Contacts of the strand formed by residues 34 - 41 (chain E) in PDB entry 4HOK
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 GLU 34 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13E ARG* 5.6 0.3 + - - -
25E LEU* 4.1 22.6 - - + +
26E GLY 3.2 9.3 - - - +
27E ALA* 4.6 5.0 - - - +
32E GLY 3.4 9.7 + - - +
33E GLU* 1.3 86.4 - - - +
35E VAL* 1.3 72.1 + - - +
84E LEU* 3.7 28.4 + - + +
103G LYS* 3.6 25.6 + - - +
283G SER* 5.8 0.7 - - - -
285G ASP* 4.6 15.3 - - - +
287G VAL* 5.2 8.0 - - + +
292G MET* 4.2 10.6 - - - +
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Residues in contact with VAL 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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9E TYR* 4.2 19.7 - - + -
25E LEU* 3.4 7.1 - - - +
26E GLY* 2.9 48.1 + - - +
27E ALA* 4.1 3.1 - - - +
33E GLU* 3.8 14.1 - - + +
34E GLU* 1.3 89.3 - - - +
36E ALA* 1.3 62.2 + - - +
37E ILE* 4.3 5.2 - - + -
69E LYS* 4.3 19.1 - - + -
81E VAL* 3.7 20.9 - - + -
82E MET 3.4 13.2 - - - +
83E GLU* 5.1 1.6 - - - -
84E LEU* 4.2 13.2 - - - +
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Residues in contact with ALA 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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15E ILE* 5.5 0.4 - - + -
23E ILE* 4.1 16.4 - - + -
24E TYR 3.4 4.7 - - - -
35E VAL* 1.3 75.2 - - - +
37E ILE* 1.3 65.4 + - - +
81E VAL* 3.4 2.3 - - - +
82E MET* 2.8 51.3 + - + +
83E GLU 3.8 17.5 - - - +
84E LEU* 4.1 14.1 - - + +
293G LEU* 4.8 2.2 - - + -
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Residues in contact with ILE 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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5E VAL* 3.9 23.1 - - + -
9E TYR* 4.4 8.1 - - + -
10E ARG 4.3 16.2 - - - +
11E LEU* 4.0 27.6 - - + -
23E ILE* 3.8 4.5 - - - -
24E TYR* 2.6 44.5 + - - +
26E GLY* 4.4 7.0 - - - -
35E VAL* 4.3 5.4 - - + +
36E ALA* 1.3 81.3 - - - +
38E LYS* 1.3 62.8 + - - +
39E LEU* 3.7 11.4 - - + -
79E VAL* 3.5 27.4 - - + -
80E MET 3.5 3.8 - - - +
81E VAL* 4.0 12.3 - - + -
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Residues in contact with LYS 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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22E ASP 4.5 9.0 - - - +
23E ILE* 3.5 28.5 - - + -
37E ILE* 1.3 73.4 - - - +
39E LEU* 1.3 78.0 + - - +
48E GLN* 5.5 5.3 + - - +
49E LEU* 3.7 34.9 - - + +
52E GLU* 4.6 18.4 - - - +
78E ASN 3.9 0.3 - - - +
79E VAL* 3.5 0.3 - - - -
80E MET* 2.8 46.1 + - + +
82E MET* 5.9 4.9 - - + +
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Residues in contact with LEU 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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234C SER* 5.1 10.7 - - - +
236C PRO* 4.2 25.1 - - + -
3E LEU* 4.7 7.4 - - + -
5E VAL* 5.2 2.2 - - + -
11E LEU* 4.4 17.3 - - + -
22E ASP 4.6 7.2 + - - +
24E TYR* 4.8 14.5 - - + -
37E ILE* 3.7 10.7 + - + -
38E LYS* 1.3 101.4 - - - +
40E GLU* 1.3 64.5 + - - +
49E LEU* 4.5 2.0 - - - +
74E GLU* 6.2 0.7 - - + -
77E TYR* 4.2 24.7 - - + -
78E ASN 3.5 2.2 - - - -
79E VAL* 3.1 40.2 - - + -
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Residues in contact with GLU 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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234C SER* 5.9 2.5 - - - +
39E LEU* 1.3 77.7 - - - +
41E CYS* 1.3 62.4 + - - +
42E VAL* 3.4 0.3 + - - -
44E THR* 3.2 25.2 + - + +
46E HIS 4.0 1.6 - - - +
47E PRO* 3.5 9.8 - - - +
48E GLN* 2.5 36.0 + - - +
49E LEU* 2.8 32.0 + - + +
50E HIS 5.0 1.4 + - - -
77E TYR* 3.6 5.8 - - - -
78E ASN* 2.8 58.8 + - + +
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Residues in contact with CYS 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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182C ILE* 6.2 2.7 - - - -
233C MET* 3.9 43.5 - - + +
234C SER* 4.9 2.0 - - - +
40E GLU* 1.3 76.1 - - - +
42E VAL* 1.3 59.9 + - - +
43E LYS* 3.7 31.9 - - - +
44E THR* 2.2 45.7 + - + +
76E ASP* 3.8 11.4 - - - -
77E TYR* 3.7 13.5 - - + -
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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