Contacts of the helix formed by residues 6 - 26 (chain B) in PDB entry 1UI6
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 ARG 6 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7B ALA* 1.3 75.4 - - - +
8B GLU* 3.3 5.6 - - - +
9B GLN* 3.0 29.2 + - - +
10B THR* 2.9 30.7 + - - +
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Residues in contact with ALA 7 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B ARG* 1.3 86.1 - - - +
8B GLU* 1.3 57.9 + - - +
10B THR* 3.1 9.6 + - - -
11B ARG 2.8 24.6 + - - -
48B PHE* 5.6 4.5 - - + -
49B HIS* 3.6 23.2 + - + -
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Residues in contact with GLU 8 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B ARG 3.3 4.6 - - - +
7B ALA* 1.3 79.4 - - - +
9B GLN* 1.3 64.3 + - + +
11B ARG* 3.2 14.6 + - + +
12B ALA* 2.9 31.9 + - + +
49B HIS* 5.4 0.4 - - - -
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Residues in contact with GLN 9 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B ARG* 3.0 27.3 + - - +
8B GLU* 1.3 79.9 - - - +
10B THR* 1.3 61.7 + - - +
12B ALA* 3.4 6.5 + - - +
13B THR* 3.0 33.2 + - - -
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Residues in contact with THR 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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6B ARG* 2.9 18.2 + - - +
7B ALA* 3.3 11.4 - - - -
9B GLN* 1.3 74.4 - - - +
11B ARG* 1.3 67.5 + - - +
13B THR* 3.2 7.4 + - - -
14B ILE* 3.0 43.4 + - + +
41B VAL* 4.1 17.2 - - + +
45B ALA* 4.6 10.5 - - + -
49B HIS* 4.2 9.9 - - + +
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Residues in contact with ARG 11 (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 ALA 2.8 13.7 + - - +
8B GLU* 3.3 18.4 - - + +
10B THR* 1.3 76.0 - - - +
12B ALA* 1.3 55.7 + - - +
14B ILE* 3.0 8.9 + - - +
15B ILE* 2.9 50.0 + - + +
49B HIS* 3.8 35.9 + - + +
50B PHE* 3.8 21.5 - - + -
59B ALA* 3.7 25.3 - - - +
62B GLU* 5.6 2.8 + - - -
63B ILE* 5.6 2.2 - - - +
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Residues in contact with ALA 12 (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 GLU* 2.9 20.1 + - + +
9B GLN* 3.6 7.9 - - - +
11B ARG* 1.3 73.9 - - - +
13B THR* 1.3 59.8 + - - +
15B ILE* 3.1 14.6 + - + +
16B GLY* 2.8 26.7 + - - -
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Residues in contact with THR 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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9B GLN* 3.0 18.3 + - - +
10B THR* 3.2 8.0 + - - +
12B ALA* 1.3 74.8 - - - +
14B ILE* 1.3 63.9 + - - +
16B GLY* 3.9 1.3 - - - +
17B ALA* 2.9 27.4 + - - +
39B ALA* 3.5 30.5 - - + +
41B VAL* 5.3 2.9 - - + -
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Residues in contact with ILE 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 THR* 3.0 28.8 + - + +
11B ARG* 3.3 6.3 - - - +
13B THR* 1.3 76.1 - - - +
15B ILE* 1.3 59.5 + - - +
17B ALA* 3.1 1.9 + - - +
18B ALA* 2.8 29.6 + - - +
35B ILE* 4.1 6.5 - - + +
39B ALA* 4.1 17.7 - - + -
41B VAL* 4.3 13.2 - - + -
45B ALA 4.2 1.6 - - - +
46B LEU* 3.6 46.0 - - + +
49B HIS* 4.0 28.3 - - + -
50B PHE* 4.0 15.7 - - + -
56B LEU* 4.1 4.5 - - + -
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Residues in contact with ILE 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 ARG* 2.9 58.6 + - + +
12B ALA* 3.4 11.4 - - - +
14B ILE* 1.3 77.8 - - - +
16B GLY* 1.3 58.5 + - - +
18B ALA* 3.7 1.9 - - - +
19B ALA* 2.8 28.1 + - - +
50B PHE* 3.8 15.0 - - + -
56B LEU* 4.5 8.1 - - + -
59B ALA* 4.4 9.2 - - + -
60B ILE* 4.1 18.1 - - + +
63B ILE* 4.0 28.9 - - + -
102B VAL* 4.4 10.8 - - + -
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Residues in contact with GLY 16 (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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12B ALA 2.8 15.5 + - - -
13B THR* 3.9 2.0 - - - -
15B ILE* 1.3 78.9 - - - +
17B ALA* 1.3 58.5 + - - +
19B ALA* 3.5 6.7 - - - +
20B ASP* 2.9 31.4 + - - +
101B PRO* 4.1 7.2 - - - +
102B VAL* 4.9 5.8 - - - -
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Residues in contact with ALA 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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13B THR* 2.9 19.4 + - + +
