Contacts of the helix formed by residues 35 - 51 (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 ASP 35 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29N PHE* 4.6 1.6 - - - -
33N GLY 3.7 3.8 + - - +
34N VAL* 1.3 78.9 - - - +
36N GLU* 1.3 62.6 + - - +
37N GLN* 2.8 50.7 + - + +
38N VAL* 3.1 27.9 + - + +
39N LEU 3.8 1.9 + - - -
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Residues in contact with GLU 36 (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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26N ARG* 2.6 51.7 + - + +
29N PHE* 5.9 0.7 - - - -
34N VAL 3.7 1.8 + - - +
35N ASP* 1.3 75.3 + - - +
37N GLN* 1.3 59.2 + - - +
38N VAL 3.3 0.2 - - - -
39N LEU* 3.3 17.3 + - + +
40N MET* 3.0 28.6 + - - +
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Residues in contact with GLN 37 (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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35N ASP* 2.8 27.1 + - - +
36N GLU* 1.3 78.2 - - - +
38N VAL* 1.3 71.8 + - + +
40N MET* 3.4 5.1 + - - +
41N GLU* 2.9 30.5 + - - +
27O GLN* 4.8 6.0 + - - +
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Residues in contact with VAL 38 (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* 4.2 3.4 - - + -
34N VAL* 3.6 23.6 - - + -
35N ASP* 3.1 15.4 + - + +
37N GLN* 1.3 86.4 - - + +
39N LEU* 1.3 59.3 + - - +
41N GLU* 3.4 6.2 + - - +
42N LEU* 2.9 28.4 + - - +
22O LEU* 3.5 26.4 - - + +
27O GLN* 3.2 38.4 - - + +
28O ILE* 4.1 10.1 - - + -
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Residues in contact with LEU 39 (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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22N ILE* 3.7 42.3 - - + +
25N VAL* 3.5 26.0 - - + -
26N ARG* 4.3 23.3 - - + -
29N PHE* 3.9 29.4 - - + -
35N ASP 3.8 1.8 + - - -
36N GLU* 3.3 20.6 + - + +
37N GLN 3.3 0.6 - - - -
38N VAL* 1.3 78.9 - - - +
40N MET* 1.3 56.6 + - - +
42N LEU* 3.4 11.9 - - + +
43N LYS* 3.1 25.6 + - - +
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Residues in contact with MET 40 (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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22N ILE* 5.5 0.4 - - - -
36N GLU 3.0 15.6 + - - +
37N GLN* 3.9 6.3 - - - +
39N LEU* 1.3 74.1 - - - +
41N GLU* 1.3 61.0 + - - +
43N LYS* 3.4 39.0 + - - +
44N THR* 2.8 41.0 + - - +
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Residues in contact with GLU 41 (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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37N GLN 2.9 17.9 + - - +
38N VAL* 3.8 6.5 - - - +
40N MET* 1.3 73.1 - - - +
42N LEU* 1.3 61.4 + - - +
44N THR* 3.9 8.7 - - - +
45N LEU* 2.8 58.3 + - + +
22O LEU* 5.3 5.8 - - + -
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Residues in contact with LEU 42 (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* 6.2 3.4 - - + -
22N ILE* 5.6 2.9 - - + -
25N VAL* 5.7 0.9 - - + -
29N PHE* 4.1 21.1 - - + -
38N VAL 2.9 18.3 + - - +
39N LEU* 3.4 14.1 - - + +
41N GLU* 1.3 76.6 - - - +
43N LYS* 1.3 58.1 + - - +
45N LEU* 3.7 6.7 - - - +
46N TRP* 2.9 35.0 + - + +
15O LEU* 4.7 9.9 - - + -
18O SER* 3.5 34.1 - - - -
19O LEU* 4.1 16.4 - - + +
22O LEU* 3.6 31.7 - - + +
36O VAL* 5.0 7.4 - - + -
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Residues in contact with LYS 43 (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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18N ILE* 3.9 25.8 - - + -
22N ILE* 3.6 38.8 - - + -
39N LEU 3.1 5.4 + - - +
40N MET* 3.5 42.1 - - - +
41N GLU 3.4 0.2 - - - -
