Contacts of the helix formed by residues 24 - 43 (chain O) in PDB entry 1IBM
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 SER 24 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
751A U 3.4 26.2 + - - -
17O ARG* 3.2 24.4 + - - +
21O ASP* 2.5 46.9 + - - -
22O THR 3.5 1.6 + - - -
23O GLY* 1.3 75.5 - - - +
25O THR* 1.3 66.5 + - - +
26O GLU* 3.3 4.5 - - - -
27O VAL* 3.3 6.8 + - - +
28O GLN* 3.1 18.2 + - - +
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Residues in contact with THR 25 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
751A U 3.5 16.0 + - - -
752A G 5.6 0.2 - - - -
754A C 5.6 1.6 - - - -
23O GLY 3.6 1.2 + - - -
24O SER* 1.3 74.5 - - - +
26O GLU* 1.3 66.4 + - - +
28O GLN* 3.3 9.2 + - - +
29O VAL* 3.0 25.1 + - + +
66O LEU* 4.3 29.6 - - + +
69O TYR* 4.1 20.2 - - + -
70O LEU* 3.6 37.8 - - + +
77O ARG* 4.7 6.3 + - - +
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Residues in contact with GLU 26 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15O PHE* 4.4 20.6 - - + +
17O ARG* 3.2 26.9 - - - +
24O SER* 3.9 0.5 - - - -
25O THR* 1.3 73.4 + - - +
27O VAL* 1.3 70.1 + - + +
29O VAL* 2.9 4.7 + - - +
30O ALA* 2.6 24.7 + - - +
70O LEU* 4.1 6.0 - - + +
77O ARG* 2.6 52.6 + - + +
81O LEU* 3.5 35.3 - - + +
84O LYS* 6.2 0.7 - - - +
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Residues in contact with VAL 27 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12O ILE* 3.7 37.7 - - + +
15O PHE* 4.1 6.0 - - + +
16O ALA* 3.9 12.8 - - - +
21O ASP* 3.1 42.2 - - - +
22O THR 3.1 21.5 - - - +
24O SER* 3.3 7.2 + - - +
26O GLU* 1.3 72.2 - - + +
28O GLN* 1.3 68.2 + - - +
30O ALA* 2.8 11.3 + - + +
31O LEU* 2.8 29.3 + - + +
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Residues in contact with GLN 28 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
656A C 2.4 41.6 + - - -
657A G 3.0 38.4 + - - +
750A G 3.4 1.0 - - - +
751A U 4.9 1.4 + - - -
23O GLY 3.1 23.4 + - - +
24O SER 3.1 7.2 + - - +
25O THR* 3.4 9.2 - - - +
27O VAL* 1.3 82.1 - - - +
29O VAL* 1.3 66.8 + - - +
31O LEU* 2.8 18.1 + - - +
32O LEU* 3.0 17.5 + - + +
66O LEU* 3.1 30.8 - - + +
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Residues in contact with VAL 29 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25O THR* 3.0 16.5 + - + +
26O GLU 2.9 3.6 + - - -
28O GLN* 1.3 75.2 - - - +
30O ALA* 1.3 57.5 + - - +
32O LEU* 3.4 7.8 + - - +
33O THR* 2.5 35.9 + - - +
63O ARG* 4.1 15.7 - - + -
66O LEU* 4.0 21.5 - - + +
67O LEU* 4.0 27.1 - - + +
81O LEU* 3.4 24.0 - - + -
85O LEU* 3.4 26.2 - - + -
87O ILE* 4.2 4.0 - - + -
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Residues in contact with ALA 30 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11O VAL* 4.0 12.4 - - + +
15O PHE* 3.5 40.6 - - + -
26O GLU 2.6 15.7 + - - +
27O VAL* 2.9 15.0 - - + +
28O GLN 2.8 0.6 + - - -
29O VAL* 1.3 76.4 - - - +
31O LEU* 1.3 61.2 + - - +
33O THR* 3.1 13.6 + - - -
34O LEU* 3.1 10.0 + - - +
81O LEU* 5.1 0.2 - - - +
85O LEU* 4.3 11.3 - - - +
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Residues in contact with LEU 31 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
657A G 3.8 10.5 - - - +
658A G 3.5 40.2 - - - +
8O LYS* 4.0 32.5 - - + +
11O VAL* 4.6 9.9 - - + -
12O ILE* 4.2 12.6 - - + -
27O VAL* 2.8 25.9 + - + +
28O GLN* 2.8 13.7 + - - +
30O ALA* 1.3 72.5 - - + +
32O LEU* 1.3 56.5 + - + +
34O LEU* 2.7 33.5 + - + +
35O ARG* 2.8 20.7 + - + +
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Residues in contact with LEU 32 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
657A G 5.7 10.1 - - - +
28O GLN* 3.0 16.0 + - + +
29O VAL* 3.8 5.6 - - - +
31O LEU* 1.3 72.3 - - + +
33O THR* 1.3 57.1 + - - +
34O LEU 2.8 5.3 + - - -
35O ARG* 3.0 15.7 + - + +
36O ILE* 2.5 44.3 + - + +
59O MET* 4.2 18.2 - - + +
62O GLN* 4.0 13.7 - - + -
63O ARG* 3.5 49.8 - - + +
66O LEU* 4.2 15.3 - - + -
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Residues in contact with THR 33 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29O VAL 2.5 22.8 + - - -
30O ALA 3.4 5.8 + - - -
32O LEU* 1.3 77.6 - - - +
34O LEU* 1.3 57.0 + - - +
36O ILE* 4.2 1.1 - - - -
37O ASN* 2.9 50.9 + - - +
63O ARG* 3.0 31.6 + - - +
