Contacts of the helix formed by residues 6 - 22 (chain J) in PDB entry 5U07
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 ILE 6 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5J TYR* 1.3 97.2 - - + +
7J LEU* 1.3 62.6 + - - +
8J GLN 3.1 1.5 + - - -
9J HIS* 3.2 11.8 + - - +
10J ALA* 2.9 20.2 + - + +
56J PRO* 4.9 10.5 - - + -
77J VAL* 5.4 3.8 - - + -
81J PHE* 4.1 21.5 - - + -
196J ILE* 5.2 0.4 - - + -
197J ARG* 4.5 16.4 - - + +
200J ALA* 4.3 30.7 - - + +
201J ARG* 6.3 1.8 - - + -
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Residues in contact with LEU 7 (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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5J TYR 2.3 18.3 + - - +
6J ILE* 1.3 73.2 - - - +
8J GLN* 1.3 56.8 + - + +
10J ALA* 3.5 5.4 - - + +
11J ASP* 2.9 37.9 + - - +
136J ARG* 3.2 31.2 - - - +
193J GLY* 3.8 34.8 - - - +
194J ILE* 4.3 3.6 - - + -
197J ARG* 3.7 39.4 - - + +
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Residues in contact with GLN 8 (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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5J TYR* 2.5 34.9 + - - +
7J LEU* 1.3 69.6 - - + +
9J HIS* 1.3 74.8 + - + +
11J ASP* 3.1 18.5 + - - +
12J ALA* 3.1 11.1 + - - +
15J LYS* 4.7 1.4 + - - -
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Residues in contact with HIS 9 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5J TYR* 4.3 13.1 + + - -
6J ILE* 3.2 10.1 + - - +
8J GLN* 1.3 86.5 - - + +
10J ALA* 1.3 63.2 + - - +
12J ALA* 3.0 11.6 + - + +
13J LEU* 3.0 23.4 + - - +
54J TYR* 3.4 32.0 + + + +
56J PRO* 3.6 27.7 - - + +
81J PHE* 4.2 10.1 - - + -
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Residues in contact with ALA 10 (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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6J ILE* 2.9 15.2 + - + +
7J LEU* 3.5 13.7 - - - +
8J GLN 3.1 0.2 - - - -
9J HIS* 1.3 77.8 - - - +
11J ASP* 1.3 57.8 + - - +
13J LEU* 3.1 4.3 + - - +
14J VAL* 2.9 32.8 + - - +
81J PHE* 3.6 11.5 - - + -
193J GLY* 4.3 11.0 - - - +
196J ILE* 3.9 33.3 - - + +
197J ARG 5.2 0.4 - - - +
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Residues in contact with ASP 11 (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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7J LEU* 2.9 36.1 + - - +
8J GLN* 3.1 10.5 + - - +
10J ALA* 1.3 73.6 - - - +
12J ALA* 1.3 65.6 + - - +
14J VAL* 3.0 16.3 - - + +
15J LYS* 3.0 38.5 + - + +
136J ARG* 4.5 10.5 + - - -
193J GLY* 4.6 6.4 - - - -
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Residues in contact with ALA 12 (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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8J GLN 3.1 10.3 + - - +
9J HIS* 3.0 14.8 + - + +
11J ASP* 1.3 77.2 - - - +
13J LEU* 1.3 56.5 + - - +
15J LYS* 3.0 23.1 - - - +
16J ARG* 2.9 33.6 + - - +
54J TYR* 3.8 23.7 + - + +
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Residues in contact with LEU 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 HIS 3.0 11.1 + - - +
10J ALA* 3.5 9.6 - - - +
12J ALA* 1.3 78.9 - - - +
14J VAL* 1.3 56.8 + - - +
16J ARG* 5.1 0.9 - - + -
17J VAL* 2.4 58.3 + - + +
50J VAL* 5.0 2.0 - - + +
51J VAL* 4.2 26.5 - - + +
54J TYR* 3.5 32.3 - - + -
81J PHE* 3.3 47.1 - - + +
85J ALA* 4.6 7.9 - - + -
196J ILE* 4.8 6.3 - - + -
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Residues in contact with VAL 14 (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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10J ALA 2.9 19.3 + - - +
