Contacts of the helix formed by residues 7 - 29 (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 ALA 7 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A SER* 1.3 66.1 + - - +
9A LEU* 3.1 12.3 - - + +
10A LEU* 3.2 32.1 + - - +
11A GLU* 3.5 5.0 + - - +
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Residues in contact with SER 8 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A ALA* 1.3 73.6 - - - +
9A LEU* 1.3 64.2 + - - +
11A GLU* 3.1 32.0 + - - +
12A LEU* 3.2 13.0 + - - +
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Residues in contact with LEU 9 (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 ALA* 3.1 9.0 - - + +
8A SER* 1.3 78.4 - - - +
10A LEU* 1.3 61.9 + - - +
12A LEU* 3.5 4.8 + - + +
13A PHE* 3.3 16.1 + - - +
50A TYR* 3.4 43.6 - - + +
53A ALA* 3.8 22.7 - - + +
54A ALA* 3.6 26.5 - - + -
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Residues in contact with LEU 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A ALA 3.2 22.9 + - - +
8A SER 3.1 0.4 - - - -
9A LEU* 1.3 78.2 - - - +
11A GLU* 1.3 65.5 + - - +
12A LEU 3.1 0.2 - - - -
13A PHE* 3.1 19.0 + - + +
14A ASN* 3.0 45.6 + - - +
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Residues in contact with GLU 11 (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 ALA 3.5 3.7 + - - +
8A SER* 3.3 28.3 + - - +
10A LEU* 1.3 80.9 - - - +
12A LEU* 1.3 60.4 + - + +
14A ASN* 3.6 10.5 + - - +
15A SER* 3.1 31.0 + - - +
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Residues in contact with LEU 12 (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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8A SER* 3.2 8.5 + - - +
9A LEU* 3.6 13.0 - - + +
10A LEU 3.1 0.6 - - - -
11A GLU* 1.3 78.7 - - + +
13A PHE* 1.3 65.9 + - - +
15A SER* 3.2 8.0 + - - -
16A ILE* 3.1 29.8 + - + +
46A LEU* 3.2 40.2 - - + +
49A SER* 4.8 11.4 - - - -
50A TYR* 3.7 23.1 - - + +
53A ALA* 5.8 4.0 - - + -
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Residues in contact with PHE 13 (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 3.3 10.5 + - - +
10A LEU* 3.1 21.7 + - + +
12A LEU* 1.3 78.8 - - - +
14A ASN* 1.3 79.7 + - - +
16A ILE* 3.3 7.1 + - - +
17A ALA* 3.1 25.6 + - + +
50A TYR* 4.1 23.0 - + + +
56A GLU* 5.9 0.9 - - - -
58A TYR* 3.4 30.6 - + - -
59A LYS 3.1 28.7 - - - -
60A ALA* 4.5 8.7 - - - -
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Residues in contact with ASN 14 (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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10A LEU* 3.0 39.8 + - - +
11A GLU* 3.9 9.0 - - - +
12A LEU 3.3 0.2 - - - -
13A PHE* 1.3 92.4 - - - +
15A SER* 1.3 58.4 + - - +
17A ALA* 3.1 7.0 + - - +
18A THR* 2.8 34.9 + - - +
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Residues in contact with SER 15 (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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11A GLU* 3.1 16.6 + - - +
12A LEU* 3.2 12.9 + - - -
14A ASN* 1.3 78.4 - - - +
16A ILE* 1.3 57.8 + - - +
18A THR* 3.7 6.8 - - - -
19A GLN* 2.9 31.4 + - - +
42A MSE 5.5 0.8 - - - +
46A LEU* 3.7 20.4 - - - +
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Residues in contact with ILE 16 (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* 3.1 16.9 + - + +
13A PHE 3.6 6.3 - - - +
14A ASN 3.2 0.2 - - - -
15A SER* 1.3 74.4 - - - +
17A ALA* 1.3 60.6 + - - +
19A GLN* 4.5 2.2 - - - -
20A GLY* 2.9 25.6 + - - -
43A LEU* 3.6 5.4 - - + +
46A LEU* 3.2 39.7 - - + +
47A LYS* 3.6 40.8 - - + -
50A TYR* 3.7 23.1 - - + -
58A TYR* 3.5 30.5 + - + -
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Residues in contact with ALA 17 (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 PHE* 3.1 19.2 + - + +
14A ASN* 3.1 12.0 + - - +
16A ILE* 1.3 76.7 - - - +
18A THR* 1.3 57.0 + - - +
20A GLY* 3.0 3.6 + - - -
21A GLU* 2.9 29.4 + - - +
58A TYR* 3.5 18.3 + - - +
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Residues in contact with THR 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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14A ASN* 2.8 21.4 + - - +
15A SER* 3.7 7.2 - - - -
17A ALA* 1.3 76.9 - - - +
19A GLN* 1.3 58.0 + - - +
21A GLU* 3.1 9.3 + - + +
22A LEU* 2.9 28.7 + - + +
356A ASN* 6.2 1.3 - - - +
