Contacts of the helix formed by residues 12 - 31 (chain J) in PDB entry 1IBL
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 12 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18C TRP* 5.6 6.2 - - - -
10J GLY 4.5 1.0 - - - -
11J PHE* 1.3 79.9 - - + +
13J HIS* 1.3 63.6 + - - +
14J LYS* 2.5 39.1 + - - +
15J THR* 2.7 43.5 + - + +
16J LEU* 3.6 10.9 + - - +
68J HIS* 4.0 1.7 - - - -
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Residues in contact with HIS 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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1152A A 2.6 65.4 + - - +
1153A C 2.8 23.4 + - - -
12J ASP* 1.3 73.4 + - - +
14J LYS* 1.3 77.8 + - + +
16J LEU* 4.0 4.0 - - - -
17J ASP* 2.6 39.3 + - + +
68J HIS* 3.7 22.1 + - + +
70J ARG* 4.5 1.7 + - - +
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Residues in contact with LYS 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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1153A C 4.8 5.4 - - - +
12J ASP* 2.5 17.2 + - - +
13J HIS* 1.3 96.7 - - + +
15J THR* 1.3 53.0 + - - +
16J LEU 2.6 16.0 + - - -
17J ASP* 4.5 3.4 - - - +
18J ALA* 3.4 26.5 + - + +
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Residues in contact with THR 15 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12J ASP* 2.7 49.8 + - + +
14J LYS* 1.3 70.6 - - - +
16J LEU* 1.3 57.7 + - + +
19J SER* 3.2 18.3 - - - -
91J PRO* 3.9 16.2 - - - +
92J THR 5.0 0.3 + - - -
93J GLY* 3.5 33.8 + - - +
94J VAL* 3.6 10.9 - - + +
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Residues in contact with LEU 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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8J LEU* 3.7 25.8 - - + +
9J ARG* 3.5 11.9 - - - +
10J GLY* 2.9 36.1 - - - +
12J ASP 3.6 11.6 + - - +
13J HIS* 4.3 2.9 - - - +
14J LYS 2.6 3.0 + - - -
15J THR* 1.3 79.5 - - + +
17J ASP* 1.3 61.3 + - - +
18J ALA 3.0 1.6 - - - -
19J SER* 2.3 30.8 + - - -
20J ALA* 2.8 13.4 + - - -
68J HIS* 5.0 7.0 - - + -
70J ARG* 4.0 16.8 - - + +
94J VAL* 3.2 40.8 - - + -
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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
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1152A A 3.2 28.2 - - - +
13J HIS* 2.6 26.1 + - + +
14J LYS* 4.4 2.9 - - - +
16J LEU* 1.3 79.2 - - - +
18J ALA* 1.3 61.2 + - - +
20J ALA* 4.2 2.7 - - - +
21J GLN* 3.2 20.3 + - - +
37J PRO* 5.6 4.3 - - - +
70J ARG* 2.7 50.9 + - - +
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Residues in contact with ALA 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 LYS* 3.4 13.1 + - + +
16J LEU 2.6 3.8 + - - -
17J ASP* 1.3 76.9 - - - +
19J SER* 1.3 61.3 + - - +
21J GLN* 2.8 39.3 + - - +
22J LYS* 3.5 9.7 + - - +
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Residues in contact with SER 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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8J LEU* 4.4 5.5 - - - +
14J LYS 4.2 0.6 + - - -
15J THR 3.2 21.5 - - - -
16J LEU* 2.3 25.6 + - - +
18J ALA* 1.3 66.9 - - - +
20J ALA* 1.3 56.1 + - - -
21J GLN 2.8 4.2 + - - -
22J LYS* 2.6 57.5 + - - +
23J ILE* 3.1 8.9 - - - +
91J PRO* 3.1 22.7 - - - +
94J VAL* 4.8 0.9 - - - +
96J ILE* 5.6 1.2 - - - +
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Residues in contact with ALA 20 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8J LEU* 3.1 38.9 - - + +
16J LEU 2.8 15.3 + - - +
17J ASP* 4.5 2.9 - - - +
19J SER* 1.3 75.1 + - - +
21J GLN* 1.3 58.0 + - - +
22J LYS 3.0 0.4 - - - -
23J ILE* 3.2 23.4 + - - +
24J VAL* 3.0 18.6 - - - +
37J PRO* 4.8 7.9 - - + -
70J ARG* 4.8 8.5 - - + -
72J VAL* 4.0 9.2 - - + +
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Residues in contact with GLN 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 ASP 3.2 17.9 + - - +
18J ALA* 2.8 28.3 - - - +
19J SER 2.8 0.2 + - - -
20J ALA* 1.3 78.6 - - - +
22J LYS* 1.3 56.7 + - - +
24J VAL* 3.1 29.3 - - + +
25J GLU* 3.7 19.0 + - + +
37J PRO* 5.4 4.3 - - + -
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Residues in contact with LYS 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 ALA* 3.8 6.5 + - - +
19J SER* 2.6 62.5 + - - +
21J GLN* 1.3 70.2 - - - +
23J ILE* 1.3 57.6 + - + +
