Contacts of the helix formed by residues 10 - 33 (chain N) in PDB entry 5IYB
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 VAL 10 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9N THR* 1.3 86.2 - - + +
11N PRO* 1.4 73.2 - - + +
12N LYS 3.0 0.9 - - - -
13N LEU* 2.9 18.9 + - + +
14N TYR* 2.9 39.2 + - + +
364N ASP 4.7 15.9 - - - +
365N TYR* 5.8 1.8 - - + -
366N ILE* 4.1 38.6 - - + -
54O ASN* 6.0 1.1 - - - +
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Residues in contact with PRO 11 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9N THR 3.9 8.3 - - - +
10N VAL* 1.4 94.1 - - + +
12N LYS* 1.3 50.1 + - - +
14N TYR* 3.1 18.8 + - + +
15N ARG* 2.6 43.0 + - + +
50N LEU* 6.4 0.2 - - + -
51N MET* 5.4 15.3 - - + -
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Residues in contact with LYS 12 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9N THR* 3.2 24.0 - - - +
11N PRO* 1.3 76.8 - - - +
13N LEU* 1.3 53.9 + - - +
15N ARG* 3.1 13.1 - - + +
16N SER* 2.6 41.1 + - - +
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Residues in contact with LEU 13 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9N THR 3.5 6.4 + - - +
10N VAL* 2.9 16.3 + - + +
12N LYS* 1.3 74.9 - - - +
14N TYR* 1.3 57.0 + - + +
16N SER* 3.1 9.4 - - - +
17N VAL* 2.7 43.6 + - + +
366N ILE* 3.9 20.4 - - + -
44O ILE* 6.1 2.0 - - + -
47O ALA* 4.3 9.6 - - + +
48O LEU* 5.1 5.2 - - + -
51O ARG* 3.5 43.1 - - + +
52O VAL* 3.7 27.4 - - + +
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Residues in contact with TYR 14 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10N VAL* 2.9 45.4 + - + +
11N PRO* 3.2 18.2 - - + +
13N LEU* 1.3 77.4 - - + +
15N ARG* 1.3 56.7 + - - +
17N VAL* 3.1 9.8 + - + +
18N ILE* 2.9 33.6 + - - +
46N TRP* 4.7 1.4 - - - -
50N LEU* 4.1 27.8 - - + -
357N ILE* 4.5 15.6 - - + +
364N ASP* 3.3 36.3 + - + +
366N ILE* 5.1 4.1 - - + +
11O LEU* 3.5 45.3 - - + -
44O ILE* 5.9 0.7 - - + -
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Residues in contact with ARG 15 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11N PRO* 2.6 25.3 + - + +
12N LYS* 3.1 15.9 - - + +
14N TYR* 1.3 70.0 - - - +
16N SER* 1.3 64.8 + - - +
18N ILE* 3.1 23.9 + - - +
19N GLU* 3.0 21.4 + - - +
47N GLU* 3.0 28.7 + - - +
50N LEU* 6.2 1.0 - - - +
51N MET* 3.5 30.5 - - - +
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Residues in contact with SER 16 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12N LYS* 2.6 27.8 + - - +
13N LEU* 3.1 23.6 - - - +
15N ARG* 1.3 73.1 - - - +
17N VAL* 1.3 53.5 + - - -
19N GLU* 3.2 13.1 + - - +
20N ASP* 3.0 25.8 + - - +
51O ARG* 3.9 35.0 + - - -
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Residues in contact with VAL 17 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13N LEU* 2.7 24.7 + - + +
14N TYR* 3.3 11.9 - - + +
16N SER* 1.3 69.7 - - - +
18N ILE* 1.3 60.2 + - - +
20N ASP* 3.8 5.9 - - - +
21N VAL* 2.9 36.8 + - + +
46N TRP* 5.6 3.1 - - + -
11O LEU* 4.9 8.5 - - + -
40O PHE* 3.9 28.5 - - + -
43O ALA* 5.2 1.6 - - + +
44O ILE* 3.5 34.5 - - + +
47O ALA* 4.1 17.7 - - + -
