Contacts of the strand formed by residues 40 - 45 (chain A) in PDB entry 3OEE
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 40 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A ALA 4.1 0.3 - - - +
36A VAL* 3.2 5.7 - - - +
37A GLY 2.8 36.3 + - - +
38A ASP* 3.0 6.5 - - + +
39A GLY* 1.3 84.4 - - - +
41A ALA* 1.3 68.7 + - - +
42A ARG* 4.1 15.1 + - + +
74A GLY* 4.9 0.9 - - - -
75A ILE 3.4 6.3 - - - +
76A VAL* 3.8 24.7 - - + -
77A LEU* 4.7 0.2 - - - -
283A LEU* 4.6 4.7 - - + +
286A LEU* 3.7 41.7 - - + +
287A LEU* 4.1 24.7 - - + -
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Residues in contact with ALA 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A VAL* 4.9 1.1 - - + -
35A ALA 3.5 7.0 - - - +
36A VAL* 4.1 10.3 - - + -
39A GLY 4.1 0.8 - - - -
40A ILE* 1.3 74.2 - - - +
42A ARG* 1.3 59.2 + - - +
43A VAL* 3.8 7.0 - - + +
57A PHE* 3.9 33.4 - - + -
73A VAL 3.5 2.8 - - - +
74A GLY 3.7 0.3 - - - -
75A ILE* 2.7 45.4 + - + +
77A LEU* 4.1 9.0 - - + -
84A VAL* 4.6 2.2 - - + -
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Residues in contact with ARG 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A VAL* 3.8 0.7 - - - -
34A LEU* 2.8 37.1 + - + +
35A ALA* 2.8 47.4 + - + +
40A ILE* 4.0 15.4 - - + +
41A ALA* 1.3 72.5 - - - +
43A VAL* 1.3 60.7 + - - +
72A GLN* 3.0 40.3 + - - +
73A VAL 3.5 5.4 - - - +
74A GLY* 4.7 4.5 - - - -
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Residues in contact with VAL 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A GLY* 4.0 2.5 - - - -
32A ARG 3.4 18.4 - - - +
33A VAL* 4.4 5.8 - - + -
34A LEU* 4.2 1.8 - - - -
41A ALA* 3.8 15.9 - - + +
42A ARG* 1.3 80.6 - - - +
44A PHE* 1.3 72.9 + - - +
45A GLY 3.9 1.4 + - - +
46A LEU* 3.8 23.1 - - + -
57A PHE* 4.7 0.4 - - + -
72A GLN* 3.2 7.4 - - - +
73A VAL* 2.7 43.3 + - + +
75A ILE* 3.5 26.7 - - + -
90A VAL* 4.0 16.4 - - + -
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Residues in contact with PHE 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A LEU* 4.0 29.7 - - + +
31A GLY* 2.9 7.3 - - - -
32A ARG* 2.8 50.3 + - + +
34A LEU* 3.8 29.3 - - + +
43A VAL* 1.3 72.6 - - - +
45A GLY* 1.3 64.7 + - - +
71A GLY* 3.7 21.5 - - - -
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Residues in contact with GLY 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A LEU* 4.0 15.9 - - - -
30A THR 3.7 4.0 - - - -
43A VAL 3.9 1.3 + - - +
44A PHE* 1.3 83.7 - - - +
46A LEU* 1.3 71.6 + - - +
47A ASN* 3.2 20.3 + - - +
71A GLY 4.7 4.0 + - - -
72A GLN* 5.4 1.1 - - - +
73A VAL* 4.4 12.1 + - - +
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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