Contacts of the helix formed by residues 6 - 22 (chain J) in PDB entry 1U8R
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 ASP 6 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1I MET* 3.5 36.3 + - + +
2J ASN* 5.5 0.2 - - - +
4J LEU* 2.9 8.2 + - - -
5J VAL* 1.3 76.3 - - - +
7J THR* 1.3 68.1 + - - +
8J THR* 3.1 17.8 + - - -
9J GLU* 3.2 33.6 + - - +
10J MET* 3.2 21.7 + - - +
106J HIS* 4.0 19.9 - - + +
22L T 4.8 2.4 + - - -
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Residues in contact with THR 7 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2J ASN* 4.1 7.5 + - - +
4J LEU* 3.8 12.4 - - + +
5J VAL 4.3 0.6 - - - -
6J ASP* 1.3 71.9 + - - +
8J THR* 1.3 67.2 + - - +
10J MET* 3.1 4.5 + - - +
11J TYR* 2.9 49.0 + - + -
44J THR* 3.9 16.6 - - + +
22L T 3.5 29.3 + - - +
23L G 3.1 33.4 + - - +
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Residues in contact with THR 8 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6J ASP* 3.1 8.5 + - - -
7J THR* 1.3 78.7 - - - +
9J GLU* 1.3 65.4 + - + +
11J TYR* 3.1 5.1 + - - +
12J LEU* 2.9 29.5 + - + +
44J THR* 5.5 1.0 - - - +
48J MET* 3.6 31.6 - - + +
53J LEU* 3.8 19.7 - - + -
71J LEU* 5.2 4.5 - - + -
22L T 4.4 15.1 + - - -
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Residues in contact with GLU 9 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6J ASP* 3.2 25.8 + - - +
8J THR* 1.3 79.5 - - + +
10J MET* 1.3 58.8 + - - +
12J LEU* 3.0 8.5 + - - +
13J ARG* 2.8 29.6 + - - +
71J LEU* 4.1 20.2 - - + +
75J VAL* 3.4 30.0 - - + +
78J LYS* 6.5 0.7 - - - -
105J GLU 4.0 1.5 - - - +
106J HIS* 2.8 48.2 + - + +
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Residues in contact with MET 10 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4J LEU* 3.7 40.8 - - + +
6J ASP 3.2 11.8 + - - +
7J THR 3.1 8.5 + - - +
9J GLU* 1.3 77.2 - - - +
11J TYR* 1.3 53.8 + - - +
13J ARG* 3.8 27.3 - - - +
14J THR* 2.6 41.6 + - - +
34J LEU* 4.4 17.9 - - + -
102J CYS* 4.0 9.0 - - - -
105J GLU* 3.1 6.1 - - - +
106J HIS* 3.2 6.7 - - + -
8002J CO 2.2 33.7 - - - +
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Residues in contact with TYR 11 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4J LEU* 4.7 0.9 - - + -
7J THR* 2.9 40.8 + - + +
8J THR 3.5 7.2 - - - +
10J MET* 1.3 73.3 - - - +
12J LEU* 1.3 67.1 + - - +
14J THR* 3.0 7.9 + - - -
15J ILE* 3.0 28.0 + - + +
30J ILE* 3.8 30.8 - - + +
34J LEU* 3.5 22.7 - - + -
36J GLN* 2.7 26.4 + - - -
41J VAL* 3.2 34.0 + - + +
44J THR* 3.5 28.8 + - + -
45J VAL* 4.4 6.3 - - + -
48J MET* 3.7 22.2 - - - -
54J LEU* 5.9 0.2 - - + -
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Residues in contact with LEU 12 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8J THR* 2.9 24.6 + - + +
9J GLU* 3.4 9.4 - - - +
11J TYR* 1.3 75.6 - - - +
13J ARG* 1.3 56.8 + - - +
15J ILE* 2.9 24.0 + - - +
16J TYR* 3.0 11.6 + - - +
48J MET* 3.7 18.8 - - + -
53J LEU* 4.2 14.6 - - + +
54J LEU* 4.7 1.6 - - + -
64J LEU* 3.7 24.9 - - + +
68J GLY* 3.9 22.2 - - - +
71J LEU* 3.5 36.1 - - + -
72J ALA* 4.1 16.9 - - + +
75J VAL* 5.9 0.7 - - + -
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Residues in contact with ARG 13 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9J GLU 2.8 19.1 + - - +
10J MET* 3.8 18.7 - - + +
12J LEU* 1.3 72.8 - - - +
14J THR* 1.3 57.7 + - - +
16J TYR* 3.4 8.2 + - + +
17J ASP* 2.8 58.2 + - - +
72J ALA* 4.6 6.0 - - - +
75J VAL* 4.1 19.7 - - + +
76J MET* 4.2 34.0 - - + +
79J HIS* 4.1 7.9 + - - -
98J HIS* 4.3 9.5 + - - -
102J CYS* 3.4 17.0 - - - -
105J GLU* 2.7 50.2 + - - +
172J GLU* 4.1 17.5 - - - +
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Residues in contact with THR 14 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10J MET* 2.6 26.3 + - - +
11J TYR* 3.0 7.4 + - - -
13J ARG* 1.3 73.7 + - - +
15J ILE* 1.3 66.9 + - - +
