Contacts of the helix formed by residues 23 - 39 (chain E) in PDB entry 4YYJ
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 THR 23 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22E SER* 1.3 78.5 - - - +
24E PRO* 1.4 71.1 - - + +
25E ILE* 3.2 25.3 - - - +
26E GLN* 2.9 19.1 + - - +
27E GLN* 2.9 26.2 + - - +
77E ASN* 4.5 12.0 + - - +
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Residues in contact with PRO 24 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23E THR* 1.4 89.2 - - - +
25E ILE* 1.3 57.7 + - - +
27E GLN* 3.4 19.1 + - + +
28E LEU* 2.9 28.2 + - - +
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Residues in contact with ILE 25 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23E THR* 3.2 15.5 - - - +
24E PRO* 1.3 80.1 - - + +
26E GLN* 1.3 65.4 + - + +
28E LEU* 3.3 8.7 + - + +
29E LEU* 2.9 51.4 + - + +
77E ASN* 5.1 4.0 - - - +
79E TYR 4.3 15.3 - - - +
80E LYS* 4.6 8.7 - - - +
81E SER* 4.2 6.3 - - - -
82E VAL* 4.0 37.7 - - + +
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Residues in contact with GLN 26 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22E SER* 3.2 19.9 + - - +
23E THR* 2.9 43.1 + - - +
25E ILE* 1.3 85.9 - - + +
27E GLN* 1.3 61.9 + - - +
29E LEU* 4.6 1.8 - - + -
30E GLU* 2.9 32.1 + - + +
74E ILE* 3.0 43.8 + - + +
75E VAL* 3.7 15.8 + - - +
77E ASN* 3.6 22.4 + - - +
79E TYR 6.0 1.1 - - - +
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Residues in contact with GLN 27 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22E SER* 3.7 24.8 + - - +
23E THR 2.9 18.8 + - - +
24E PRO* 3.4 21.0 + - + +
26E GLN* 1.3 72.4 - - - +
28E LEU* 1.4 58.7 + - - +
30E GLU* 3.5 6.0 + - - +
31E HIS* 3.0 28.8 + - - +
34E ARG* 4.9 1.9 + - - -
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Residues in contact with LEU 28 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24E PRO 2.9 16.6 + - - +
25E ILE* 3.3 11.2 + - + +
27E GLN* 1.4 76.6 - - - +
29E LEU* 1.3 58.6 + - + +
31E HIS* 3.2 14.5 + - + +
32E PHE* 2.9 55.9 + - + -
82E VAL* 3.7 28.3 - - + -
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Residues in contact with LEU 29 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25E ILE* 2.9 40.0 + - + +
26E GLN* 4.0 3.1 - - + +
28E LEU* 1.3 69.2 - - - +
30E GLU* 1.3 61.0 + - - +
32E PHE* 3.3 9.7 + - + +
33E LEU* 2.8 30.7 + - - +
74E ILE* 3.8 23.8 - - + +
79E TYR* 3.4 41.5 - - + +
81E SER 4.5 1.1 - - - +
82E VAL* 4.0 27.4 - - + -
85E PHE* 3.8 32.7 - - + -
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Residues in contact with GLU 30 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22E SER* 5.9 1.6 - - - +
26E GLN* 2.9 24.3 + - + +
27E GLN* 3.7 7.0 - - - +
29E LEU* 1.3 76.7 - - - +
31E HIS* 1.3 60.8 + - - +
33E LEU* 3.3 20.4 + - - +
34E ARG* 3.0 48.5 + - - +
71E LYS* 2.8 33.6 + - - +
74E ILE* 4.0 18.9 - - + +
75E VAL* 4.4 10.0 - - - +
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Residues in contact with HIS 31 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27E GLN 3.0 14.5 + - - +
28E LEU* 3.3 16.8 - - + +
30E GLU* 1.3 73.0 - - - +
32E PHE* 1.3 76.0 + + - +
34E ARG* 3.4 28.8 + - - +
35E GLN* 3.1 60.4 + - + +
