Contacts of the helix formed by residues 9 - 31 (chain B) in PDB entry 1RIO
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 THR 9 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B LEU* 1.3 75.5 - - - +
10B GLN* 1.3 61.0 + - - +
11B GLU* 3.7 10.3 + - - +
12B GLN* 2.8 43.5 + - - +
13B LEU* 2.7 28.4 + - - +
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Residues in contact with GLN 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B LEU 3.8 0.8 + - - -
9B THR* 1.3 73.5 - - - +
11B GLU* 1.3 56.9 - - - +
13B LEU* 3.0 18.5 + - - +
14B GLU* 2.8 66.1 + - - +
17B ARG* 3.8 16.4 + - - +
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Residues in contact with GLU 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B THR* 3.1 9.4 + - - +
10B GLN* 1.3 78.8 - - - +
12B GLN* 1.3 68.5 + - - +
14B GLU* 3.1 14.2 + - - +
15B ASP* 2.8 37.2 + - - +
18B ARG* 5.5 2.2 - - - +
80B SER* 3.6 31.6 + - - +
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Residues in contact with GLN 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B LEU* 3.4 26.8 - - + +
9B THR* 2.8 52.8 + - - +
11B GLU* 1.3 82.1 - - - +
13B LEU* 1.3 58.7 + - - +
15B ASP* 3.2 14.5 + - - +
16B ALA* 2.9 28.8 + - - +
57B ALA* 3.6 27.4 - - - +
58B LEU* 5.0 6.2 + - - +
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Residues in contact with LEU 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B PRO* 5.9 3.6 - - + -
8B LEU* 4.3 20.6 - - + +
9B THR 2.7 15.8 + - - +
10B GLN* 3.5 23.6 - - - +
12B GLN* 1.3 77.2 - - - +
14B GLU* 1.3 57.0 + - - +
16B ALA* 3.4 5.1 + - - +
17B ARG* 3.0 47.1 + - - +
53B ASN 5.1 1.6 - - - +
54B GLY* 3.3 33.2 - - - +
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Residues in contact with GLU 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B GLN* 2.8 49.9 + - - +
11B GLU* 3.1 13.0 + - - +
13B LEU* 1.3 73.9 - - - +
15B ASP* 1.3 67.1 + - - +
17B ARG* 3.1 16.0 + - - +
18B ARG* 3.0 52.7 + - - +
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Residues in contact with ASP 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B GLU* 2.8 26.4 + - - +
12B GLN* 3.3 15.4 - - - +
14B GLU* 1.3 73.0 - - - +
16B ALA* 1.3 63.5 + - - +
18B ARG* 3.0 23.4 + - - +
19B LEU* 2.9 22.8 + - - +
58B LEU* 4.5 12.8 - - + -
77B PHE* 3.3 15.7 - - - +
78B SER* 2.6 36.4 + - - -
79B PRO* 4.4 1.2 - - - +
80B SER* 4.0 8.4 + - - -
81B ILE* 4.3 7.4 - - - +
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Residues in contact with ALA 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B LEU* 6.1 0.7 - - + -
12B GLN 2.9 15.1 + - - +
13B LEU 3.8 3.1 - - - +
15B ASP* 1.3 76.8 - - - +
17B ARG* 1.3 65.5 + - - +
19B LEU* 3.1 9.9 + - - +
20B LYS 2.9 21.1 + - - -
51B LEU 3.5 23.6 - - - +
52B PHE 3.5 9.1 - - - +
53B ASN 4.6 0.2 - - - -
54B GLY* 3.7 26.2 - - - +
58B LEU* 5.0 4.7 - - + -
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Residues in contact with ARG 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B GLN* 3.8 26.4 + - - +
13B LEU* 3.0 40.1 + - - +
14B GLU* 3.1 11.9 + - - +
16B ALA* 1.3 77.4 - - - +
18B ARG* 1.3 56.8 + - + +
20B LYS* 3.6 6.4 + - + +
21B ALA* 3.0 29.3 + - - +
52B PHE 5.0 1.3 - - - -
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Residues in contact with ARG 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A HIS* 6.3 1.8 - - - -
11B GLU* 4.6 3.4 + - - +
14B GLU* 3.0 36.6 + - - +
15B ASP* 3.0 38.0 + - - +
17B ARG* 1.3 74.9 - - + +
19B LEU* 1.3 63.5 + - - +
21B ALA* 3.3 5.8 + - - +
22B ILE* 3.0 30.0 + - + +
76B GLU 4.0 13.9 - - - +
77B PHE* 2.7 29.5 + - - -
79B PRO* 3.9 15.3 - - - +
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Residues in contact with LEU 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B ASP 2.9 14.3 + - - +
16B ALA* 3.1 8.3 + - - +
18B ARG* 1.3 75.7 - - - +
20B LYS* 1.3 63.3 + - - +
22B ILE* 3.2 7.9 + - + +
23B TYR* 2.9 19.8 + - - +
51B LEU 4.2 11.4 - - - +
52B PHE* 3.7 25.1 - - + -
58B LEU* 4.0 23.8 - - + -
66B LEU* 3.8 27.1 - - + -
70B LEU* 4.0 22.2 - - + +
77B PHE* 3.6 32.2 - - + +
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Residues in contact with LYS 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B ALA 2.9 12.8 + - - +
17B ARG* 3.9 7.0 - - + +