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Residues in contact with ILE 18 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14N TYR 2.9 20.9 + - - +
15N ARG* 3.2 34.1 - - - +
17N VAL* 1.3 76.7 - - - +
19N GLU* 1.3 62.8 + - - +
21N VAL* 4.0 4.2 - - - +
22N ILE* 3.0 28.3 + - + +
43N LYS* 3.9 39.7 - - + -
46N TRP* 3.4 37.5 - - + -
47N GLU* 4.6 14.4 - - + -
50N LEU* 5.2 2.7 - - + -
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Residues in contact with GLU 19 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15N ARG 3.0 11.7 + - - +
16N SER* 3.2 14.6 + - - +
18N ILE* 1.3 77.7 - - - +
20N ASP* 1.3 60.9 + - - +
22N ILE* 4.0 2.0 - - - +
23N ASN* 2.7 44.9 + - - +
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Residues in contact with ASP 20 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16N SER 3.0 13.0 + - - +
17N VAL* 3.8 7.6 - - - +
19N GLU* 1.3 76.9 - - - +
21N VAL* 1.3 57.7 + - - +
23N ASN* 4.0 3.4 - - - +
24N ASP* 2.9 37.9 + - - +
43O ALA* 3.8 33.1 - - + +
46O ALA* 5.3 3.8 - - - +
47O ALA* 5.7 1.0 - - - +
51O ARG* 4.6 12.8 + - - +
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Residues in contact with VAL 21 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17N VAL* 2.9 28.4 + - + +
18N ILE* 4.0 4.0 - - - +
20N ASP* 1.3 72.7 - - - +
22N ILE* 1.3 68.8 - - + +
24N ASP* 3.3 3.9 + - - -
25N VAL* 3.2 37.7 + - + +
42N LEU* 6.2 3.4 - - + -
15O LEU* 5.3 7.9 - - + -
36O VAL* 4.7 12.8 - - + -
39O GLN 5.6 0.4 - - - -
40O PHE* 3.4 48.7 - - + +
43O ALA* 4.5 5.4 - - + -
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Residues in contact with ILE 22 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18N ILE* 3.0 24.6 + - + +
19N GLU* 4.0 4.0 - - - +
21N VAL* 1.3 81.3 - - + +
23N ASN* 1.3 69.3 + - - +
25N VAL* 3.5 6.3 - - + +
26N ARG* 3.4 16.5 + - - +
39N LEU* 3.7 42.7 - - + +
40N MET* 5.5 0.2 - - - -
42N LEU* 5.6 2.9 - - + -
43N LYS* 3.6 46.7 - - + +
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Residues in contact with ASN 23 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19N GLU* 2.7 43.6 + - - +
20N ASP* 4.0 5.2 - - - +
22N ILE* 1.3 85.4 - - - +
24N ASP* 1.3 62.1 + - - +
25N VAL 3.3 0.9 + - - -
26N ARG* 3.5 20.7 + - - +
27N ASP* 4.7 1.7 + - - +
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Residues in contact with ASP 24 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20N ASP* 2.9 25.9 + - - +
21N VAL* 3.9 4.3 - - - +
22N ILE 3.3 0.4 - - - -
23N ASN* 1.3 77.2 - - - +
25N VAL* 1.3 60.0 + - - +
26N ARG 3.5 0.2 - - - -
27N ASP* 4.9 4.8 + - - +
28N ILE* 3.6 14.4 - - - +
39O GLN* 2.8 47.8 - - + +
42O LYS* 5.4 2.4 - - - +
43O ALA* 5.2 2.4 - - + +
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Residues in contact with VAL 25 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21N VAL* 3.2 25.8 - - + +
22N ILE* 3.5 8.5 - - - +
24N ASP* 1.3 78.6 - - - +
26N ARG* 1.3 68.5 + - - +
27N ASP 3.3 2.7 - - - -
28N ILE* 2.9 15.0 + - + +
29N PHE* 2.8 29.1 + - + -
39N LEU* 3.5 25.8 - - + -
42N LEU* 5.7 0.9 - - + -
36O VAL* 3.7 43.7 - - + -