42N LEU* 1.3 82.0 - - - +
44N THR* 1.3 58.4 + - - +
46N TRP* 3.6 7.3 - - - +
47N GLU* 2.9 44.3 + - - +
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Residues in contact with THR 44 (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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40N MET* 2.8 36.9 + - - +
41N GLU* 3.9 10.9 - - - +
43N LYS* 1.3 76.2 + - - +
45N LEU* 1.3 65.3 + - - +
47N GLU* 3.6 8.9 + - + +
48N ASN* 3.1 24.8 + - + +
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Residues in contact with LEU 45 (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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41N GLU* 2.8 47.0 + - + +
42N LEU* 3.7 7.2 - - - +
44N THR* 1.3 72.2 - - - +
46N TRP* 1.3 52.1 + - - +
48N ASN* 3.2 9.0 + - + +
49N LYS* 2.8 50.6 + - + +
18O SER* 4.3 10.5 - - - +
21O GLU* 4.5 23.8 - - + -
22O LEU* 5.2 6.3 - - + -
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Residues in contact with TRP 46 (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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14N TYR* 4.7 4.0 - - + -
17N VAL* 5.6 2.2 - - + -
18N ILE* 3.4 37.2 - - + -
42N LEU* 2.9 20.6 + - + +
43N LYS* 3.6 7.6 - - - +
45N LEU* 1.3 78.3 - - - +
47N GLU* 1.3 64.3 + - + +
49N LYS* 3.2 4.1 + - - +
50N LEU* 2.8 54.1 + - + -
11O LEU* 3.3 36.8 + - + -
14O SER* 3.6 15.6 + - - -
15O LEU* 3.4 56.4 - - + +
18O SER* 3.4 15.0 + - - +
40O PHE* 5.2 6.4 - + - -
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Residues in contact with GLU 47 (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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15N ARG* 3.0 44.1 + - - +
18N ILE* 4.6 13.9 - - + +
43N LYS* 2.9 38.3 + - - +
44N THR* 3.8 9.4 - - + +
45N LEU 3.4 0.2 - - - -
46N TRP* 1.3 85.0 - - + +
48N ASN* 1.3 60.8 + - - +
50N LEU* 3.5 5.8 + - + +
51N MET* 3.3 26.3 + - + +
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Residues in contact with ASN 48 (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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44N THR* 3.1 20.6 + - + +
45N LEU* 3.6 8.0 - - - +
47N GLU* 1.3 75.4 - - - +
49N LYS* 1.3 62.1 + - + +
51N MET 3.2 25.6 - - - +
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Residues in contact with LYS 49 (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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45N LEU* 2.8 27.6 + - + +
46N TRP* 3.5 6.3 - - - +
48N ASN* 1.3 77.4 - - + +
50N LEU* 1.3 65.5 + - - +
51N MET* 3.4 1.2 + - - -
14O SER* 4.0 21.6 - - - +
17O GLU* 3.6 30.3 + - + +
18O SER* 3.5 25.6 - - - +
21O GLU* 4.3 20.5 + - - +
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Residues in contact with LEU 50 (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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14N TYR* 4.1 28.0 - - + -
15N ARG* 6.2 0.9 - - - +
18N ILE* 5.2 2.9 - - + -
46N TRP* 2.8 51.9 + - + +
47N GLU* 3.6 8.1 - - + +
48N ASN 3.4 0.4 - - - -
49N LYS* 1.3 76.6 - - - +
51N MET* 1.3 81.2 + - + +
364N ASP* 5.6 5.2 - - - +
10O THR* 5.6 4.0 - - - +
11O LEU* 4.7 14.1 - - + +
14O SER* 4.7 13.8 - - - +
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Residues in contact with MET 51 (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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11N PRO* 5.4 15.3 - - + -
15N ARG* 3.5 31.0 - - - +
47N GLU* 3.3 18.9 + - + +
48N ASN* 3.2 27.1 - - - +
49N LYS 3.2 1.5 - - - -
50N LEU* 1.3 102.0 - - + +
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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