17J ASP* 3.2 8.7 + - + +
18J LEU* 3.0 29.3 + - + +
30J ILE* 4.2 33.9 - - + +
33J ARG* 4.3 25.7 - - + +
34J LEU* 3.8 17.9 - - + +
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Residues in contact with ILE 15 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11J TYR* 3.0 21.1 + - + +
12J LEU* 2.9 8.9 + - - +
14J THR* 1.3 77.8 - - - +
16J TYR* 1.3 61.5 + - - +
18J LEU* 3.4 9.1 + - + +
19J GLU* 3.1 32.5 + - - +
25J PRO* 4.4 14.3 - - + +
30J ILE* 3.8 12.8 - - + -
54J LEU* 4.7 9.4 - - + -
62J LEU* 3.3 47.8 - - + +
64J LEU* 3.3 39.5 - - + -
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Residues in contact with TYR 16 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12J LEU 3.0 7.9 + - - +
13J ARG* 3.5 12.6 - - + +
15J ILE* 1.3 78.6 - - - +
17J ASP* 1.3 64.3 + - - +
19J GLU* 3.1 14.7 + - - +
20J GLU* 2.9 44.3 + - + -
64J LEU* 4.6 2.2 - - + +
69J ARG* 4.3 20.6 - - - -
72J ALA* 4.3 22.7 - - + -
73J ILE* 4.0 21.3 - - + +
76J MET* 3.4 36.1 - - + -
80J ARG* 5.6 0.2 + - - -
133J PRO* 3.6 23.4 - - + +
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Residues in contact with ASP 17 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13J ARG* 2.8 54.8 + - - +
14J THR* 3.2 8.7 + - - +
16J TYR* 1.3 71.6 - - - +
18J LEU* 1.3 63.9 + - - +
20J GLU* 3.1 13.3 + - - +
21J GLU* 2.9 37.1 + - - +
33J ARG* 4.4 5.8 - - - +
76J MET* 3.6 7.8 - - - +
171J THR* 5.4 1.0 - - - -
172J GLU* 3.1 35.5 + - - +
173J HIS* 4.6 1.9 + - - +
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Residues in contact with LEU 18 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14J THR* 3.0 25.4 + - + +
15J ILE* 3.5 9.4 - - + +
17J ASP* 1.3 77.2 - - - +
19J GLU* 1.3 62.4 + - - +
21J GLU* 3.0 6.0 + - - +
22J GLY 2.9 17.5 + - - -
23J VAL* 3.1 37.6 + - + +
24J THR 4.1 0.7 - - - +
25J PRO* 3.6 23.8 - - + -
26J LEU 4.2 2.0 - - - +
29J ARG* 3.3 36.8 - - + -
30J ILE* 5.0 2.5 - - + +
33J ARG* 3.2 37.5 - - - +
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Residues in contact with GLU 19 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15J ILE* 3.1 28.0 - - - +
16J TYR* 3.1 16.4 + - - +
18J LEU* 1.3 76.2 - - - +
20J GLU* 1.3 57.8 - - - +
22J GLY* 2.9 21.2 + - - +
23J VAL 4.3 4.5 + - - -
25J PRO* 4.1 16.3 - - + +
62J LEU 5.0 3.5 - - - +
63J GLU* 5.6 2.9 - - - +
64J LEU* 4.4 3.0 + - - +
69J ARG* 3.0 42.4 + - - -
153J ARG* 4.5 2.1 + - - -
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Residues in contact with GLU 20 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16J TYR* 2.9 37.1 + - + +
17J ASP* 3.2 23.0 - - - +
19J GLU* 1.3 77.7 - - - +
21J GLU* 1.3 54.8 + - - +
76J MET* 3.9 0.5 - - - +
80J ARG* 2.8 38.9 + - - -
130J ASN* 5.2 2.2 - - - +
131J PRO* 5.5 3.7 - - - +
153J ARG* 2.9 19.9 + - - -
169J GLN* 5.5 1.8 - - - +
171J THR* 3.9 26.0 - - + +
223J HIS 4.9 0.2 - - - +
226J LYS* 3.9 15.6 + - - -
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Residues in contact with GLU 21 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17J ASP* 2.9 22.2 + - - +
18J LEU* 3.0 7.8 + - - +
20J GLU* 1.3 76.1 - - - +
22J GLY* 1.3 58.5 + - - +
23J VAL* 3.9 12.2 - - + +
33J ARG* 2.7 48.3 + - - -
153J ARG* 3.0 17.4 + - - -
171J THR* 4.0 20.3 - - - +
173J HIS* 2.9 28.5 + - - +
220J GLU 4.9 0.7 - - - +
223J HIS* 3.1 33.9 + - - +
224J ALA* 4.1 6.9 - - + +
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Residues in contact with GLY 22 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19J GLU* 2.9 17.2 + - - -
20J GLU 3.2 0.8 + - - -
21J GLU* 1.3 80.8 - - - +
23J VAL* 1.3 62.4 + - - +
153J ARG* 4.1 13.7 - - - -
223J HIS* 4.2 10.4 - - - -
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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
------------------------------------------------------------
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