Contacts of the helix formed by residues 22 - 35 (chain A) in PDB entry 2PEA
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 THR 22 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20A SER 4.4 4.3 - - - +
21A ASP* 1.3 75.6 - - - +
23A ILE* 1.3 66.7 + - - +
24A GLU* 3.8 5.6 + - - +
25A ASN* 2.4 48.9 + - - +
26A VAL* 2.9 23.7 + - - +
52A ASP 4.4 6.3 - - - +
53A GLY 5.7 3.4 - - - +
54A ARG 3.6 9.2 - - - +
55A THR* 4.2 13.7 - - + +
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Residues in contact with ILE 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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22A THR* 1.3 71.6 - - - +
24A GLU* 1.3 58.5 + - - +
26A VAL* 3.0 8.8 + - + +
27A LYS* 2.8 32.4 + - - +
43A LEU* 4.1 19.5 - - + -
50A LEU* 4.0 34.3 - - + +
51A GLU 3.0 30.3 - - - +
52A ASP* 3.9 14.1 - - - +
54A ARG 3.0 17.1 + - - +
55A THR 4.7 2.0 - - - +
56A LEU* 3.9 31.0 - - + +
59A TYR* 4.7 5.8 - - + -
67A LEU* 5.6 0.7 - - + -
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Residues in contact with GLU 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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22A THR* 3.2 5.1 + - - +
23A ILE* 1.3 79.8 - - - +
25A ASN* 1.3 67.2 + - - +
27A LYS* 3.3 10.5 + - + +
28A ALA* 3.0 22.8 + - + +
38A PRO* 5.7 5.7 - - + +
52A ASP* 3.6 36.4 + - + +
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Residues in contact with ASN 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 ASP* 4.8 15.7 + - + +
22A THR* 2.4 43.0 + - - +
24A GLU* 1.3 85.0 - - - +
26A VAL* 1.3 62.4 + - - +
28A ALA* 3.1 9.7 + - - +
29A LYS* 3.0 31.8 + - - +
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Residues in contact with VAL 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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3A ILE* 4.7 9.9 - - + -
5A VAL* 5.5 2.2 - - + -
15A LEU* 4.5 18.4 - - + -
17A VAL* 4.4 12.8 - - + -
21A ASP* 4.7 4.5 - - + -
22A THR 2.9 18.3 + - - +
23A ILE* 3.0 11.0 + - + +
25A ASN* 1.3 76.2 - - - +
27A LYS* 1.3 62.7 + - - +
29A LYS* 3.1 12.4 + - + +
30A ILE* 3.0 24.4 + - + +
43A LEU* 4.2 16.8 - - + -
56A LEU* 4.2 32.8 - - + -
67A LEU* 5.5 4.7 - - + -
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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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23A ILE* 2.8 21.8 + - - +
24A GLU* 3.5 9.2 - - - +
26A VAL* 1.3 75.9 - - - +
28A ALA* 1.3 57.9 + - - +
30A ILE* 3.1 12.4 + - - +
31A GLN* 2.9 27.8 + - - +
38A PRO* 3.6 38.3 - - + +
41A GLN* 3.5 35.3 + - + +
42A ARG* 4.3 0.2 - - - +
43A LEU* 3.4 40.6 - - + +
50A LEU 4.8 3.4 + - - -
52A ASP* 3.2 33.8 + - - +
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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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24A GLU* 3.0 15.0 + - + +
25A ASN* 3.1 12.8 + - - +
27A LYS* 1.3 77.2 - - - +
29A LYS* 1.3 61.4 + - + +
31A GLN* 3.2 14.9 + - - +
32A ASP* 3.0 21.8 + - - +
38A PRO* 4.8 4.0 - - + +
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Residues in contact with LYS 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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15A LEU* 4.6 17.3 - - + -
16A GLU 3.5 25.3 + - - +
17A VAL* 4.4 11.2 - - + -
21A ASP* 4.4 18.1 + - - -
25A ASN* 3.0 21.4 + - - +
26A VAL* 3.1 11.0 + - - +
28A ALA* 1.3 79.1 - - + +
30A ILE* 1.3 62.0 + - - +
32A ASP* 3.3 8.2 + - - +
33A LYS* 3.1 30.8 + - + +
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Residues in contact with ILE 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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5A VAL* 4.2 23.1 - - + -
13A ILE* 5.1 7.9 - - + -
15A LEU* 3.9 18.6 - - + -
26A VAL* 3.0 17.0 + - + +
27A LYS* 3.1 10.7 + - - +
29A LYS* 1.3 74.3 - - - +
31A GLN* 1.3 55.6 + - - +
33A LYS* 3.1 5.8 + - - +
34A GLU* 2.7 40.4 + - + +
36A ILE* 4.2 14.4 - - + -
41A GLN* 3.0 35.2 - - - +
43A LEU* 4.2 22.7 - - + -
69A LEU* 4.3 6.3 - - + -
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Residues in contact with GLN 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 12.2 + - - +
28A ALA* 3.4 14.6 - - - +
30A ILE* 1.3 76.2 - - - +
32A ASP* 1.3 61.7 + - - +
35A GLY* 2.8 32.7 + - - +
36A ILE 3.6 25.8 - - - +
37A PRO* 4.6 5.3 - - - +
38A PRO* 3.1 30.9 - - + +
41A GLN* 4.2 0.2 - - - +
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Residues in contact with ASP 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 ALA 3.0 9.3 + - - +
29A LYS* 3.4 12.6 - - - +
30A ILE 3.2 0.2 - - - -
31A GLN* 1.3 82.8 - - - +
33A LYS* 1.3 63.7 + - + +
35A GLY 4.8 0.3 + - - -
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Residues in contact with LYS 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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13A ILE* 4.5 13.4 - - + +
14A THR 3.3 22.0 + - - -
15A LEU* 3.5 24.3 - - + +
16A GLU 5.5 1.2 - - - +
29A LYS* 3.1 18.1 + - - +
30A ILE* 3.1 5.5 + - - +
32A ASP* 1.3 83.7 - - + +
34A GLU* 1.3 73.8 + - + +
35A GLY 3.8 0.2 - - - -
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Residues in contact with GLU 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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7A THR* 6.0 2.0 - - + -
11A LYS* 3.8 23.9 - - - +
13A ILE* 3.5 36.4 - - + +
30A ILE* 2.7 18.9 + - + +
33A LYS* 1.3 82.6 - - + +
35A GLY* 1.3 60.5 + - - +
36A ILE* 3.4 31.7 + - + +
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Residues in contact with GLY 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 GLN* 2.8 28.3 + - - -
32A ASP 4.8 0.2 + - - -
33A LYS 3.8 0.6 - - - -
34A GLU* 1.3 73.2 - - - +
36A ILE* 1.3 61.5 + - - +
37A PRO* 3.4 9.9 - - - +
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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