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Residues in contact with GLN 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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15A SER 2.9 19.1 + - - +
16A ILE 3.9 3.1 - - - +
18A THR* 1.3 77.7 - - - +
20A GLY* 1.3 58.1 + - - +
22A LEU* 3.4 23.7 - - - +
23A VAL* 3.0 34.4 + - - +
39A ALA* 2.8 41.6 + - - +
42A MSE 3.6 32.7 - - + +
43A LEU* 3.9 29.4 - - + +
46A LEU* 4.4 7.4 - - + -
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Residues in contact with GLY 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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16A ILE 2.9 16.5 + - - -
17A ALA* 3.0 4.7 + - - -
19A GLN* 1.3 76.7 - - - +
21A GLU* 1.3 62.8 + - - +
23A VAL* 3.4 2.8 + - - +
24A ARG* 3.0 22.9 + - - +
43A LEU* 4.0 18.6 - - - +
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Residues in contact with GLU 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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17A ALA 2.9 11.9 + - - +
18A THR* 3.1 11.9 + - + +
20A GLY* 1.3 76.5 - - - +
22A LEU* 1.3 62.9 + - - +
24A ARG* 2.7 66.9 + - - +
25A SER* 3.0 7.4 + - - -
355A PRO* 3.4 12.3 - - + +
356A ASN* 2.6 53.2 + - - +
360A PHE* 5.3 1.9 - - - -
371A LYS* 6.0 0.2 + - - -
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Residues in contact with LEU 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 THR* 2.9 14.4 + - + +
19A GLN* 3.4 34.5 - - - +
21A GLU* 1.3 74.8 - - - +
23A VAL* 1.3 65.0 + - - +
25A SER* 2.7 27.5 + - - +
26A LEU* 2.9 37.1 + - + +
39A ALA* 5.4 1.1 - - + -
355A PRO* 4.4 13.9 - - + -
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Residues in contact with VAL 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 GLN* 3.0 22.7 + - - +
20A GLY* 3.8 6.1 - - - +
22A LEU* 1.3 75.0 - - - +
24A ARG* 1.3 64.7 + - - +
26A LEU* 3.2 9.4 + - - +
27A LYS* 3.0 51.9 + - + +
36A ILE* 4.9 3.1 - - + +
39A ALA* 3.8 36.3 - - + +
40A VAL* 4.0 13.5 - - + +
43A LEU* 4.2 19.3 - - + -
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Residues in contact with ARG 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 GLY 3.0 16.3 + - - +
21A GLU* 2.7 65.6 + - - -
22A LEU 3.2 0.2 - - - -
23A VAL* 1.3 79.7 - - - +
25A SER* 1.3 68.5 + - - +
27A LYS* 3.3 9.5 + - - +
28A ALA* 3.1 22.5 + - + +
352A ALA* 2.8 30.5 + - - +
354A ASP 4.1 5.3 + - - -
358A SER* 5.4 1.0 + - - +
360A PHE* 3.2 39.8 - - - -
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Residues in contact with SER 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 GLU 3.0 13.6 + - - -
22A LEU* 2.7 25.1 + - - +
24A ARG* 1.3 81.0 - - - +
26A LEU* 1.3 61.1 + - - +
28A ALA* 3.1 2.8 + - - +
29A GLY* 2.8 26.7 + - - -
352A ALA 3.5 16.4 - - - -
353A SER* 3.3 27.9 + - - +
355A PRO* 3.5 22.1 - - - +
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Residues in contact with LEU 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 LEU* 2.9 39.6 + - + +
23A VAL* 3.2 8.5 + - - +
25A SER* 1.3 77.7 + - - +
27A LYS* 1.3 61.4 + - - +
29A GLY* 3.1 17.0 + - - +
31A ALA* 3.6 34.3 + - + +
35A GLU* 4.6 11.4 - - + +
36A ILE* 4.2 13.3 - - + +
39A ALA* 3.6 31.4 - - + -
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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 VAL* 3.0 38.4 + - + +
24A ARG* 3.7 10.1 - - - +
26A LEU* 1.3 76.7 - - - +
28A ALA* 1.3 56.9 + - - +
36A ILE* 3.9 35.5 - - + +
40A VAL* 4.8 5.7 - - - +
165A SER* 4.7 0.7 + - - -
204A LYS* 2.9 24.8 + - - -
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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 ARG* 3.1 14.8 + - + +
25A SER 3.6 1.8 - - - +
27A LYS* 1.3 74.3 - - - +
29A GLY* 1.3 65.0 + - - +
165A SER* 4.0 12.4 + - - -
168A ALA* 4.2 11.7 - - + -
200A LYS* 4.8 7.3 + - - -
204A LYS* 3.7 7.3 + - - -
352A ALA* 3.6 42.0 - - + +
353A SER* 3.9 5.4 + - - -
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Residues in contact with GLY 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 SER 2.8 12.6 + - - -
26A LEU* 3.1 8.9 + - - +
28A ALA* 1.3 78.0 - - - +
30A ASN* 1.3 61.7 + - - -
31A ALA 3.4 6.8 + - - +
204A LYS* 3.0 26.2 - - - -
353A SER* 3.4 20.4 + - - -
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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