39O GLN* 4.2 9.2 - - + -
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Residues in contact with ARG 26 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22N ILE 3.4 12.9 + - - +
23N ASN* 3.5 16.7 + - - +
25N VAL* 1.3 77.7 - - - +
27N ASP* 1.3 59.8 + - - +
29N PHE* 3.2 5.1 + - - +
30N LEU* 2.9 40.2 + - + +
36N GLU* 2.6 36.8 + - + +
39N LEU* 4.3 17.3 - - + -
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Residues in contact with ASP 27 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23N ASN 4.7 1.8 + - - +
24N ASP 4.9 3.6 + - - +
25N VAL 3.3 0.2 - - - -
26N ARG* 1.3 80.7 - - - +
28N ILE* 1.3 59.7 + - + +
30N LEU* 3.3 22.7 - - - +
31N ASP* 3.0 28.0 + - - +
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Residues in contact with ILE 28 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24N ASP 3.6 16.2 - - - +
25N VAL* 3.2 19.1 - - + +
27N ASP* 1.3 75.4 - - + +
29N PHE* 1.3 65.4 + - - +
31N ASP* 3.1 17.3 + - + +
32N ASP* 3.2 10.0 + - - +
32O LEU* 3.4 24.5 - - + +
35O GLN* 3.4 50.5 - - + +
36O VAL* 4.8 0.9 - - + +
39O GLN* 3.5 32.5 - - + -
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Residues in contact with PHE 29 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25N VAL* 2.8 27.3 + - + +
26N ARG* 3.5 9.9 - - - +
28N ILE* 1.3 72.2 - - - +
30N LEU* 1.3 60.2 + - - +
32N ASP* 3.2 2.8 + - - +
33N GLY 2.9 8.0 + - - -
34N VAL* 2.9 55.0 + - + +
35N ASP 4.6 0.7 - - - -
36N GLU* 6.3 0.7 - - - -
38N VAL* 4.2 5.6 - - + -
39N LEU* 3.9 44.0 - - + -
42N LEU* 4.1 15.7 - - + -
22O LEU* 4.9 0.7 - - + -
28O ILE* 4.0 27.1 - - + -
32O LEU* 4.0 17.3 - - + -
36O VAL* 3.6 27.8 - - + -
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Residues in contact with LEU 30 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26N ARG* 2.9 26.0 + - + +
27N ASP* 3.3 26.0 - - - +
29N PHE* 1.3 76.8 - - - +
31N ASP* 1.3 58.0 + - - +
33N GLY* 3.0 20.5 + - - +
34N VAL 4.8 3.1 - - - -
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Residues in contact with ASP 31 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27N ASP* 3.0 14.2 + - - +
28N ILE* 3.1 14.5 + - + +
30N LEU* 1.3 76.6 - - - +
32N ASP* 1.3 59.1 + - - +
35O GLN* 5.7 1.4 - - - +
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Residues in contact with ASP 32 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28N ILE 3.2 8.6 + - - +
29N PHE 3.7 2.7 - - - +
30N LEU 3.2 0.2 - - - -
31N ASP* 1.3 76.5 - - - +
33N GLY* 1.3 60.8 + - - +
34N VAL* 3.4 20.7 + - + +
28O ILE* 4.7 0.2 - - - -
29O THR* 3.7 28.0 + - - +
32O LEU* 3.3 28.8 - - + +
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Residues in contact with GLY 33 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29N PHE 2.9 4.0 + - - -
30N LEU* 3.0 16.2 + - - -
31N ASP 3.4 0.2 - - - -
32N ASP* 1.3 78.1 - - - +
34N VAL* 1.3 62.1 + - - +
35N ASP* 3.7 2.9 + - - +
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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
------------------------------------------------------------
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