Contacts of the helix formed by residues 17 - 28 (chain J) 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 LYS 17 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C GLU* 6.0 0.2 + - - -
142C TYR* 3.8 22.1 - - + -
12J LYS* 5.1 9.9 - - + -
13J ILE* 4.5 17.3 - - - +
14J VAL* 5.0 6.3 - - + -
15J GLY* 2.9 3.6 + - - +
16J ASN* 1.3 101.5 - - + +
18J TRP* 1.3 62.9 + - - +
19J GLU 3.8 0.7 - - - -
20J ALA* 4.3 5.2 - - - -
21J TYR* 3.3 21.7 + - - +
38J LEU* 3.1 33.1 + - + +
39J GLY* 5.0 4.3 - - - -
40J LEU* 3.5 26.5 - - + -
49J LEU* 3.9 17.7 - - + +
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Residues in contact with TRP 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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149C LEU* 5.6 4.3 - - + -
152C LYS* 6.1 0.4 - - - +
2J ILE* 6.1 0.4 - - + -
3J ILE* 3.3 52.7 - - + +
14J VAL 4.9 1.3 + - - +
15J GLY* 3.0 7.2 + - - +
16J ASN 3.6 1.0 + - - -
17J LYS* 1.3 74.2 - - - +
19J GLU* 1.3 90.8 + - + +
20J ALA 3.1 1.8 - - - -
21J TYR* 2.9 37.0 + + - +
22J LEU* 3.1 51.5 + - + +
49J LEU* 3.7 38.3 - - + +
52J HIS* 4.1 23.1 - + + -
54J ASP* 4.4 29.0 + - + -
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Residues in contact with GLU 19 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114C HIS* 3.2 34.4 + - + -
143C VAL* 5.4 1.3 - - + -
144C GLU* 5.9 5.6 - - + -
146C ASP* 4.3 20.6 + - - +
149C LEU* 4.3 6.6 - - + +
152C LYS* 3.7 14.8 + - - -
15J GLY 4.8 0.4 + - - -
18J TRP* 1.3 97.9 + - + +
20J ALA* 1.3 56.3 + - - +
22J LEU* 3.4 17.9 + - - +
23J GLY* 2.9 27.4 + - - -
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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
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142C TYR* 5.4 2.7 - - + +
143C VAL* 3.5 33.0 - - + +
16J ASN 5.1 3.8 + - - +
17J LYS* 4.0 9.6 - - - +
18J TRP 3.1 0.4 - - - -
19J GLU* 1.3 75.4 - - - +
21J TYR* 1.3 64.7 + - - +
23J GLY* 3.5 1.4 + - - -
24J LEU* 3.0 26.5 + - - +
38J LEU* 3.9 19.2 - - + +
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Residues in contact with TYR 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 LYS 3.3 7.4 + - - +
18J TRP* 2.9 30.0 + + - +
20J ALA* 1.3 80.2 - - - +
22J LEU* 1.3 88.8 + - + +
24J LEU* 3.1 4.7 + - - +
25J LEU* 3.0 59.1 + - + +
31J GLU* 2.8 28.9 + - + -
34J ALA* 5.0 0.4 - - + -
35J LEU* 4.2 14.4 - - + -
38J LEU* 3.4 29.8 - - + +
49J LEU* 3.3 34.8 - - + -
50J LEU* 4.3 11.7 + - - +
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Residues in contact with LEU 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 TRP* 3.1 58.9 + - + +
19J GLU* 3.7 19.3 - - - +
21J TYR* 1.3 90.1 - - + +
23J GLY* 1.3 57.5 + - - +
25J LEU* 3.6 5.9 + - + +
26J GLN* 3.1 28.7 + - - +
54J ASP* 5.1 6.1 - - + +
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Residues in contact with GLY 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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19J GLU 2.9 17.2 + - - -
20J ALA* 3.9 2.2 - - - -
22J LEU* 1.3 73.3 - - - +
24J LEU* 1.3 58.5 + - - +
26J GLN* 3.4 12.1 + - - +
27J ALA* 3.0 28.3 + - - +
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Residues in contact with LEU 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 19.3 + - - +
21J TYR* 3.1 4.5 + - - +
23J GLY* 1.3 74.6 - - - +
25J LEU* 1.3 54.5 + - - +
27J ALA* 4.4 6.1 - - + +
28J GLU* 2.5 69.5 + - + +
34J ALA* 3.8 39.3 - - + +
37J ALA* 4.4 13.5 - - + -
38J LEU* 4.9 8.1 - - + -
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Residues in contact with LEU 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 TYR* 3.0 56.5 + - + +
22J LEU* 4.0 6.3 - - + +
24J LEU* 1.3 74.5 - - - +
26J GLN* 1.3 65.5 + - - +
27J ALA 3.4 0.2 + - - -
28J GLU 3.5 18.7 + - - +
29J TYR* 4.3 10.6 + - + +
30J THR 5.7 0.7 - - - +
31J GLU* 3.7 28.7 - - + +
34J ALA* 3.5 30.1 - - + -
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Residues in contact with GLN 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 LEU 3.1 15.5 + - - +
23J GLY* 3.6 12.9 - - - +
24J LEU 3.3 0.2 - - - -
25J LEU* 1.3 78.6 - - - +
27J ALA* 1.3 58.5 + - - +
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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 GLY 3.0 16.6 + - - +
24J LEU* 3.8 8.1 - - + +
25J LEU 4.1 0.2 - - - -
26J GLN* 1.3 79.3 - - - +
28J GLU* 1.3 62.0 + - + +
29J TYR 4.3 0.4 + - - -
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Residues in contact with GLU 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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24J LEU* 2.5 52.7 + - + +
25J LEU* 3.5 14.6 + - - +
27J ALA* 1.3 77.5 - - + +
29J TYR* 1.3 59.7 + - - +
30J THR* 3.3 35.2 + - + +
33J ASP* 4.3 8.1 - - - +
34J ALA* 5.1 1.3 - - - +
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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