Contacts of the strand formed by residues 34 - 40 (chain E) in PDB entry 4MJI
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 ALA 34 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28E PRO* 5.7 0.2 - - - +
32E HIS* 4.4 2.1 - - - +
33E THR* 1.3 78.6 + - - +
35E LEU* 1.3 59.5 + - - +
36E TYR* 3.9 7.6 - - + +
51E TYR* 3.6 25.8 - - + -
52E PHE 3.1 7.0 - - - -
53E GLN* 3.4 11.2 - - - +
72E ARG* 4.4 0.8 + - - -
97E SER* 3.3 5.5 - - - -
98E SER* 2.9 50.6 + - - +
99E LEU 4.5 1.2 + - - -
101E GLY* 4.0 6.3 - - - -
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Residues in contact with LEU 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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26E CYS* 4.4 2.5 - - - -
28E PRO* 3.4 23.6 - - + -
33E THR 3.5 0.8 + - - -
34E ALA* 1.3 74.3 - - - +
36E TYR* 1.3 76.0 + - - +
37E TRP* 4.0 6.5 - - + +
51E TYR* 3.6 1.0 - - - -
52E PHE* 2.7 39.6 + - + +
72E ARG* 3.3 23.3 - - - +
76E SER 3.2 27.4 - - - +
78E SER* 3.6 32.3 - - - +
95E CYS* 3.8 12.8 - - - -
96E ALA 3.4 10.1 - - - +
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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
----------------------------------------------------------
97D ARG 3.2 19.6 + - - -
98D GLN* 4.4 3.6 - - - -
99D LEU 4.9 1.1 - - - -
34E ALA* 3.9 6.2 - - + +
35E LEU* 1.3 86.0 - - - +
37E TRP* 1.3 60.8 + - - +
38E TYR* 3.8 24.5 - + + -
48E PHE* 4.2 8.7 - + - -
50E ILE 3.5 5.2 - - - +
51E TYR* 3.4 41.2 - + + -
95E CYS* 3.6 2.6 - - - -
96E ALA* 3.0 38.8 + - + +
97E SER 4.5 0.2 - - - -
98E SER* 3.7 16.8 - - - -
101E GLY* 3.7 5.5 - - - -
102E GLY* 2.7 32.1 + - - -
105E LEU* 3.6 35.7 - - + -
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Residues in contact with TRP 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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9E GLN* 3.9 20.0 - - - -
24E LEU* 3.5 37.5 - - + -
25E ARG 3.9 12.3 - - - -
26E CYS* 4.0 18.2 - - + -
35E LEU* 4.0 10.1 - - + +
36E TYR* 1.3 72.6 - - - +
38E TYR* 1.3 67.4 + - - +
48E PHE* 4.4 0.9 - - - -
49E LEU* 3.1 34.5 + - + +
50E ILE* 2.8 36.8 + - + +
52E PHE* 4.7 2.2 - + - -
70E ALA* 4.5 6.7 - - + -
78E SER* 2.7 29.0 + - - -
79E THR 4.4 1.0 - - - -
80E LEU* 3.8 30.6 - - + +
93E TYR* 4.0 19.1 - - + -
94E LEU 3.2 20.0 - - - -
95E CYS* 4.3 4.7 - - + -
111E SER* 6.1 0.4 - - - -
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Residues in contact with TYR 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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99D LEU* 2.7 49.2 + - - +
101D PHE* 3.7 17.7 - + - -
36E TYR* 3.8 18.8 - - + -
37E TRP* 1.3 78.6 - - - +
39E ARG* 1.3 60.9 + - - +
46E PRO* 3.9 21.5 - - + -
47E GLU 3.2 26.9 - - - +
48E PHE* 3.5 24.5 - + - -
49E LEU* 4.2 6.9 - - - +
93E TYR* 3.4 4.7 - - - +
94E LEU* 2.6 44.0 + - + +
96E ALA* 5.1 0.7 - - + -
105E LEU* 3.7 22.6 - - + +
107E PHE* 3.9 14.1 - + - -
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Residues in contact with ARG 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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38E TYR* 1.3 77.1 - - - +
40E GLN* 1.3 60.4 + - - +
46E PRO* 3.4 1.3 - - - +
47E GLU* 2.7 59.8 + - + +
49E LEU* 4.3 17.2 - - + +
64E PRO* 3.6 29.6 - - - +
68E PHE* 3.9 16.6 - - - -
88E GLY 4.9 3.4 + - - -
89E ASP* 4.4 13.1 + - - +
91E ALA* 4.7 7.8 - - + +
92E VAL 3.2 8.5 - - - +
93E TYR* 3.3 49.3 + - + -
94E LEU* 4.3 1.3 - - - +
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Residues in contact with GLN 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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38D ASN* 3.3 29.5 + - - +
88D PHE* 3.3 13.9 - - - -
39E ARG* 1.3 78.2 - - - +
41E SER* 1.3 66.2 + - - +
43E GLY 5.6 1.3 - - - +
44E GLN 2.7 30.9 + - - +
45E GLY 3.9 6.1 - - - +
46E PRO* 3.7 16.9 - - + +
47E GLU* 5.3 2.7 - - - -
91E ALA* 3.0 4.5 - - - +
92E VAL* 2.7 47.9 + - + +
94E LEU* 4.0 18.1 - - + +
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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