Contacts of the helix formed by residues 32 - 49 (chain A) in PDB entry 1TV9
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 ALA 32 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26A GLU* 2.9 31.6 + - - +
27A LYS* 4.5 0.4 + - - -
30A SER* 4.3 6.1 - - - +
31A GLN* 1.3 77.0 - - - +
33A ILE* 1.3 65.0 + - - +
34A HIS 3.2 2.9 - - - -
35A LYS* 3.0 20.1 + - + +
36A TYR* 3.0 20.1 + - - +
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Residues in contact with ILE 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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27A LYS* 4.0 22.0 - - + +
31A GLN 3.8 2.2 + - - -
32A ALA* 1.3 74.9 - - - +
34A HIS* 1.3 88.6 + - + +
36A TYR* 3.4 31.5 - - + +
37A ASN* 3.0 35.2 + - - +
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Residues in contact with HIS 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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32A ALA 3.2 0.8 - - - -
33A ILE* 1.3 95.7 - - + +
35A LYS* 1.3 61.9 + - + +
37A ASN* 3.5 10.7 + - - +
38A ALA* 3.0 25.3 + - - +
1D G 4.0 13.6 - - + +
5T C 3.3 79.0 + + + +
6T A 5.0 3.8 + - - -
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Residues in contact with LYS 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A GLU* 3.6 30.4 + - + +
32A ALA* 3.0 20.9 + - + +
34A HIS* 1.3 76.2 - - - +
36A TYR* 1.3 67.1 + - - +
38A ALA* 3.6 6.8 - - - +
39A TYR* 3.0 32.3 + - + -
1D G 2.6 78.0 + - + +
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Residues in contact with TYR 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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23A ALA* 3.3 41.3 - - + +
24A ASN* 4.0 10.5 - - - -
26A GLU* 3.8 2.6 - - - +
27A LYS* 3.4 41.7 - - + +
32A ALA 3.0 11.0 + - - +
33A ILE* 3.4 29.8 - - + +
35A LYS* 1.3 79.5 - - - +
37A ASN* 1.3 87.8 + - - +
39A TYR 3.3 0.3 + - - -
40A ARG* 3.0 67.9 + - + +
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Residues in contact with ASN 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 ILE* 3.0 30.8 + - - +
34A HIS* 4.0 11.8 + - - +
35A LYS 3.2 0.2 - - - -
36A TYR* 1.3 85.9 - - - +
38A ALA* 1.3 55.1 + - - +
40A ARG* 3.0 38.0 + - - +
41A LYS* 2.7 37.0 + - - +
5T C 6.4 0.4 - - - +
6T A 5.4 5.1 + - - -
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Residues in contact with ALA 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A HIS 3.0 17.9 + - - +
35A LYS* 3.3 6.0 + - - +
37A ASN* 1.3 73.9 - - - +
39A TYR* 1.3 64.3 + - - +
41A LYS* 3.2 9.6 + - - +
42A ALA* 3.0 23.4 + - - +
64A GLY 4.4 4.6 - - - +
69A ILE* 4.6 2.6 - - + +
1D G 3.5 43.7 + - + +
2D T 4.7 9.0 - - - +
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Residues in contact with TYR 39 (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 LEU* 3.6 23.5 - - + +
22A LEU* 3.7 28.6 - - + +
23A ALA* 3.5 25.6 - - + -
26A GLU* 3.7 30.8 + - + -
35A LYS* 3.0 24.4 + - + +
38A ALA* 1.3 77.3 - - - +
40A ARG* 1.3 57.1 + - - +
42A ALA* 3.3 4.5 + - - +
43A ALA* 2.8 30.8 + - - +
69A ILE* 3.9 30.3 - - + -
72A LYS* 3.4 24.5 + - + +
1D G 3.4 33.2 + - - -
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Residues in contact with ARG 40 (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 THR* 6.0 3.4 - - + +
23A ALA* 4.1 8.1 - - + -
36A TYR* 3.0 56.6 + - + +
37A ASN* 3.0 31.3 + - - +
39A TYR* 1.3 76.3 - - - +
41A LYS* 1.3 59.1 + - - +
43A ALA* 3.3 7.4 + - - +
44A SER* 2.9 35.5 + - - +
276A ASP* 4.9 13.3 + - - -
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Residues in contact with LYS 41 (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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37A ASN 2.7 21.5 + - - +
38A ALA* 3.5 8.7 - - - +
40A ARG* 1.3 72.1 - - - +
42A ALA* 1.3 61.5 + - - +
