Contacts of the strand formed by residues 52 - 58 (chain E) in PDB entry 4GKH
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 LEU 52 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22E ASP* 4.2 10.8 - - + +
26E TYR* 3.5 37.9 - - + +
42E ARG* 3.8 0.5 - - - -
43E LEU* 2.9 45.1 + - + +
50E PRO* 4.3 10.8 - - + +
51E GLU* 1.3 86.2 - - - +
53E PHE* 1.3 69.8 + - - +
85E LYS* 4.8 11.0 - - + -
97E LEU* 4.2 22.2 - - + -
98E THR 3.4 15.9 - - - +
99E THR* 3.8 18.2 - - + -
100E ALA 4.1 1.6 - - - +
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Residues in contact with PHE 53 (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 ASP* 3.6 22.0 - - - -
40E ILE* 4.0 17.3 - - + -
41E TYR 3.3 12.8 - - - -
42E ARG* 3.7 24.7 - - + -
43E LEU* 5.0 0.4 - - - -
51E GLU* 3.8 7.6 - - - -
52E LEU* 1.3 73.8 - - - +
54E LEU* 1.3 60.8 + - - +
55E LYS* 4.2 4.9 - - + +
96E LEU 3.6 1.4 - - - +
97E LEU* 3.4 6.4 - - - +
98E THR* 2.9 43.2 + - - +
99E THR 4.8 1.1 - - - -
100E ALA* 3.6 34.3 - - + -
101E ILE 5.4 1.6 - - - -
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Residues in contact with LEU 54 (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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19E LEU* 4.5 14.4 - - + -
23E LEU* 4.8 5.2 - - + -
28E TRP* 3.6 32.1 - - + -
39E THR 3.6 1.6 - - - +
40E ILE* 3.7 0.9 - - - -
41E TYR* 2.8 49.7 + - + +
43E LEU* 4.4 4.9 - - + +
53E PHE* 1.3 73.4 - - - +
55E LYS* 1.3 62.3 + - - +
95E TRP* 3.9 37.5 - - + -
96E LEU 3.4 27.4 - - - +
97E LEU* 3.9 22.9 - - + -
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Residues in contact with LYS 55 (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 GLY* 5.4 0.2 - - - -
35E GLN* 4.8 19.8 + - - +
36E SER* 4.7 10.9 + - - -
38E ALA* 4.5 13.5 - - + -
39E THR 3.4 4.3 - - - +
40E ILE* 4.2 30.5 - - + -
53E PHE* 5.7 4.7 - - + -
54E LEU* 1.3 77.9 - - - +
56E HIS* 1.3 59.6 - - - +
57E GLY 4.2 0.4 - - - -
65E VAL* 4.5 11.8 - - + +
68E GLU* 3.2 33.3 + - - +
94E ALA 3.7 0.5 - - - +
95E TRP* 3.3 4.3 - - - -
96E LEU* 2.9 49.7 + - + +
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Residues in contact with HIS 56 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38E ALA* 3.4 5.4 - - - +
39E THR* 2.9 48.4 + - - +
41E TYR* 4.4 13.1 + - + -
55E LYS* 1.3 73.8 - - - +
57E GLY* 1.3 74.7 + - - +
58E LYS* 4.3 15.3 + - + -
93E ASP* 2.8 28.5 + - - -
94E ALA 3.3 12.6 - - - -
95E TRP* 3.4 52.4 - + + -
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Residues in contact with GLY 57 (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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56E HIS* 1.3 77.2 - - - +
58E LYS* 1.3 60.1 + - - -
61E VAL* 3.7 25.8 - - - -
62E ALA* 3.4 8.3 - - - +
65E VAL* 3.9 9.0 - - - +
93E ASP* 3.4 3.6 - - - -
94E ALA 2.9 36.1 + - - -
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Residues in contact with LYS 58 (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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56E HIS* 4.2 13.1 + - + +
57E GLY* 1.3 72.8 - - - -
59E GLY* 1.3 71.0 + - - +
60E SER 3.4 0.5 + - - -
61E VAL* 3.1 18.7 + - - +
92E ASP* 3.3 14.8 - - + +
93E ASP* 3.7 19.1 - - - +
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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