Contacts of the helix formed by residues 32 - 54 (chain A) in PDB entry 1R6T
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 SER 32 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A ASN 3.6 2.5 + - - -
31A ALA* 1.3 76.0 - - - +
33A LYS* 1.3 66.1 + - - +
34A ASP* 3.7 9.9 + - - +
35A GLU* 2.7 40.7 + - - +
36A ILE* 3.1 22.4 + - - +
205A ASP* 4.1 18.8 - - - -
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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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32A SER* 1.3 74.3 - - - +
34A ASP* 1.3 56.8 + - - +
36A ILE* 3.4 11.5 + - + +
37A ASP* 2.6 46.3 + - - +
205A ASP* 2.9 49.3 + - + +
206A LEU* 4.2 4.0 - - - +
207A THR* 4.6 8.1 - - - +
210A GLN* 3.4 29.2 + - - +
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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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32A SER* 3.2 9.8 + - - +
33A LYS* 1.3 77.1 - - - +
35A GLU* 1.3 66.3 + - + +
37A ASP* 3.4 9.5 + - - +
38A SER* 3.0 28.2 + - - -
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Residues in contact with GLU 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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26A LEU* 4.6 7.1 - - + +
30A ASN 4.9 0.3 - - - +
31A ALA* 3.6 16.7 - - + +
32A SER* 2.7 44.5 + - - +
34A ASP* 1.3 77.2 - - + +
36A ILE* 1.3 63.0 + - - +
38A SER* 3.3 7.8 + - - -
39A ALA* 3.1 21.7 + - - +
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Residues in contact with ILE 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 VAL* 4.9 2.9 - - + -
26A LEU* 4.2 22.4 - - + +
27A LYS* 3.9 50.7 - - + +
31A ALA* 3.8 15.7 - - + +
32A SER 3.1 16.9 + - - +
33A LYS* 3.7 12.1 - - + +
35A GLU* 1.3 76.1 - - - +
37A ASP* 1.3 67.0 + - - +
39A ALA* 3.1 8.5 + - - +
40A VAL* 3.0 33.3 + - + +
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Residues in contact with ASP 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A LYS* 2.6 40.9 + - - +
34A ASP* 3.6 11.4 + - - +
36A ILE* 1.3 77.1 - - - +
38A SER* 1.3 61.7 + - - +
40A VAL* 3.2 10.0 + - - +
41A LYS* 3.0 44.0 + - - +
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Residues in contact with SER 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A ASP 3.0 16.9 + - - -
35A GLU* 3.7 7.4 - - - -
36A ILE 3.2 0.2 - - - -
37A ASP* 1.3 75.8 - - - +
39A ALA* 1.3 61.4 + - - +
41A LYS* 3.4 24.0 + - - +
42A MSE 3.5 12.0 + - - +
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Residues in contact with ALA 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 GLN* 2.8 34.4 + - - +
22A LEU* 5.4 2.5 - - + -
23A VAL* 3.8 10.7 - - + +
26A LEU* 3.6 29.8 - - + -
35A GLU 3.1 7.1 + - - +
36A ILE* 3.1 9.7 + - - +
38A SER* 1.3 77.8 - - - +
40A VAL* 1.3 62.1 + - - +
42A MSE 3.4 2.5 + - - -
43A LEU* 3.1 12.1 + - - +
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Residues in contact with VAL 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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23A VAL* 4.0 22.0 - - + -
27A LYS* 4.8 5.8 - - - +
36A ILE* 3.0 24.4 + - + +
37A ASP* 3.5 11.7 - - - +
38A SER 3.2 0.2 - - - -
39A ALA* 1.3 74.0 - - - +
41A LYS* 1.3 56.0 + - + +
42A MSE 3.0 1.8 - - - -
43A LEU* 2.8 14.8 + - + +
44A VAL* 2.7 49.0 + - + +
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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 ASP* 3.0 37.7 + - - +
38A SER* 3.6 15.8 + - - +
39A ALA 3.4 0.2 - - - -
40A VAL* 1.3 77.7 - - + +
42A MSE 1.3 57.2 + - - +
44A VAL* 3.8 7.6 - - - +
45A SER* 3.0 28.6 + - - -
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Residues in contact with MSE 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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15A SER* 5.5 1.1 - - - +
19A GLN* 3.6 28.5 - - + +
38A SER 3.5 8.3 + - - +
39A ALA* 3.4 10.4 + - - +
40A VAL 3.0 0.4 - - - -
41A LYS* 1.3 76.9 - - - +
43A LEU* 1.3 58.3 + - - +
45A SER* 3.7 5.2 - - - -
46A LEU* 2.7 68.6 + - + +
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Residues in contact with LEU 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 ILE* 3.6 29.4 - - + +
19A GLN* 3.9 13.2 - - + +
20A GLY* 4.0 17.5 - - - +
23A VAL* 4.2 21.5 - - + -
39A ALA 3.1 10.3 + - - +
40A VAL* 2.8 16.5 + - + +
42A MSE 1.3 80.5 - - - +
44A VAL* 1.3 64.7 + - + +
46A LEU* 3.3 3.5 + - - +
