Contacts of the strand formed by residues 32 - 37 (chain E) in PDB entry 1OFG
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 PHE 32 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31E ARG* 1.3 73.6 - - + +
33E GLY* 1.3 57.8 + - - +
34E TYR* 3.6 31.1 - + - -
56E HIS 2.9 18.9 + - - +
57E SER* 3.4 3.0 - - - -
58E ARG* 2.7 35.6 + - - +
100E ASP* 3.7 21.3 - - + -
101E ALA* 3.5 33.7 - - + -
124E HIS* 4.2 4.0 - + - -
332E LEU* 4.2 6.7 - - + -
333E ALA* 3.5 33.9 - - + -
336E VAL* 3.5 43.7 - - + -
337E ILE* 4.8 7.2 - - + -
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Residues in contact with GLY 33 (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 PHE* 1.3 73.1 - - - +
34E TYR* 1.3 62.1 + - - -
58E ARG* 3.4 26.7 - - - +
60E GLU* 4.1 5.2 - - - -
98E LYS 3.7 2.9 - - - -
99E ILE* 3.8 0.4 - - - -
100E ASP* 2.6 44.5 + - - +
101E ALA* 3.0 9.9 + - - +
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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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32E PHE* 3.6 24.4 - + - -
33E GLY* 1.3 74.2 - - - -
35E ALA* 1.3 58.4 + - - +
36E ILE* 4.0 6.5 - - + +
51E PHE* 3.5 29.6 - + + -
57E SER* 3.8 13.5 - - - -
58E ARG 2.8 16.3 + - - +
59E ILE* 3.6 1.6 - - - -
60E GLU* 2.6 30.5 + - - +
61E ALA 3.0 7.7 + - - +
99E ILE* 4.9 0.9 - - - -
101E ALA* 3.4 25.6 - - + -
103E TYR* 4.1 19.1 - - + -
126E MET* 3.3 29.1 - - + +
329E LEU* 2.7 37.4 + - + -
332E LEU* 3.5 18.2 - - + +
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Residues in contact with ALA 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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34E TYR* 1.3 73.7 - - - +
36E ILE* 1.3 64.6 + - - +
37E VAL* 3.6 2.8 + - + +
61E ALA* 3.3 19.5 - - + +
63E VAL* 4.8 12.3 - - + -
93E ILE* 5.3 2.9 - - + -
99E ILE* 3.8 20.0 - - + -
101E ALA 2.9 13.8 + - - +
102E VAL* 3.5 12.8 - - + -
103E TYR* 2.9 25.8 + - - +
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Residues in contact with ILE 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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34E TYR* 4.0 9.0 - - + +
35E ALA* 1.3 75.9 - - - +
37E VAL* 1.3 62.4 + - - +
38E GLY 3.9 7.6 + - - +
39E LEU* 3.9 23.1 - - + +
43E ALA* 4.7 2.7 - - + -
47E ILE* 4.8 5.4 - - + -
48E LEU* 3.9 23.6 - - + -
51E PHE* 3.6 34.5 - - + -
59E ILE* 4.0 16.4 - - + -
61E ALA 2.9 13.2 + - - +
62E LEU* 3.5 8.0 - - + +
63E VAL 2.8 29.3 + - - +
103E TYR* 3.8 13.0 - - + -
105E ILE* 4.4 12.8 - - + -
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Residues in contact with VAL 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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35E ALA 3.9 4.3 - - - +
36E ILE* 1.3 75.7 - - - +
38E GLY* 1.3 63.0 + - - +
63E VAL* 3.8 33.9 - - + -
87E TYR* 4.5 4.3 - - + -
90E PHE* 4.2 7.6 - - + -
102E VAL* 3.8 25.1 - - + -
103E TYR 2.8 17.6 + - - +
104E ILE* 4.1 9.2 - - + -
105E ILE* 2.7 32.9 + - - -
106E LEU* 3.8 25.5 + - + -
114E PHE* 4.6 10.5 - - + -
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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