Contacts of the strand formed by residues 89 - 96 (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 LEU 89 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30A THR* 3.8 28.0 - - + -
31A GLY 3.4 14.1 - - - +
32A ARG* 3.4 27.7 - - - +
56A GLU 4.3 0.2 - - - +
57A PHE* 3.8 1.2 - - - -
58A SER* 3.0 37.6 + - - +
88A GLU* 1.3 75.9 - - - +
90A VAL* 1.3 61.0 + - - +
91A LYS* 4.7 19.1 - - + +
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Residues in contact with VAL 90 (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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30A THR* 3.3 6.7 - - - +
31A GLY 3.0 33.6 + - - +
33A VAL* 3.7 16.6 - - + -
43A VAL* 4.0 18.2 - - + -
46A LEU* 3.7 5.0 - - + +
55A VAL* 3.8 26.2 - - + -
56A GLU 3.3 14.4 - - - +
57A PHE* 3.6 37.0 - - + -
75A ILE* 4.6 6.1 - - + -
88A GLU 3.9 2.7 - - - +
89A LEU* 1.3 78.1 - - - +
91A LYS* 1.3 61.7 + - - +
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Residues in contact with LYS 91 (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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29A GLU 3.8 4.7 - - - +
30A THR* 4.1 13.7 - - + -
46A LEU* 4.2 3.6 - - - -
55A VAL* 3.4 7.4 - - - +
56A GLU* 2.8 65.6 + - + +
57A PHE 6.4 0.4 - - - -
89A LEU* 4.7 19.3 - - + +
90A VAL* 1.3 77.2 - - - +
92A ARG* 1.3 69.4 + - - +
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Residues in contact with ARG 92 (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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28A ASN 3.9 11.4 - - - -
29A GLU* 2.7 55.4 + - + +
46A LEU* 3.8 19.6 - - + +
48A ASN* 3.3 24.0 + - - +
49A ILE* 3.5 19.5 - - + +
50A GLN* 4.2 9.7 + - - +
53A GLU* 2.8 36.2 + - - +
54A LEU 4.3 2.5 - - - -
55A VAL* 4.8 2.2 - - - -
56A GLU* 5.6 0.2 - - - +
91A LYS* 1.3 84.1 - - - +
93A THR* 1.3 61.2 + - - +
94A GLY* 4.0 14.2 + - - +
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Residues in contact with THR 93 (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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53A GLU* 3.7 0.2 + - - -
54A LEU* 2.6 46.7 + - + +
55A VAL 4.1 13.2 - - - +
56A GLU* 4.2 10.5 - - + +
62A LYS* 5.5 8.1 - - - -
92A ARG* 1.3 76.7 - - - +
94A GLY* 1.3 61.2 + - - +
95A ASN* 3.2 32.2 + - - +
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Residues in contact with GLY 94 (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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50A GLN* 3.5 12.7 - - - +
53A GLU* 3.0 22.3 + - - -
92A ARG* 3.4 15.8 + - - +
93A THR* 1.3 79.3 - - - +
95A ASN* 1.3 63.2 + - - +
96A ILE* 5.6 0.2 - - - +
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Residues in contact with ASN 95 (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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53A GLU* 3.8 5.1 - - - +
54A LEU* 2.8 37.1 + - + +
93A THR* 3.2 28.6 + - - +
94A GLY* 1.3 84.0 - - - +
96A ILE* 1.3 69.7 - - - +
98A ASP* 5.3 9.2 - - - +
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Residues in contact with ILE 96 (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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50A GLN* 3.8 34.8 - - + +
51A ALA 3.7 19.1 - - - +
52A GLU* 3.4 27.1 - - + +
53A GLU* 4.3 2.9 - - - -
54A LEU* 5.2 1.0 - - - +
64A MET* 5.6 0.2 - - + -
95A ASN* 1.3 84.3 - - - +
97A VAL* 1.3 73.7 + - + +
98A ASP* 3.1 9.4 + - - +
130A ARG* 3.7 47.8 + - + +
132A GLN* 6.0 5.6 - - + -
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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