47A LYS* 3.0 61.8 + - + +
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Residues in contact with VAL 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 VAL* 2.7 37.5 + - + +
41A LYS* 3.8 7.6 - - - +
43A LEU* 1.3 73.9 - - + +
45A SER* 1.3 63.3 + - - +
47A LYS* 3.2 9.9 + - + +
48A MSE 3.0 25.6 + - + +
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Residues in contact with SER 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 3.0 19.9 + - - -
42A MSE 3.7 6.7 - - - -
44A VAL* 1.3 78.0 - - - +
46A LEU* 1.3 64.2 + - - +
48A MSE 3.2 15.8 + - - +
49A SER* 3.2 26.9 + - - -
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Residues in contact with LEU 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 LEU* 3.2 28.6 - - + +
15A SER* 3.7 40.8 - - - +
16A ILE* 3.2 24.7 - - + +
19A GLN* 4.4 4.7 - - + -
42A MSE 2.7 50.2 + - + +
43A LEU* 3.6 5.6 - - - +
45A SER* 1.3 74.9 - - - +
47A LYS* 1.3 58.9 + - - +
49A SER* 3.9 5.8 + - - +
50A TYR 3.6 4.2 + - - -
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Residues in contact with LYS 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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16A ILE* 3.6 38.4 - - + -
43A LEU* 3.0 45.1 + - + +
44A VAL* 3.2 7.8 + - + +
46A LEU* 1.3 76.0 - - - +
48A MSE 1.3 61.2 + - - +
49A SER 3.3 0.4 - - - -
50A TYR* 3.3 3.2 + - - +
51A LYS* 3.0 27.5 + - - +
57A ASP 4.0 3.7 - - - +
58A TYR* 3.8 27.8 - - + -
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Residues in contact with MSE 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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44A VAL* 3.0 16.7 + - + +
45A SER* 3.2 18.1 + - - +
47A LYS* 1.3 76.9 - - - +
49A SER* 1.3 64.4 + - - +
51A LYS* 3.4 11.6 + - + +
52A ALA* 3.3 21.0 + - - +
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Residues in contact with SER 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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12A LEU* 4.8 12.8 - - - -
45A SER* 3.2 15.8 + - - -
46A LEU* 4.0 10.5 - - - +
47A LYS 3.3 0.2 - - - -
48A MSE 1.3 82.6 - - - +
50A TYR* 1.3 59.0 + - - +
52A ALA* 3.4 5.8 + - - +
53A ALA* 2.9 31.2 + - - +
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Residues in contact with TYR 50 (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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9A LEU* 3.4 50.5 + - + +
12A LEU* 3.7 22.4 - - + +
13A PHE* 4.1 23.6 - + + +
16A ILE* 3.7 20.2 - - + -
46A LEU 3.6 2.0 + - - -
47A LYS 3.3 8.4 + - - +
48A MSE 3.2 0.4 - - - -
49A SER* 1.3 77.4 - - - +
51A LYS* 1.3 56.5 + - - +
52A ALA 3.0 4.9 - - - -
53A ALA* 4.8 1.6 - - - -
54A ALA* 2.9 41.9 + - + +
56A GLU* 3.6 27.2 + - + -
57A ASP 2.8 24.2 - - - +
58A TYR* 3.9 19.1 - + + -
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Residues in contact with LYS 51 (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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47A LYS 3.0 16.7 + - - +
48A MSE 3.4 12.5 + - + +
50A TYR* 1.3 75.3 - - - +
52A ALA* 1.3 53.5 - - - +
54A ALA 2.5 20.2 - - - +
55A GLY* 3.6 8.4 - - - +
56A GLU 3.3 17.0 - - - +
57A ASP* 3.3 31.9 + - + +
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Residues in contact with ALA 52 (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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48A MSE 3.3 10.5 + - - +
49A SER* 3.7 8.5 - - - +
50A TYR 3.0 0.4 - - - -
51A LYS* 1.3 76.7 - - - +
53A ALA* 1.3 56.2 + - - +
54A ALA 2.7 21.8 + - - +
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Residues in contact with ALA 53 (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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9A LEU* 3.8 20.6 - - + +
12A LEU* 5.8 4.5 - - + -
49A SER 2.9 20.4 + - - +
50A TYR* 4.4 2.7 - - - +
52A ALA* 1.3 71.8 - - - +
54A ALA* 1.3 58.1 + - - +
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Residues in contact with ALA 54 (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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9A LEU* 3.6 28.0 - - + -
50A TYR* 2.9 30.2 + - + +
51A LYS 2.5 26.6 - - - +
52A ALA 2.7 7.5 - - - +
53A ALA* 1.3 77.0 - - - +
55A GLY* 1.3 59.3 + - - +
56A GLU* 4.5 4.9 - - + +
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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