14B ILE 3.6 2.9 - - - +
16B GLY* 1.3 73.2 - - - +
18B ALA* 1.3 68.0 + - - +
20B ASP* 3.3 2.1 + - - -
21B LEU* 3.1 20.5 + - - +
35B ILE* 4.1 7.4 - - + +
38B HIS* 3.6 33.1 - - + +
39B ALA* 3.8 25.6 - - + +
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Residues in contact with ALA 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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14B ILE 2.8 20.0 + - - +
15B ILE 3.7 3.6 - - - +
17B ALA* 1.3 72.4 - - - +
19B ALA* 1.3 56.7 + - - +
21B LEU* 3.2 2.0 + - - -
22B PHE* 2.8 49.5 + - + -
35B ILE* 3.6 37.3 - - + +
56B LEU* 4.0 14.8 - - + -
60B ILE* 4.3 2.9 - - + -
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Residues in contact with ALA 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 ILE 2.8 17.5 + - - +
16B GLY 3.5 4.5 - - - +
17B ALA 3.2 0.2 - - - -
18B ALA* 1.3 74.9 - - - +
20B ASP* 1.3 60.0 + - - +
22B PHE 3.4 0.2 + - - -
23B ASP* 2.9 32.4 + - - +
60B ILE* 3.8 9.6 - - + +
101B PRO* 4.0 5.2 - - + +
102B VAL* 3.9 29.2 - - + +
105B ALA* 3.4 25.9 - - + +
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Residues in contact with ASP 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 GLY 2.9 16.6 + - - +
17B ALA 3.8 3.8 - - - +
19B ALA* 1.3 76.4 - - - +
21B LEU* 1.3 57.2 + - - +
23B ASP* 3.5 2.3 + - - +
24B ARG* 2.7 64.1 + - - +
38B HIS* 2.7 28.7 + - + +
101B PRO* 3.9 20.0 - - + +
104B ARG* 5.1 4.9 + - - -
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Residues in contact with LEU 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 ALA 3.1 15.2 + - - +
18B ALA 3.7 2.9 - - - +
19B ALA 3.1 0.4 - - - -
20B ASP* 1.3 75.7 - - - +
22B PHE* 1.3 61.0 + - - +
23B ASP 3.0 1.8 - - - -
24B ARG* 3.8 21.5 - - - +
25B ARG* 2.8 66.4 + - - +
26B GLY 3.4 0.5 + - - -
30B THR* 3.6 19.6 + - + +
34B GLU* 3.9 18.6 - - + +
35B ILE* 3.8 30.3 - - + +
38B HIS* 3.8 24.0 - - + -
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Residues in contact with PHE 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 ALA* 2.8 32.0 + - + +
19B ALA 3.9 3.4 - - - +
21B LEU* 1.3 73.2 - - - +
23B ASP* 1.3 59.0 + - - +
26B GLY* 3.0 27.6 + - - -
27B TYR* 3.7 48.7 - + - +
30B THR* 3.6 34.1 - - + -
35B ILE* 3.8 19.7 - - + -
53B LYS* 4.2 10.5 - - + -
56B LEU* 4.3 10.5 - - + -
57B ALA 4.6 2.0 - - - -
60B ILE* 3.8 21.5 - - + -
105B ALA* 4.4 9.2 - - + +
108B ARG* 3.5 14.3 - - + +
109B LEU* 4.2 13.9 - - + -
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Residues in contact with ASP 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 ALA 2.9 18.5 + - - +
20B ASP* 3.8 5.6 - - - +
21B LEU 3.0 0.2 - - - -
22B PHE* 1.3 79.5 - - - +
24B ARG* 1.3 66.8 + - - +
101B PRO* 4.5 1.7 - - + +
104B ARG* 3.0 62.6 + - + +
105B ALA* 4.3 4.7 - - - +
108B ARG* 3.1 43.1 + - - -
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Residues in contact with ARG 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 ASP* 2.7 50.6 + - - +
21B LEU* 3.8 15.3 - - - +
23B ASP* 1.3 86.4 - - - +
25B ARG* 1.3 81.5 + - + +
26B GLY 3.8 0.2 - - - -
38B HIS* 3.6 18.0 + - - -
108B ARG* 4.1 8.9 + - - +
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Residues in contact with ARG 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B LEU* 2.8 39.8 + - + +
24B ARG* 1.3 100.0 - - + +
26B GLY* 1.3 58.6 + - - +
29B SER* 3.0 23.1 + - - -
30B THR* 4.1 9.2 - - - +
34B GLU* 4.2 25.6 + - - +
108B ARG* 5.1 2.5 - - - -
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Residues in contact with GLY 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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113A GLY* 6.0 6.7 - - - -
21B LEU 3.4 0.4 + - - -
22B PHE* 3.0 21.4 + - - -
23B ASP 4.5 0.6 + - - -
24B ARG 3.8 0.6 - - - -
25B ARG* 1.3 79.4 - - - +
27B TYR* 1.3 64.1 + - - -
28B GLU 3.6 1.8 - - - -
29B SER* 4.3 3.1 - - - -
30B THR* 2.9 26.2 + - - -
108B ARG* 4.6 11.9 - - - +
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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
------------------------------------------------------------
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