19B LEU* 1.3 74.0 - - - +
21B ALA* 1.3 59.1 + - - +
23B TYR* 2.8 10.3 + - + +
24B GLU* 2.8 52.4 + - + +
34B GLN* 5.0 0.9 - - - +
52B PHE* 3.4 41.7 - - + +
53B ASN* 2.7 24.2 + - - +
9T A 2.6 36.3 + - - -
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Residues in contact with ALA 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B ARG 3.0 19.5 + - - +
18B ARG* 3.7 6.3 - - - +
20B LYS* 1.3 77.8 - - - +
22B ILE* 1.3 63.7 + - + +
24B GLU* 4.5 0.7 - - - -
25B LYS* 2.3 59.6 + - + +
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Residues in contact with ILE 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B ARG* 3.0 26.6 + - - +
19B LEU* 3.2 8.5 + - - +
21B ALA* 1.3 77.4 - - + +
23B TYR* 1.3 65.3 + - - +
25B LYS* 3.2 5.7 + - - +
26B LYS* 3.1 34.3 + - + +
70B LEU* 4.5 12.3 - - + -
72B VAL* 3.8 36.8 - - + -
76B GLU* 4.5 27.8 - - + +
77B PHE* 5.0 4.9 - - + -
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Residues in contact with TYR 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B LEU 2.9 11.7 + - - +
20B LYS* 2.8 12.6 + - + +
22B ILE* 1.3 76.5 - - - +
24B GLU* 1.3 78.4 + - - +
27B LYS* 2.9 58.0 + - + +
32B LEU* 3.8 17.5 + - + -
33B SER* 3.2 12.3 - - - -
34B GLN* 3.0 34.0 + - + -
37B VAL* 4.3 5.4 - - + -
52B PHE* 3.7 35.0 - + + -
70B LEU* 4.2 24.2 - - + +
8T A 2.6 28.2 + - - -
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Residues in contact with GLU 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B LYS* 2.8 43.7 + - + +
21B ALA* 4.8 0.2 - - - -
23B TYR* 1.3 90.6 - - - +
25B LYS* 1.3 89.2 + - + +
26B LYS 3.4 0.3 + - - -
27B LYS* 2.7 45.8 + - - +
28B ASN* 5.1 4.0 + - - -
34B GLN* 5.1 1.7 + - - -
8T A 5.6 3.1 - - - +
9T A 5.0 1.4 + - - -
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Residues in contact with LYS 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B ALA* 2.3 49.3 + - + +
22B ILE* 3.6 7.4 - - + +
24B GLU* 1.3 99.5 - - + +
26B LYS* 1.3 64.1 + - + +
28B ASN* 5.3 2.8 + - - +
29B GLU* 4.4 6.9 - - - +
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Residues in contact with LYS 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A HIS* 5.0 6.1 + - - -
22B ILE* 3.1 30.9 + - + +
23B TYR 4.4 0.4 - - - +
25B LYS* 1.3 84.6 - - + +
27B LYS* 1.3 64.9 + - - +
28B ASN 3.3 2.9 - - - -
29B GLU* 3.1 32.3 - - + +
30B LEU* 2.9 38.4 + - + +
32B LEU* 5.7 0.2 - - - -
70B LEU* 2.8 32.5 + - + +
71B LYS* 3.3 23.8 + - - +
72B VAL* 3.9 6.2 - - + +
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Residues in contact with LYS 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B TYR* 2.9 33.5 + - + +
24B GLU* 2.7 49.8 + - - +
25B LYS 3.8 0.2 - - - -
26B LYS* 1.3 76.2 - - - +
28B ASN* 1.3 68.9 + - - +
30B LEU* 4.8 0.7 - - - -
31B GLY* 2.7 29.5 + - - -
32B LEU* 3.0 30.0 + - - +
70B LEU* 5.7 0.2 - - - +
7T C 4.8 1.1 + - - -
8T A 3.1 33.7 + - - -
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Residues in contact with ASN 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B GLU 5.1 4.0 + - - -
25B LYS 5.3 2.8 + - - +
26B LYS 3.3 1.2 + - - -
27B LYS* 1.3 93.9 - - - +
29B GLU* 1.3 63.1 + - - +
31B GLY* 3.2 13.3 + - - -
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Residues in contact with GLU 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B LYS 4.4 5.5 - - - +
26B LYS* 3.1 47.5 - - - +
28B ASN* 1.3 78.3 - - - +
30B LEU* 1.3 69.5 + - + +
31B GLY* 4.7 0.2 - - - -
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Residues in contact with LEU 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B LYS* 2.9 36.0 + - + +
29B GLU* 1.3 89.7 - - + +
31B GLY* 1.3 63.9 + - - +
32B LEU* 3.8 26.0 - - + +
69B ILE 3.8 7.0 - - - +
70B LEU* 3.5 39.7 - - + +
71B LYS* 3.9 26.7 - - + -
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Residues in contact with GLY 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B LYS 2.7 12.8 + - - -
28B ASN 3.2 11.0 + - - -
29B GLU 3.2 0.6 - - - -
30B LEU* 1.3 81.0 - - - +
32B LEU* 1.3 61.0 + - - +
36B SER* 4.2 4.7 + - - -
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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
------------------------------------------------------------
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