44A SER* 3.4 6.9 + - - -
45A VAL* 3.1 23.2 + - + +
63A PRO* 4.2 12.9 - - - +
64A GLY* 4.1 26.1 - - - +
3D C 4.4 18.0 - - - -
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Residues in contact with ALA 42 (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 LEU* 4.0 11.7 - - + -
38A ALA 3.0 11.6 + - - +
39A TYR 3.7 3.4 - - - +
41A LYS* 1.3 73.7 - - - +
43A ALA* 1.3 66.7 + - - +
45A VAL* 3.4 8.7 - - - +
46A ILE* 3.1 29.5 + - - +
64A GLY 3.7 13.4 + - - +
65A VAL* 4.2 9.0 - - + -
69A ILE* 3.5 31.4 - - + -
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Residues in contact with ALA 43 (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 THR* 4.0 12.5 - - - +
19A LEU* 3.9 19.7 - - + +
20A THR* 4.0 20.9 - - - +
39A TYR 2.8 21.0 + - - +
40A ARG* 3.3 8.7 + - - +
42A ALA* 1.3 74.2 - - - +
44A SER* 1.3 57.8 + - - +
46A ILE* 3.3 3.8 + - - +
47A ALA* 2.9 30.8 + - - +
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Residues in contact with SER 44 (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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40A ARG* 2.9 21.3 + - - +
41A LYS* 3.7 6.5 - - - -
42A ALA 3.2 0.2 - - - -
43A ALA* 1.3 74.9 - - - +
45A VAL* 1.3 65.1 + - - +
47A ALA* 3.3 7.6 + - - +
48A LYS* 3.2 27.6 + - - +
277A ILE* 5.9 5.3 - - - +
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Residues in contact with VAL 45 (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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41A LYS* 3.1 10.0 + - + +
42A ALA* 3.4 13.0 - - - +
44A SER* 1.3 79.1 - - - +
46A ILE* 1.3 67.4 + - - +
48A LYS* 3.3 8.5 + - + +
49A TYR* 3.2 20.4 + - - +
62A LEU* 4.0 23.7 - - + +
63A PRO* 3.8 44.2 - - + +
65A VAL* 4.1 9.9 - - + -
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Residues in contact with ILE 46 (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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12A ASN* 3.8 15.1 + - + +
15A ILE* 3.8 14.1 - - + -
16A THR* 3.6 19.5 - - + -
19A LEU* 3.6 24.2 - - + -
42A ALA 3.1 17.3 + - - +
43A ALA* 3.7 3.4 - - - +
45A VAL* 1.3 90.0 - - + +
47A ALA* 1.3 62.4 + - - +
49A TYR* 3.1 24.6 + - - +
53A ILE* 3.7 26.5 - - + -
59A ALA* 4.9 0.4 - - + -
62A LEU* 4.2 8.7 - - + -
65A VAL* 4.2 11.0 - - + -
69A ILE* 5.0 0.2 - - + -
73A ILE* 3.9 16.8 - - + -
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Residues in contact with ALA 47 (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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6A ALA* 4.6 5.9 - - + +
7A PRO* 3.3 24.1 - - - +
12A ASN* 5.9 0.7 - - - -
16A THR* 4.1 14.8 - - + -
43A ALA 2.9 18.8 + - - +
44A SER* 3.6 9.9 - - - +
45A VAL 3.3 0.2 - - - -
46A ILE* 1.3 78.7 - - - +
48A LYS* 1.3 59.9 + - + +
49A TYR 3.7 0.7 + - - +
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Residues in contact with LYS 48 (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 LYS* 4.5 20.0 - - - +
6A ALA* 4.8 18.4 - - + +
7A PRO* 3.7 11.5 - - + +
44A SER* 3.2 17.4 + - - +
45A VAL* 3.7 8.5 - - + +
46A ILE 3.1 0.8 - - - -
47A ALA* 1.3 78.0 - - + +
49A TYR* 1.3 64.0 + - - +
50A PRO* 3.3 9.0 - - - +
277A ILE* 6.4 0.9 - - - -
335A GLU* 2.5 39.8 + - - -
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Residues in contact with TYR 49 (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 PRO* 3.8 8.6 - - - +
11A LEU* 4.3 1.7 - - - +
12A ASN* 3.9 4.6 + - - -
45A VAL 3.2 10.8 + - - +
46A ILE* 3.1 20.8 + - - +
47A ALA 4.4 0.7 - - - +
48A LYS* 1.3 76.2 - - - +
50A PRO* 1.3 68.5 - - + +
51A HIS* 3.2 54.1 + + + +
53A ILE* 3.6 26.7 - - + -
58A GLU* 2.7 39.7 + - + +
62A LEU* 3.9 33.4 - - + -
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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