP 5.2 2.3 - - - +
42A TYR 4.2 3.8 - - - +
43A HIS* 3.5 23.6 - - - +
44A SER* 2.8 51.4 + - - -
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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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32A GLY 3.1 16.0 + - - +
33A GLU* 3.1 36.2 + - - +
35A ASN* 1.3 76.0 - - - +
37A ALA* 1.3 62.3 + - + +
38A SER 3.5 5.7 + - - +
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Residues in contact with ALA 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 GLU 3.0 16.2 + - - +
34A TYR* 3.9 5.6 - - - +
36A LYS* 1.3 75.6 - - - +
38A SER* 1.3 64.3 + - - +
39A ASN* 3.8 5.9 + - - -
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Residues in contact with SER 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A TYR* 3.1 26.1 + - - -
35A ASN* 3.4 18.8 + - - +
36A LYS 3.2 8.9 - - - +
37A ALA* 1.3 82.5 - - - +
39A ASN* 1.3 63.4 + - - +
40A ASP* 3.2 28.4 + - - +
42A TYR 5.0 0.7 + - - -
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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