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Residues in contact with PHE 32 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28E LEU* 2.9 48.6 + - + -
29E LEU* 3.6 18.8 - - + +
31E HIS* 1.3 81.3 - + - +
33E LEU* 1.3 57.7 + - - +
35E GLN* 3.1 11.3 + - - +
36E LEU* 2.9 34.8 + - + +
82E VAL* 4.1 20.4 - - + -
85E PHE* 3.9 13.7 - + + -
120E MET* 3.8 25.7 - - + +
121E MET* 3.7 42.6 - - + -
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Residues in contact with LEU 33 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29E LEU 2.8 20.9 + - - +
30E GLU* 3.3 13.9 + - - +
32E PHE* 1.3 71.8 - - - +
34E ARG* 1.3 57.9 + - + +
36E LEU* 3.9 2.6 - - + +
37E GLN* 2.9 45.7 + - - +
67E PHE* 3.5 41.7 - - + +
70E MET* 4.6 5.8 - - + -
71E LYS* 3.5 44.0 - - + +
74E ILE* 3.7 14.6 - - + -
85E PHE* 4.2 15.0 - - + -
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Residues in contact with ARG 34 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27E GLN 4.9 1.6 + - - -
30E GLU* 3.0 40.5 + - - +
31E HIS* 3.4 37.9 + - - +
32E PHE 3.2 0.2 - - - -
33E LEU* 1.3 78.1 - - + +
35E GLN* 1.3 64.2 + - + +
37E GLN* 3.5 6.2 + - - +
38E ARG* 3.1 31.1 + - + +
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Residues in contact with GLN 35 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31E HIS* 3.1 46.4 + - + +
32E PHE* 3.1 8.9 + - - +
34E ARG* 1.3 78.8 - - + +
36E LEU* 1.3 62.2 + - - +
38E ARG* 3.4 28.7 - - - +
39E LYS* 3.6 16.5 + - - +
120E MET* 3.4 39.1 - - + +
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Residues in contact with LEU 36 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32E PHE 2.9 21.3 + - - +
33E LEU* 3.9 2.9 - - - +
35E GLN* 1.3 75.6 - - - +
37E GLN* 1.3 56.8 + - - +
39E LYS* 3.0 34.6 + - + +
40E ASP 3.8 1.2 + - - -
67E PHE* 3.9 21.3 - - + -
85E PHE* 4.1 27.4 - - + -
89E PHE* 3.8 32.1 - - + -
113E ILE* 3.5 9.8 - - + +
117E GLY* 3.5 25.6 - - - +
120E MET* 3.4 22.9 - - + -
121E MET* 4.3 7.2 - - + -
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Residues in contact with GLN 37 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33E LEU* 2.9 34.3 + - + +
34E ARG* 3.8 6.6 - - - +
36E LEU* 1.3 71.9 - - - +
38E ARG* 1.3 65.8 + - + +
40E ASP* 3.0 26.6 + - - +
41E PRO* 4.2 1.2 - - - +
43E GLY* 6.1 0.8 - - - -
46E ALA* 4.4 15.6 - - - +
67E PHE* 3.4 49.6 - - + +
71E LYS* 5.6 4.5 - - - +
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Residues in contact with ARG 38 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34E ARG* 3.1 17.5 + - + +
35E GLN* 3.4 20.5 - - - +
37E GLN* 1.3 76.6 - - + +
39E LYS* 1.3 60.5 + - + +
40E ASP 3.2 1.1 + - - -
41E PRO* 3.9 13.3 - - - +
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Residues in contact with LYS 39 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35E GLN* 3.9 18.6 + - - +
36E LEU* 3.0 25.9 + - + +
38E ARG* 1.3 76.4 - - + +
40E ASP* 1.3 55.7 + - - +
41E PRO* 3.3 10.8 - - - +
109E LEU* 3.5 20.6 - - + +
113E ILE* 3.6 30.7 - - + -
116E ALA* 4.5 23.4 - - + +
117E GLY 4.7 2.5 - - - +
120E MET* 4.6 14.6 - - - +
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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