Contacts of the strand formed by residues 34 - 42 (chain E) in PDB entry 5AK9
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 34 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27E LEU 3.3 13.5 - - - -
28E LYS* 4.3 14.8 - - - -
29E TYR* 4.2 5.5 - - - +
32E ASN 4.9 0.4 - - - -
33E ARG* 1.3 78.7 - - - +
35E GLU* 1.3 62.4 + - - +
36E TYR* 3.8 5.9 - - - -
3H C 3.6 7.3 - - - +
4H G 2.8 44.7 + - - +
5H C 2.9 28.9 + - - -
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Residues in contact with GLU 35 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26E LYS* 3.5 3.1 - - - +
27E LEU* 2.7 41.0 + - + +
29E TYR* 2.7 36.6 + - + +
34E SER* 1.3 77.9 - - - +
36E TYR* 1.3 69.5 + - - +
37E ARG* 3.0 33.8 + - + +
70E GLN* 5.0 0.2 + - - -
81E ARG* 4.7 1.6 - - - -
83E SER* 2.9 31.8 + - - +
4H G 5.0 0.4 - - - -
5H C 4.1 9.6 - - + -
6H C 3.0 36.2 + - - -
7H G 5.0 0.2 - - - +
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Residues in contact with TYR 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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25E TYR 3.4 3.6 - - - -
26E LYS* 3.6 35.3 + - + -
28E LYS* 3.8 13.0 + - - -
34E SER* 3.8 10.5 - - - -
35E GLU* 1.3 78.8 - - - +
37E ARG* 1.3 61.7 + - - +
82E VAL 3.7 0.2 - - - +
83E SER* 3.4 5.8 + - - -
84E SER 2.9 47.7 + - - +
85E LYS* 3.5 42.1 + - + +
88E TYR* 3.7 26.0 - + + -
89E TYR* 4.0 12.2 + + - -
4H G 2.9 35.1 + - - -
5H C 4.0 8.8 + - - -
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Residues in contact with ARG 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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23E GLY 3.8 0.7 - - - +
24E LEU* 3.4 6.4 - - - +
25E TYR* 2.7 47.7 + - + +
27E LEU* 3.9 14.4 - - + -
29E TYR* 4.3 0.2 - - - -
35E GLU* 3.0 34.4 + - - +
36E TYR* 1.3 78.3 - - - +
38E VAL* 1.3 61.6 - - - +
39E VAL* 4.0 16.4 - - + -
79E GLU* 4.9 0.2 + - - -
81E ARG* 3.4 44.4 - - + +
82E VAL 3.7 2.0 - - - +
83E SER* 4.8 0.9 - - - +
88E TYR* 3.9 4.9 - - - -
17G T 3.4 22.3 + - - -
18G C 3.5 11.2 - - - +
7H G 3.0 20.6 + - - -
8H G 2.7 30.9 + - - -
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Residues in contact with VAL 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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18E ILE* 3.4 33.7 - - + -
23E GLY 3.8 2.7 - - - -
24E LEU* 3.9 8.1 - - + -
37E ARG* 1.3 73.5 - - - +
39E VAL* 1.3 60.0 + - - +
56E MET* 4.1 13.7 - - + -
80E LEU* 3.9 2.8 - - - +
81E ARG* 3.4 4.5 - - - -
82E VAL* 2.9 39.4 + - + +
84E SER 5.0 0.7 - - - +
87E LEU* 3.9 21.5 - - + +
88E TYR* 3.7 33.0 - - + +
91E PHE* 3.9 10.3 - - + -
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Residues in contact with VAL 39 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18E ILE* 3.9 5.4 - - - +
22E GLY* 3.2 6.9 - - - -
23E GLY 2.9 35.7 + - - +
25E TYR* 3.7 32.8 - - + -
37E ARG* 4.0 13.5 - - + -
38E VAL* 1.3 80.3 - - - +
40E ILE* 1.3 71.3 + - - +
41E THR* 3.8 26.2 - - + -
79E GLU* 3.8 22.7 - - + +
80E LEU 3.4 7.9 - - - +
81E ARG* 4.3 6.3 - - + -
16G T 4.5 4.9 - - + -
17G T 5.8 0.9 - - + +
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Residues in contact with ILE 40 (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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14E LEU* 4.2 6.7 - - + +
17E LEU* 3.9 31.2 - - + +
18E ILE* 3.6 26.9 - - + +
21E ASP* 4.7 2.5 - - + -
22E GLY* 4.1 3.6 - - - -
38E VAL 4.4 0.2 + - - -
39E VAL* 1.3 77.4 - - - +
41E THR* 1.3 74.8 + - - +
42E ALA* 5.4 0.2 - - + -
48E ILE* 4.0 3.2 - - + +
52E ILE* 3.9 41.5 - - + -
56E MET* 4.2 18.6 - - + -
79E GLU* 3.8 0.2 - - - -
80E LEU* 2.9 41.0 + - + +
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Residues in contact with THR 41 (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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21E ASP* 2.5 42.7 + - - +
22E GLY* 5.0 0.4 - - - -
39E VAL* 3.8 19.5 - - + -
40E ILE* 1.3 81.1 - - - +
42E ALA* 1.3 64.3 + - - +
77E ARG* 3.7 22.2 - - - +
78E TYR 3.4 7.0 - - - +
79E GLU* 3.8 19.3 - - + -
14F A 3.4 31.8 - - - +
15G G 4.0 9.7 - - + -
16G T 4.9 1.1 - - + -
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Residues in contact with ALA 42 (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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21E ASP* 5.5 1.3 - - - +
41E THR* 1.3 78.2 - - - +
43E LYS* 1.3 59.3 + - - +
44E SER 4.4 6.1 - - - +
47E LEU* 4.8 15.0 - - + -
48E ILE* 3.7 24.0 - - + +
52E ILE* 5.1 6.1 - - + -
77E ARG* 3.8 5.6 - - - +
78E TYR* 2.8 42.3 + - - +
14F A 3.5 11.6 - - - +
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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