11J ASP* 3.0 36.3 - - + +
13J LEU* 1.3 75.3 - - - +
15J LYS* 1.3 60.0 + - + +
17J VAL* 4.8 1.3 - - - -
18J SER* 2.8 34.3 + - - +
88J MET* 5.2 5.6 - - + -
192J TRP* 4.2 18.2 - - + -
193J GLY* 4.0 25.4 - - - +
196J ILE* 4.0 12.8 - - + -
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Residues in contact with LYS 15 (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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8J GLN 4.7 1.6 + - - -
11J ASP* 3.0 28.0 + - + +
12J ALA* 3.0 36.2 - - - +
14J VAL* 1.3 75.9 - - + +
16J ARG* 1.3 81.9 + - - +
18J SER* 3.6 2.1 - - - -
19J LYS* 2.7 27.2 + - + +
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Residues in contact with ARG 16 (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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12J ALA 2.9 21.8 + - - +
13J LEU* 3.9 2.2 - - + +
15J LYS* 1.3 82.6 - - + +
17J VAL* 1.3 54.9 + - + +
19J LYS* 2.7 5.6 + - - +
20J LEU* 2.4 38.3 + - + +
50J VAL* 6.5 0.7 - - + -
54J TYR* 4.3 20.2 - - + +
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Residues in contact with VAL 17 (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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13J LEU* 2.4 57.3 + - + +
16J ARG* 1.3 69.6 - - + +
18J SER* 1.3 51.8 + - - +
19J LYS 2.5 2.6 + - - -
20J LEU* 2.4 32.4 + - + +
21J ILE* 2.6 21.9 + - + +
31J LEU* 3.9 28.0 - - + -
50J VAL* 5.3 6.9 - - + +
51J VAL* 4.8 6.7 - - + -
85J ALA* 4.5 9.9 - - + +
88J MET* 3.6 22.4 - - + -
89J ALA* 5.1 1.3 - - + -
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Residues in contact with SER 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 VAL* 2.8 22.3 + - - -
15J LYS* 4.0 2.0 - - - -
17J VAL* 1.3 78.3 - - - +
19J LYS* 1.3 55.8 + - - +
21J ILE* 4.1 6.6 - - - +
22J VAL* 4.0 18.5 + - - +
88J MET* 3.8 19.4 - - - +
192J TRP* 5.3 10.1 - - - -
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Residues in contact with LYS 19 (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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15J LYS* 2.7 22.0 + - + +
16J ARG* 2.7 9.1 + - - +
17J VAL 2.5 4.2 + - - -
18J SER* 1.3 72.5 - - - +
20J LEU* 1.3 53.8 + - - -
21J ILE 3.2 3.8 - - - -
22J VAL* 5.4 0.6 - - - +
23J ASN* 3.0 29.4 + - - +
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Residues in contact with LEU 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 ARG* 2.4 19.0 + - + +
17J VAL* 2.4 25.9 + - + +
19J LYS* 1.3 69.0 - - - +
21J ILE* 1.3 55.1 + - - -
23J ASN* 4.1 2.2 - - - -
24J GLU* 2.9 29.7 - - + +
27J ALA* 4.5 8.7 - - + +
50J VAL* 5.0 14.4 - - + -
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Residues in contact with ILE 21 (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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17J VAL* 2.6 25.5 + - + +
18J SER* 4.4 6.5 - - - +
20J LEU* 1.3 71.2 - - - +
22J VAL* 1.3 58.5 + - - +
23J ASN 2.7 4.6 + - - -
24J GLU 2.6 39.7 + - - +
28J ARG* 4.3 13.6 - - + +
31J LEU* 5.8 1.6 - - + -
88J MET* 5.9 2.7 - - - -
89J ALA* 5.5 11.7 - - + +
96J ARG* 4.6 13.5 + - - +
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Residues in contact with VAL 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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18J SER 4.0 12.4 + - - +
19J LYS* 5.4 0.4 - - - +
21J ILE* 1.3 78.6 - - - +
23J ASN* 1.3 57.1 + - - +
24J GLU 3.4 0.8 + - - -
96J ARG* 4.1 28.8 - - + +
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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