Contacts of the strand formed by residues 74 - 80 (chain E) in PDB entry 4R3O
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 ILE 74 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69E GLU* 3.7 1.2 - - - -
70E ILE* 2.8 49.1 + - + -
71E ASP* 2.9 20.3 + - + +
73E HIS* 1.3 114.2 - - + +
75E GLY* 1.3 65.9 + - - +
96E THR* 5.1 2.5 - - + -
107E MET 4.3 0.4 - - - +
109E VAL* 3.8 31.6 - - + +
112E VAL* 3.6 30.5 - - + -
143E PHE* 4.2 11.9 - - + -
144E GLY 3.6 8.3 - - - +
226E PHE* 4.4 3.5 - - - +
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Residues in contact with GLY 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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48E LEU* 4.1 6.5 - - - -
68E VAL 3.4 9.9 - - - -
70E ILE* 4.2 2.0 - - - -
74E ILE* 1.3 79.4 - - - +
76E CYS* 1.3 61.5 + - - +
143E PHE* 3.4 4.5 - - - -
144E GLY 2.9 35.3 + - - -
220E VAL* 4.5 0.6 - - - +
226E PHE* 3.5 22.3 - - - -
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Residues in contact with CYS 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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48E LEU* 4.2 4.5 - - - +
66E LYS 3.7 0.7 - - - +
67E ILE* 3.2 4.0 - - - +
68E VAL* 2.9 35.7 + - + +
70E ILE* 3.8 22.0 - - + -
75E GLY* 1.3 75.4 - - - +
77E ALA* 1.3 63.4 + - - +
78E MET* 4.9 1.0 - - - +
89E ILE* 3.7 16.6 - - + -
141E LEU* 3.6 32.5 - - - -
142E LEU 3.3 9.9 - - - -
143E PHE* 3.7 20.2 - - + -
226E PHE* 4.8 0.6 - - - -
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Residues in contact with ALA 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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37E ALA* 4.5 17.5 - - + -
38E ILE 5.8 0.4 - - - +
48E LEU* 4.1 23.5 - - + +
49E ALA 5.6 0.9 - - - +
50E VAL* 5.3 1.3 - - + -
66E LYS 3.2 8.7 - - - +
67E ILE* 4.1 14.6 - - + -
76E CYS* 1.3 75.9 - - - +
78E MET* 1.3 60.1 + - - +
140E ALA 3.9 0.5 - - - +
141E LEU* 3.6 4.0 - - - -
142E LEU* 2.9 38.8 + - + +
170E ILE* 4.1 2.6 - - - +
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Residues in contact with MET 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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35E SER 4.8 0.2 - - - +
37E ALA* 5.0 1.0 - - - +
50E VAL* 4.7 6.1 - - - +
65E GLU 3.3 24.9 - - - +
66E LYS* 2.9 38.7 + - + +
68E VAL* 3.7 36.3 - - + -
76E CYS* 4.9 0.9 - - - +
77E ALA* 1.3 74.6 - - - +
79E SER* 1.3 61.4 + - - +
82E ILE* 4.3 20.0 - - + +
85E ALA* 3.5 29.6 - - + -
86E LYS* 5.0 1.8 - - - -
89E ILE* 4.2 13.5 - - + -
139E VAL* 4.3 1.3 - - + -
140E ALA 3.5 4.7 - - - +
141E LEU* 3.7 17.3 - - + -
170E ILE* 4.5 1.6 - - - -
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Residues in contact with SER 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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31E ILE* 4.3 5.5 + - - +
34E GLY* 3.5 10.6 - - - -
35E SER* 2.7 29.8 + - - +
37E ALA* 5.1 0.7 - - - -
78E MET* 1.3 75.7 - - - +
80E GLY* 1.3 61.4 + - - +
82E ILE* 4.8 2.9 - - - -
139E VAL* 3.3 7.7 - - - +
140E ALA* 2.9 35.1 + - - +
170E ILE* 3.7 26.5 - - - -
171E GLY* 3.6 8.7 - - - -
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Residues in contact with GLY 80 (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 ALA 4.7 3.4 - - - -
31E ILE* 4.6 10.5 - - - -
34E GLY* 3.7 23.4 - - - -
35E SER 4.5 1.0 - - - +
79E SER* 1.3 78.1 + - - +
81E LEU* 1.3 65.9 + - - +
82E ILE* 3.3 17.4 + - - +
138E GLY 3.9 4.7 - - - -
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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