Contacts of the helix formed by residues 21 - 32 (chain A) in PDB entry 3A4T
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 21 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15A VAL* 4.2 1.1 - - - -
17A THR* 5.8 4.0 + - - -
20A ILE* 1.3 81.8 - - - +
22A PRO* 1.3 75.2 - - + +
23A GLU* 3.1 5.4 + - + +
24A VAL* 3.2 30.9 + - + +
25A LEU* 3.2 11.8 + - - +
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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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15A VAL* 3.8 12.1 - - + -
17A THR* 4.2 10.5 - - + -
20A ILE 4.1 4.7 - - - +
21A ASN* 1.3 89.5 - - + +
23A GLU* 1.3 63.6 - - + +
25A LEU* 3.7 1.2 + - - +
26A LYS* 3.0 29.2 + - - +
42A ASP* 3.3 32.1 - - + +
43A TYR* 3.7 23.3 - - + -
45A PHE* 3.8 12.1 - - + -
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Residues in contact with GLU 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 ASN* 3.2 3.4 - - + +
22A PRO* 1.3 80.3 - - + +
24A VAL* 1.3 66.1 + - + +
26A LYS* 4.0 15.7 - - - +
27A LYS* 3.2 24.9 + - - +
38A LYS* 3.1 28.2 + - - -
42A ASP 5.3 1.2 - - - +
45A PHE* 4.5 5.2 - - - -
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Residues in contact with VAL 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 ILE* 4.2 17.7 - - + -
21A ASN* 3.2 27.3 + - + +
23A GLU* 1.3 76.9 - - + +
25A LEU* 1.3 64.2 + - - +
27A LYS* 3.7 4.0 + - - +
28A ARG* 3.1 27.8 + - - +
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Residues in contact with LEU 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 ILE* 4.6 3.4 - - + -
15A VAL* 3.5 31.2 - - + -
20A ILE* 3.5 16.9 - - + +
21A ASN 3.2 12.4 + - - +
22A PRO 3.9 2.5 - - - +
24A VAL* 1.3 72.5 - - - +
26A LYS* 1.3 67.9 + - - +
28A ARG* 3.1 5.7 + - + +
29A LEU* 2.9 51.0 + - + +
45A PHE* 5.4 0.9 - - + -
59A GLU* 3.9 20.4 - - + -
64A TYR* 3.7 35.7 - - + +
65A TYR* 3.9 16.4 - - + -
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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 PRO 3.0 19.8 + - - +
23A GLU* 4.0 16.2 - - - +
24A VAL 3.4 0.2 - - - -
25A LEU* 1.3 77.6 - - - +
27A LYS* 1.3 56.2 + - - +
29A LEU 3.4 0.2 + - - -
30A GLU* 2.9 59.7 + - - +
36A LEU* 3.7 31.9 + - + +
37A GLU* 5.5 0.2 - - - +
38A LYS* 3.5 34.6 - - - +
45A PHE* 3.6 38.8 - - + -
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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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23A GLU 3.2 18.4 + - - +
24A VAL* 3.9 5.4 - - - +
26A LYS* 1.3 72.5 - - - +
28A ARG* 1.3 66.4 + - - +
30A GLU* 4.0 8.4 - - - +
31A ASN* 2.9 63.0 + - - +
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Residues in contact with ARG 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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20A ILE* 5.6 2.2 - - - -
24A VAL* 3.1 24.3 + - - +
25A LEU* 3.1 7.8 + - - +
27A LYS* 1.3 80.1 - - - +
29A LEU* 1.3 63.4 + - + +
31A ASN* 3.5 6.3 + - - +
32A LYS* 3.3 29.8 + - - +
58A PRO* 4.9 2.2 - - - +
59A GLU* 2.7 38.8 + - + +
62A PHE* 3.5 28.7 - - - -
64A TYR* 3.8 22.9 + - - -
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Residues in contact with LEU 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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13A ILE* 4.1 19.3 - - + -
25A LEU* 2.9 46.9 + - + +
26A LYS 4.1 2.2 - - - +
28A ARG* 1.3 74.5 - - - +
30A GLU* 1.3 60.9 + - - +
32A LYS* 3.0 22.1 + - + +
33A GLY 3.5 0.2 + - - -
34A VAL* 3.0 40.9 + - + +
36A LEU* 4.3 11.7 - - + -
52A PHE* 6.3 0.2 - - + -
57A THR* 4.8 9.9 - - + -
59A GLU* 3.9 36.6 - - + +
65A TYR* 4.2 11.9 - - + +
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Residues in contact with GLU 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 LYS* 2.9 46.8 + - - +
27A LYS* 4.1 8.2 + - - +
29A LEU* 1.3 75.4 - - - +
31A ASN* 1.3 61.1 + - - +
33A GLY* 3.1 17.8 + - - -
34A VAL 3.3 19.8 - - - +
35A VAL* 4.8 1.2 - - - +
36A LEU* 3.7 33.4 + - + +
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Residues in contact with ASN 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 55.6 + - - +
28A ARG* 3.9 7.0 - - - +
29A LEU 3.2 0.4 - - - -
30A GLU* 1.3 80.5 - - - +
32A LYS* 1.3 59.3 + - - +
33A GLY 3.3 1.4 + - - -
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Residues in contact with LYS 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 ARG* 3.3 21.6 + - - +
29A LEU* 3.0 14.7 + - + +
31A ASN* 1.3 78.4 - - + +
33A GLY* 1.3 55.7 + - - +
34A VAL* 3.4 1.8 - - + -
51A PRO* 3.5 6.8 - - - +
52A PHE* 3.3 45.8 - - + -
57A THR* 5.1 0.9 - - + -
58A PRO* 3.9 19.8 - - - +
59A GLU* 2.9 41.2 + - - +
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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