Contacts of the helix formed by residues 20 - 34 (chain A) in PDB entry 2P2B
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 ASN 20 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17A CYS* 4.0 12.0 + - - -
19A ILE* 1.3 76.9 - - - +
21A PRO* 1.4 76.0 - - + +
22A GLU* 3.1 21.3 + - - +
23A GLN* 2.9 50.3 + - - +
24A TYR 2.9 18.7 + - - -
428A GLY 3.5 3.8 - - - +
429A ALA* 3.5 4.4 - - - +
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Residues in contact with PRO 21 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A ILE* 4.1 12.1 - - + -
20A ASN* 1.4 89.9 - - + +
22A GLU* 1.3 71.9 + - - +
24A TYR* 3.2 4.9 + - + +
25A GLU* 3.0 35.9 + - + +
428A GLY 3.3 11.7 - - - +
429A ALA* 3.4 26.4 - - + +
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Residues in contact with GLU 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 ASN* 3.1 24.5 + - - +
21A PRO* 1.3 88.0 - - - +
23A GLN* 1.3 59.4 + - + +
25A GLU* 3.3 9.3 + - - +
26A THR* 3.0 33.6 + - - +
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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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18A LEU 3.5 17.0 - - - +
19A ILE* 3.5 9.3 - - + +
20A ASN* 2.9 48.3 + - - +
22A GLU* 1.3 74.5 - - + +
24A TYR* 1.3 64.7 + - - +
26A THR* 4.6 4.7 - - - +
27A LYS* 3.0 39.4 + - + +
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Residues in contact with TYR 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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19A ILE* 3.5 8.2 - - + +
20A ASN 2.9 17.4 + - - +
21A PRO* 3.2 8.0 + - + +
23A GLN* 1.3 73.4 - - - +
25A GLU* 1.3 82.7 + - - +
28A TYR* 2.8 51.4 + + + +
426A LEU* 4.4 14.6 - - + -
429A ALA* 3.7 16.6 - - + -
430A ILE* 4.0 26.2 - - + -
439A ARG* 3.4 26.6 - - - +
440A PRO* 2.7 32.8 + - - +
441A PHE* 5.1 0.9 - - - -
442A PHE* 3.5 30.6 - + - -
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Residues in contact with GLU 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 PRO* 3.0 18.4 + - + +
22A GLU* 3.6 9.9 - - - +
24A TYR* 1.3 95.4 - - - +
26A THR* 1.3 58.9 + - - +
28A TYR* 3.8 4.8 - - - +
29A LYS* 3.0 29.1 + - - +
439A ARG* 4.4 15.1 + - - -
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Residues in contact with THR 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 GLU 3.0 17.6 + - - -
23A GLN* 4.0 6.1 - - - -
24A TYR 3.3 0.2 - - - -
25A GLU* 1.3 73.6 - - - +
27A LYS* 1.3 64.7 + - + +
29A LYS* 3.4 5.8 + - - +
30A GLN* 3.0 28.8 + - + +
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Residues in contact with LYS 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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19A ILE* 4.3 25.3 - - + +
23A GLN* 3.0 28.6 + - - +
26A THR* 1.3 75.4 - - + +
28A TYR* 1.3 61.0 + - - +
30A GLN* 3.4 8.7 + - - +
31A SER* 2.9 30.8 + - - -
38A PHE* 3.9 24.6 - - + -
42A GLN* 4.9 8.7 - - - +
291A TYR* 4.3 16.8 + - - -
442A PHE* 3.8 15.7 - - + -
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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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24A TYR* 2.8 35.8 + + + +
25A GLU* 3.8 6.3 - - - +
27A LYS* 1.3 76.4 - - - +
29A LYS* 1.3 67.4 + - - +
31A SER* 2.6 23.7 + - - -
32A ILE* 3.2 35.8 + - + +
440A PRO* 3.7 29.3 - - + +
441A PHE 3.3 30.1 - - - -
442A PHE* 3.6 9.1 - + + -
444A VAL 2.7 23.0 + - - -
445A GLN* 4.1 6.6 - - - +
446A PRO* 4.3 1.4 - - - +
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Residues in contact with LYS 29 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25A GLU 3.0 17.6 + - - +
26A THR* 3.8 5.6 - - - +
27A LYS 3.4 0.2 - - - -
28A TYR* 1.3 81.5 - - + +
30A GLN* 1.3 57.8 + - - +
32A ILE* 3.3 4.2 + - - +
33A ASN* 2.8 48.2 + - - +
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Residues in contact with GLN 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 THR* 3.0 19.2 + - + +
27A LYS* 3.8 6.8 - - - +
29A LYS* 1.3 73.3 - - - +
31A SER* 1.3 59.2 + - - +
33A ASN* 4.8 2.2 - - - -
34A ASP* 2.8 49.8 + - + +
37A THR* 3.6 27.5 - - - +
38A PHE* 3.5 29.0 - - + -
41A GLU* 4.4 9.4 + - - +
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Residues in contact with SER 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 LYS 2.9 18.6 + - - -
28A TYR* 2.6 23.6 + - - -
30A GLN* 1.3 72.4 - - - +
32A ILE* 1.3 64.5 + - - +
35A PRO* 3.4 23.7 - - - +
38A PHE* 3.6 34.2 - - - +
39A TRP* 4.6 0.7 + - - -
442A PHE* 3.6 1.9 - - - -
443A GLY* 2.9 34.4 + - - -
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Residues in contact with ILE 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 TYR* 3.2 44.3 + - + +
29A LYS* 3.7 4.9 - - - +
30A GLN 3.2 0.4 - - - -
31A SER* 1.3 90.0 + - - +
33A ASN* 1.3 75.1 + - - +
35A PRO* 3.4 11.6 - - - +
443A GLY* 3.7 21.8 - - - +
445A GLN* 3.4 50.2 + - + +
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Residues in contact with ASN 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 LYS* 2.8 34.9 + - - +
30A GLN* 4.8 2.0 - - - -
32A ILE* 1.3 84.1 - - - +
34A ASP* 1.3 60.3 + - + +
35A PRO* 3.6 3.5 - - - +
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Residues in contact with ASP 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 GLN* 2.8 31.2 + - + +
33A ASN* 1.3 78.2 - - + +
35A PRO* 1.4 63.2 - - - +
36A ASP* 3.7 7.6 + - - +
37A THR* 2.6 35.5 + - - +
38A PHE 3.0 15.6 + - - -
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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