85O LEU* 3.6 26.6 - - + +
86O GLY 5.8 1.6 - - - +
87O ILE* 4.6 11.0 - - + -
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Residues in contact with LEU 34 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3O ILE* 3.4 41.5 - - + -
7O GLU* 4.4 10.3 - - - +
8O LYS* 4.6 4.7 - - + -
11O VAL* 3.8 33.2 - - + -
30O ALA 3.1 7.8 + - - +
31O LEU* 2.7 25.1 + - + +
33O THR* 1.3 74.9 - - - +
35O ARG* 1.3 63.1 + - + +
37O ASN* 3.2 4.5 + - - +
38O ARG* 3.0 38.5 + - + +
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Residues in contact with ARG 35 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
741A G 3.4 28.3 + - - +
742A G 2.8 40.2 + - - -
3O ILE* 3.9 24.0 - - + -
31O LEU* 2.8 19.0 + - + +
32O LEU* 3.9 16.1 - - + +
34O LEU* 1.3 71.4 - - + +
36O ILE* 1.3 70.4 + - - +
38O ARG* 3.4 2.5 + - - +
39O LEU* 3.1 22.2 + - - +
59O MET* 3.9 25.3 - - - +
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Residues in contact with ILE 36 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32O LEU* 2.5 24.2 + - + +
33O THR* 4.0 2.7 - - - +
35O ARG* 1.3 74.9 - - - +
37O ASN* 1.3 62.2 + - - +
39O LEU* 3.4 1.2 - - - +
40O SER* 2.5 52.0 + - - +
56O LEU* 4.3 10.1 - - + -
59O MET* 3.6 29.8 - - + +
60O VAL* 3.7 38.8 - - + +
63O ARG* 3.9 33.9 - - + +
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Residues in contact with ASN 37 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33O THR* 2.9 35.0 + - - +
34O LEU* 3.7 4.5 - - - +
36O ILE* 1.3 87.0 - - - +
38O ARG* 1.3 67.0 + - - +
40O SER* 3.3 11.1 + - - -
41O GLU* 3.1 22.2 + - - +
63O ARG* 5.3 0.6 - - - +
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Residues in contact with ARG 38 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
740A U 4.7 17.3 + - - +
741A G 6.1 0.2 - - - +
2O PRO* 2.6 33.7 + - - +
3O ILE* 3.1 21.7 - - + +
7O GLU* 2.7 36.4 + - - +
34O LEU* 3.0 33.7 + - + +
35O ARG* 3.7 5.8 - - - +
36O ILE 3.2 0.2 - - - -
37O ASN* 1.3 75.8 - - - +
39O LEU* 1.3 54.8 + - - +
41O GLU* 2.7 34.6 + - - +
42O HIS* 3.0 6.0 + - - +
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Residues in contact with LEU 39 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
740A U 4.3 14.1 - - - +
741A G 3.4 33.4 - - - +
35O ARG 3.1 12.6 + - - +
36O ILE 3.1 1.6 + - - +
38O ARG* 1.3 74.4 - - - +
40O SER* 1.3 71.4 + - - +
41O GLU 2.8 3.5 + - - -
42O HIS* 3.0 20.0 + - + -
43O LEU* 3.1 24.5 + - + +
52O SER* 3.6 20.6 - - - +
56O LEU* 3.3 41.7 - - + -
59O MET* 3.5 15.0 - - + -
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Residues in contact with SER 40 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36O ILE* 2.5 48.1 + - - +
37O ASN* 3.3 15.4 + - - -
38O ARG 3.1 0.2 - - - -
39O LEU* 1.3 79.5 - - - +
41O GLU* 1.3 62.5 + - - +
43O LEU* 3.9 4.5 + - - +
44O LYS* 3.2 30.2 + - - +
56O LEU* 4.6 7.6 - - - +
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Residues in contact with GLU 41 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37O ASN 3.1 12.3 + - - +
38O ARG* 2.7 16.6 + - - +
40O SER* 1.3 75.6 - - - +
42O HIS* 1.3 56.1 + - - +
43O LEU 2.9 2.5 - - - -
44O LYS* 2.5 58.9 + - + +
45O VAL* 3.6 7.0 + - + +
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Residues in contact with HIS 42 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
667A G 3.1 10.0 + - - -
739A C 2.7 44.6 + - - +
740A U 3.1 41.1 + - - +
38O ARG 3.0 6.6 + - - +
39O LEU* 3.0 12.5 + - + +
41O GLU* 1.3 75.6 - - - +
43O LEU* 1.3 71.9 + - + +
45O VAL* 3.8 3.4 + - - +
46O HIS* 3.2 45.9 + + - +
49O ASP* 2.8 27.8 + - - -
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Residues in contact with LEU 43 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39O LEU* 3.3 35.9 - - + +
40O SER 4.3 4.0 - - - +
41O GLU 2.7 2.2 + - - -
42O HIS* 1.3 96.2 - - + +
44O LYS* 1.3 69.0 + - - +
45O VAL 2.8 9.3 + - - -
46O HIS 3.5 19.2 - - - +
47O LYS* 3.6 9.5 + - - +
49O ASP* 4.0 22.4 - - - +
52O SER* 4.2 6.5 - - - -
53O HIS* 4.0 23.8 - - + -
56O LEU* 3.7 16.2 - - + -
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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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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