Contacts of the helix formed by residues 17 - 29 (chain A) in PDB entry 1TF5
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 17 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15A THR 4.0 1.2 + - - -
16A LEU* 1.3 74.4 - - - +
18A ARG* 1.3 64.2 + - - +
19A TYR* 2.8 33.4 + - + +
20A GLU* 2.9 40.7 + - - +
21A LYS* 3.1 20.3 + - - +
87A MET* 6.0 0.2 - - - -
393A PRO* 6.3 0.8 - - - +
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Residues in contact with ARG 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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17A ASN* 1.3 75.1 - - - +
19A TYR* 1.3 80.1 + - + +
21A LYS* 3.7 8.1 + - - +
22A ILE* 3.0 48.6 + - + +
59A ASP* 4.3 14.5 + - - -
62A LEU* 5.3 5.3 - - - +
90A VAL* 3.9 14.2 - - - +
94A ASP* 2.9 42.0 + - - -
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Residues in contact with TYR 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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17A ASN* 2.8 25.4 + - + +
18A ARG* 1.3 88.8 - - + +
20A GLU* 1.3 62.4 + - - +
21A LYS 3.2 0.4 - - - -
22A ILE* 3.6 4.9 + - - +
23A ALA* 3.1 23.7 + - - +
87A MET* 3.4 40.5 - - + +
90A VAL* 3.9 17.5 - - + -
91A ALA* 4.1 14.8 - - + -
94A ASP* 3.9 22.0 + - - -
96A ASN* 4.8 5.2 + - - -
390A VAL* 3.5 37.5 - - + +
392A ILE* 5.3 1.3 - - + -
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Residues in contact with GLU 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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15A THR 4.7 1.0 - - - +
16A LEU* 3.5 32.5 - - + +
17A ASN* 2.9 47.6 + - - +
19A TYR* 1.3 74.9 - - - +
21A LYS* 1.3 58.5 + - - +
23A ALA* 3.4 6.8 + - - +
24A ASN* 3.0 36.9 + - - +
87A MET* 4.3 19.2 - - + +
393A PRO* 6.6 0.2 - - + -
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Residues in contact with LYS 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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14A ARG* 5.8 15.4 - - + +
16A LEU* 4.5 11.8 - - + +
17A ASN 3.1 15.6 + - - +
18A ARG* 3.7 8.3 - - - +
19A TYR 3.2 0.2 - - - -
20A GLU* 1.3 73.8 - - - +
22A ILE* 1.3 72.8 + - + +
24A ASN* 3.1 10.0 + - - +
25A ASP* 3.0 44.6 + - - +
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Residues in contact with ILE 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 ARG* 3.0 41.6 + - + +
19A TYR 4.1 1.6 - - - +
21A LYS* 1.3 83.3 - - + +
23A ALA* 1.3 62.8 + - - +
25A ASP* 3.2 15.0 + - - +
26A ILE* 3.0 29.5 + - + +
62A LEU* 3.5 32.5 - - + -
63A VAL* 4.3 12.8 - - + -
90A VAL* 3.8 24.7 - - + -
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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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19A TYR 3.1 19.7 + - - +
20A GLU* 3.4 7.0 - - - +
21A LYS 3.1 0.2 - - - -
22A ILE* 1.3 78.2 - - - +
24A ASN* 1.3 63.8 + - - +
26A ILE* 3.4 3.6 + - - +
27A ASP* 3.0 23.3 + - - +
83A LYS* 3.9 32.7 - - + +
86A LEU* 4.0 19.8 - - + +
87A MET* 3.9 8.5 - - + +
90A VAL* 5.6 0.4 - - - +
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Residues in contact with ASN 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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16A LEU* 3.3 28.9 - - - +
20A GLU* 3.0 23.6 + - - +
21A LYS* 3.7 5.4 - - - +
23A ALA* 1.3 74.5 - - - +
25A ASP* 1.3 56.7 + - - +
27A ASP* 3.1 9.4 + - - +
28A ALA* 2.7 38.0 + - - +
83A LYS* 6.1 1.2 - - - +
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Residues in contact with ASP 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 LYS* 3.0 43.1 + - - +
22A ILE* 3.4 15.4 - - - +
24A ASN* 1.3 76.9 - - - +
26A ILE* 1.3 62.9 + - - +
28A ALA* 3.0 22.8 + - - +
29A ILE* 3.4 12.1 + - - +
63A VAL* 4.0 22.0 - - + +
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Residues in contact with ILE 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 ILE* 3.0 34.5 + - + +
23A ALA 3.7 4.0 - - - +
25A ASP* 1.3 74.8 - - - +
27A ASP* 1.3 63.2 + - - +
28A ALA 3.3 0.3 + - - -
29A ILE* 3.3 18.1 + - - +
30A ARG* 3.7 5.4 + - - -
62A LEU* 4.3 1.6 - - + -
63A VAL* 3.5 27.8 - - + +
66A PHE* 3.5 34.8 - - + -
67A ALA* 3.8 29.1 - - + +
70A ARG* 4.2 10.8 + - - +
86A LEU* 4.2 26.7 - - + -
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Residues in contact with ASP 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 ALA 3.0 18.5 + - - +
24A ASN* 3.5 10.0 - - - +
26A ILE* 1.3 77.7 - - - +
28A ALA* 1.3 63.5 + - - +
30A ARG* 3.0 62.2 + - - +
70A ARG* 3.1 29.7 + - - +
83A LYS* 5.5 7.3 - - + +
86A LEU* 5.2 0.9 - - + -
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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 ASN 2.7 12.3 + - - +
25A ASP* 3.0 17.2 + - - +
27A ASP* 1.3 79.6 - - - +
29A ILE* 1.3 59.7 + - + +
30A ARG* 3.3 2.8 + - - +
31A GLY 4.8 2.1 + - - -
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Residues in contact with ILE 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 ASP 3.9 8.1 - - - +
26A ILE 3.4 12.8 - - - +
28A ALA* 1.3 80.3 - - + +
30A ARG* 1.3 63.9 + - - +
31A GLY 3.2 3.6 - - - +
32A ASP* 3.1 30.5 + - - +
33A TYR* 3.3 25.9 - - + +
63A VAL* 3.8 25.1 - - + -
64A GLU* 4.1 11.9 - - + -
67A ALA* 3.9 19.1 - - + -
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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