Contacts of the strand formed by residues 70 - 79 (chain E) in PDB entry 3OF6
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 TRP 70 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35E ASP 3.9 1.7 + - - -
36E VAL* 3.2 42.4 + - + +
38E PRO* 3.5 23.2 - - + +
39E PRO* 3.1 40.0 - - + +
62E PRO* 4.0 10.5 - - + -
63E SER 3.6 7.4 - - - -
64E PRO* 3.3 37.9 - - + -
65E ALA 4.2 0.7 - - - +
68E GLY 3.8 9.9 + - - -
69E THR* 1.3 94.6 + - - +
71E THR* 1.3 70.2 + - - +
64F PRO* 3.5 31.4 - - + +
70F TRP* 3.3 32.3 - + - -
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Residues in contact with THR 71 (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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196B ARG* 3.7 25.0 + - - -
198B ARG* 5.7 3.4 - - - +
32E LEU* 4.0 11.0 - - + -
33E VAL 3.4 10.1 - - - +
34E LEU* 3.5 28.5 - - + -
36E VAL* 4.2 1.6 - - - -
61E GLY 3.9 1.4 - - - +
62E PRO* 4.1 2.0 - - - -
63E SER* 2.8 38.3 + - - -
65E ALA* 4.4 16.5 - - + +
69E THR* 4.8 4.5 - - + -
70E TRP* 1.3 81.5 - - - +
72E ASN* 1.3 60.7 + - - +
73E LEU* 4.2 0.3 + - - +
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Residues in contact with ASN 72 (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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32E LEU* 3.5 4.8 - - - +
33E VAL* 3.2 46.7 + - + +
36E VAL* 4.1 6.7 - - + +
42E ASP* 4.6 3.6 + - - +
43E SER 3.2 31.0 + - - +
44E PRO* 4.3 4.2 - - - +
45E ILE* 3.6 9.1 - - - +
59E THR* 4.8 6.8 - - - +
61E GLY* 3.1 25.7 + - - -
62E PRO* 3.8 23.3 - - + +
71E THR* 1.3 74.3 - - - +
73E LEU* 1.3 81.9 + - - +
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Residues in contact with LEU 73 (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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147B VAL* 3.7 27.4 - - + -
149B LEU* 3.9 7.0 - - + -
194B SER* 3.6 31.2 - - - +
196B ARG* 4.4 14.6 - - + +
30E VAL* 3.4 17.5 - - + -
31E CYS 3.3 18.6 - - - +
32E LEU* 3.6 26.7 - - + -
45E ILE* 3.9 2.0 - - - -
59E THR* 3.4 1.6 - - - -
60E TYR* 2.8 37.8 + - + -
61E GLY 4.1 4.2 + - - +
71E THR 4.2 0.4 + - - +
72E ASN* 1.3 85.9 + - - +
74E ALA* 1.3 65.9 + - - +
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Residues in contact with ALA 74 (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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30E VAL* 4.1 3.1 - - - -
31E CYS 3.0 28.7 + - - +
45E ILE* 3.8 25.6 - - + +
47E PHE* 3.8 12.8 - - + -
57E ALA* 5.1 0.9 - - + -
58E PHE 3.2 15.5 - - - +
59E THR* 3.6 18.6 - - + +
60E TYR* 4.1 2.5 - - - -
73E LEU* 1.3 80.8 - - - +
75E HIS* 1.3 59.8 + - - +
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Residues in contact with HIS 75 (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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149B LEU* 3.6 26.5 - - + -
151B THR* 4.6 13.6 - - + +
182B GLU* 6.0 1.6 - - + -
28E VAL* 4.4 13.2 - - + -
29E VAL 3.5 9.2 - - - +
30E VAL* 4.2 3.1 - - + +
57E ALA* 3.4 4.9 - - - +
58E PHE* 3.0 59.0 + + + -
60E TYR* 3.1 29.1 + - + -
74E ALA* 1.3 73.9 - - - +
76E LEU* 1.3 73.8 + - - +
77E SER* 4.3 9.7 - - - -
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Residues in contact with LEU 76 (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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27E MET* 3.9 0.7 - - - +
28E VAL* 3.4 4.0 - - - +
29E VAL* 2.8 45.8 + - + +
47E PHE* 3.8 32.1 - - + -
55E LEU* 3.8 34.5 - - + -
56E ASP 3.2 28.0 - - - +
57E ALA* 4.1 4.9 - - + -
74E ALA 4.3 0.2 + - - -
75E HIS* 1.3 79.0 - - - +
77E SER* 1.3 78.0 + - - +
78E LEU* 5.3 5.7 - - + +
89E LEU* 4.0 18.6 - - + -
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Residues in contact with SER 77 (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 GLN* 2.7 35.8 + - - +
27E MET 3.6 2.7 - - - -
28E VAL* 3.8 10.7 - - - +
75E HIS* 4.3 12.1 - - - -
76E LEU* 1.3 86.3 - - - +
78E LEU* 1.3 63.5 + - - +
79E PRO* 4.6 1.4 - - - +
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Residues in contact with LEU 78 (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 GLN* 3.6 5.4 - - - -
27E MET* 2.7 66.8 + - + +
55E LEU* 5.2 13.7 - - + -
76E LEU* 5.3 8.1 - - + +
77E SER* 1.3 78.9 + - - +
79E PRO* 1.3 87.4 - - + +
82E GLU* 3.9 16.2 - - + +
83E LEU* 4.2 20.6 - - + +
86E TRP* 4.0 25.1 - - + +
89E LEU* 5.9 7.2 - - + -
109E LEU* 5.1 4.7 - - + -
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Residues in contact with PRO 79 (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 GLN* 3.8 18.1 - - - +
77E SER 4.6 1.1 - - - +
78E LEU* 1.3 108.9 - - + +
80E SER* 1.3 58.4 + - - +
81E GLU* 3.0 30.8 + - - +
82E GLU* 3.2 38.3 + - + +
83E LEU* 4.0 2.1 + - - -
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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