24J VAL 2.5 17.9 + - - -
25J GLU* 3.2 3.7 + - - +
26J ALA* 2.8 32.5 + - + +
88J LEU 5.2 4.5 - - - +
89J ASP* 5.9 1.6 - - - -
90J LEU* 3.5 39.2 - - + +
91J PRO* 3.6 12.2 - - + +
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Residues in contact with ILE 23 (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* 3.3 30.2 - - + +
8J LEU* 4.3 11.2 - - + -
19J SER* 3.1 25.8 - - - +
20J ALA* 3.2 17.9 + - - +
22J LYS* 1.3 76.9 - - + +
24J VAL* 1.3 59.7 + - - +
26J ALA* 4.5 0.4 - - - -
27J ALA* 4.5 4.2 - - - +
34J VAL* 4.4 4.2 - - - +
72J VAL* 3.5 16.9 - - + +
74J ILE* 4.7 1.3 - - + +
85J LEU* 3.7 34.8 - - + -
89J ASP* 6.1 0.9 - - - +
96J ILE* 5.0 10.1 - - + -
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Residues in contact with VAL 24 (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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20J ALA 3.0 21.1 - - - +
21J GLN* 3.1 21.1 - - + +
22J LYS 2.5 7.5 + - - -
23J ILE* 1.3 76.2 - - - +
25J GLU* 1.3 54.4 + - + +
26J ALA 3.2 0.4 - - - -
27J ALA 3.2 4.2 - - - -
28J ARG* 2.6 73.0 + - + +
34J VAL* 3.5 16.9 - - + +
36J GLY* 5.7 0.2 - - - -
37J PRO* 4.1 25.8 - - + -
72J VAL* 4.9 4.5 - - + -
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Residues in contact with GLU 25 (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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21J GLN* 3.7 19.1 + - + +
22J LYS* 3.2 4.9 + - - +
24J VAL* 1.3 75.7 - - + +
26J ALA* 1.3 53.1 + - - +
27J ALA 2.7 16.3 + - - -
28J ARG* 3.0 29.5 + - + +
29J ARG* 2.9 42.9 + - - +
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Residues in contact with ALA 26 (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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22J LYS* 2.8 23.5 + - + +
23J ILE* 4.5 0.2 - - - -
25J GLU* 1.3 74.8 - - - +
27J ALA* 1.3 58.6 + - - +
29J ARG* 3.8 12.1 - - - +
84J GLN* 3.0 36.4 - - - +
85J LEU* 2.9 27.0 - - + +
88J LEU* 5.3 5.4 - - + -
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Residues in contact with ALA 27 (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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23J ILE 4.5 3.4 - - - +
24J VAL 3.2 7.1 + - - +
25J GLU 2.7 1.4 + - - -
26J ALA* 1.3 78.9 - - - +
28J ARG* 1.3 63.7 + - - +
30J SER* 3.0 16.4 - - - -
31J GLY* 3.2 22.0 + - - -
32J ALA 4.5 0.5 + - - -
33J GLN 4.8 0.9 + - - -
34J VAL* 4.2 6.4 - - - +
74J ILE* 4.0 20.5 - - + +
81J THR* 3.6 17.6 - - + +
84J GLN* 3.6 0.2 + - - -
85J LEU* 3.5 16.6 - - + -
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Residues in contact with ARG 28 (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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1123A A 5.0 13.7 + - - -
24J VAL* 2.6 43.7 + - + +
25J GLU* 3.0 25.5 + - - +
27J ALA* 1.3 76.6 - - - +
29J ARG* 1.3 65.9 + - + +
31J GLY 3.2 17.5 - - - +
32J ALA 3.6 8.7 - - - +
33J GLN* 3.3 42.9 + - - +
34J VAL* 4.2 6.7 - - + +
36J GLY* 5.7 4.8 - - - -
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Residues in contact with ARG 29 (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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25J GLU* 2.9 43.1 + - - +
26J ALA* 3.8 7.5 - - - +
28J ARG* 1.3 77.2 - - + +
30J SER* 1.3 64.1 + - - +
31J GLY 3.3 4.8 + - - +
84J GLN* 2.6 52.0 + - - +
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Residues in contact with SER 30 (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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27J ALA* 3.0 23.2 - - - -
29J ARG* 1.3 81.9 - - - +
31J GLY* 1.3 52.8 + - - +
78J ASN* 3.0 14.9 + - - +
80J LYS* 3.4 13.7 - - - +
81J THR* 2.5 44.5 + - - -
84J GLN* 2.9 31.0 + - - +
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Residues in contact with GLY 31 (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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27J ALA 3.2 12.0 + - - -
28J ARG 3.2 8.0 - - - +
29J ARG 3.8 4.2 - - - +
30J SER* 1.3 84.3 + - - +
32J ALA* 1.3 71.3 + - - +
33J GLN 3.8 0.2 - - - -
76J ASN 4.0 2.7 - - - -
78J ASN* 2.9 16.8 - - - -
81J THR* 3.0 10.2 + - - -
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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