Contacts of the strand formed by residues 32 - 38 (chain E) in PDB entry 4JFF
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 ASN 32 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A ALA* 5.6 1.6 - - - +
31E PRO* 1.3 70.0 - - - +
33E LEU* 1.3 68.8 + - - +
34E TYR* 3.5 17.5 + - + +
49E TYR* 3.8 18.2 + - + -
50E TRP 3.4 7.0 - - - +
51E GLY* 3.9 11.6 - - - -
52E PRO* 4.0 6.2 - - - +
56E ILE* 5.1 1.2 - - - +
93E TRP* 3.1 5.0 - - - +
94E SER* 2.7 50.7 + - - +
95E GLU 2.8 23.2 + - - -
96E THR* 4.5 2.0 - - - -
97E GLY 3.3 21.9 + - - +
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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
----------------------------------------------------------
23E CYS* 5.9 1.3 - - - -
25E VAL* 5.2 5.2 - - + -
31E PRO* 3.2 34.3 - - + +
32E ASN* 1.3 85.8 - - - +
34E TYR* 1.3 63.2 + - - +
49E TYR* 3.6 1.7 - - - -
50E TRP* 2.8 38.4 + - - +
68E ARG* 3.4 31.2 - - + +
71E ASP 4.0 6.5 - - - +
72E ARG 4.9 2.7 - - - +
73E GLN 4.7 2.9 - - - +
74E PHE* 3.5 48.3 - - + +
91E CYS* 5.4 3.4 - - - -
92E ALA 3.5 6.3 - - - +
93E TRP* 4.5 5.4 - - + -
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Residues in contact with TYR 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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95D GLY 2.8 24.9 + - - -
96D ARG* 4.0 9.6 - - + -
32E ASN* 3.5 25.4 + - + +
33E LEU* 1.3 74.9 - - - +
35E TRP* 1.3 60.4 + - - +
36E TYR* 3.7 24.9 - + + -
46E LEU* 4.1 8.7 - - + -
48E PHE 3.2 6.3 - - - +
49E TYR* 3.2 41.0 - + + -
74E PHE* 3.8 5.1 - - - -
90E LEU 4.4 0.2 - - - -
91E CYS* 3.3 10.2 - - - -
92E ALA* 3.0 46.5 + - + +
93E TRP 4.3 0.7 - - - -
94E SER* 3.0 25.2 + - - -
103E TRP* 3.2 19.3 - + - -
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Residues in contact with TRP 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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6E GLN* 3.7 23.8 - - - -
21E LEU* 3.9 26.5 - - + -
22E GLU 4.2 4.0 - - - -
23E CYS* 3.7 20.0 - - + -
34E TYR* 1.3 71.8 - - - +
36E TYR* 1.3 54.4 + - - +
46E LEU* 3.7 2.8 - - - +
47E LEU* 2.7 49.2 + - + -
48E PHE* 2.9 16.2 + + + +
66E ALA* 4.1 8.3 - - + -
74E PHE* 3.0 58.0 - + - -
75E ILE 3.5 11.7 + - - -
76E LEU* 3.6 44.6 - - + -
89E TYR* 4.8 2.5 - - + -
90E LEU 3.5 14.8 - - - -
91E CYS* 3.8 6.5 - - + -
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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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96D ARG* 4.5 1.7 - - - +
97D LEU* 2.5 48.7 + - + +
99D PHE* 3.7 16.8 - + - -
34E TYR* 3.7 28.8 - + + -
35E TRP* 1.3 78.8 - - - +
37E ARG* 1.3 60.3 + - - +
44E PRO* 3.8 26.2 - - + -
45E GLN 3.2 8.3 - - - +
46E LEU* 3.3 38.6 - - + +
47E LEU* 4.1 5.3 - - - +
89E TYR* 3.5 4.3 - - - +
90E LEU* 2.8 41.4 + - + +
92E ALA* 4.7 3.8 - - + -
103E TRP* 5.6 0.7 - - - -
105E PHE* 4.0 19.3 - + - -
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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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36E TYR* 1.3 74.4 - - - +
38E GLN* 1.3 60.8 + - - +
39E ALA 4.3 0.5 + - - -
43E GLY 4.3 0.3 - - - +
44E PRO* 4.3 0.7 - - - -
45E GLN* 2.7 47.0 + - + +
47E LEU* 3.7 22.6 - - + +
61E PRO* 5.2 8.9 - - - +
62E GLN* 5.4 5.7 - - - +
64E LEU* 3.7 17.4 - - - +
84E SER* 5.0 6.1 + - - -
85E ASP* 3.6 24.2 + - - +
86E SER 5.4 5.8 - - - -
87E GLY* 5.6 1.6 - - - -
88E PHE 3.5 6.3 - - - +
89E TYR* 3.1 45.3 + - + -
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Residues in contact with GLN 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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38D GLN* 2.8 43.4 + - - -
88D LEU* 4.3 0.7 - - - +
37E ARG* 1.3 77.1 - - - +
39E ALA* 1.3 64.9 + - - +
42E ARG 3.0 28.0 - - - +
43E GLY* 4.1 1.5 - - - -
44E PRO* 3.5 26.9 - - + +
87E GLY* 3.8 4.0 - - - -
88E PHE* 2.9 61.8 + - + +
90E LEU* 3.7 13.1 - - + +
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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