Contacts of the strand formed by residues 84 - 91 (chain A) in PDB entry 3OAN
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 84 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A LEU* 4.4 5.6 - - + -
76A PRO* 3.2 3.3 - - - +
77A ILE* 2.8 51.7 + - + +
81A ASN* 3.1 29.7 + - + +
82A GLU 3.2 1.0 - - - -
83A ASN* 1.3 106.3 - - - +
85A ILE* 1.3 58.3 + - - +
99A ILE* 3.8 17.5 - - + -
100A ILE 3.5 4.0 - - - -
101A LYS* 3.8 34.8 - - + -
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Residues in contact with ILE 85 (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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74A TYR* 4.2 4.7 - - + -
75A GLN 3.7 14.1 - - - +
76A PRO* 4.0 7.0 - - + -
82A GLU 3.4 25.1 - - - +
83A ASN 4.7 1.1 - - - +
84A LEU* 1.3 77.6 - - - +
86A LYS* 1.3 75.1 + - - +
87A TRP* 3.4 15.6 + - + +
99A ILE* 3.3 5.1 - - - +
100A ILE* 2.8 45.1 + - + +
102A VAL* 5.3 1.3 - - + -
108A GLY* 3.7 12.6 - - - +
111A LEU* 4.0 24.7 - - + -
112A VAL* 3.6 28.0 - - + -
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Residues in contact with LYS 86 (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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73A LYS 5.4 0.7 - - - +
74A TYR* 3.6 18.5 - - - -
75A GLN* 2.8 45.6 + - + +
76A PRO 3.0 21.4 + - - -
77A ILE* 3.6 35.3 + - + +
85A ILE* 1.3 75.3 - - - +
87A TRP* 1.3 59.2 + - - +
88A PRO* 3.5 12.9 - - + +
97A THR* 3.6 21.3 - - + -
98A PHE 3.6 4.5 - - - -
99A ILE* 4.7 3.4 - - + -
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Residues in contact with TRP 87 (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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52A VAL* 3.4 40.8 - - + +
64A LEU* 4.8 6.7 - - + -
66A THR* 3.6 25.2 - - + +
67A SER 5.1 0.6 + - - -
68A VAL* 4.2 13.7 - - + -
74A TYR* 3.3 38.0 + + + -
85A ILE* 4.3 15.0 - - + +
86A LYS* 1.3 73.5 - - - +
88A PRO* 1.3 76.2 + - - +
89A ILE* 3.5 7.6 + - + +
97A THR* 3.9 1.1 - - - +
98A PHE* 2.7 47.8 + + + +
100A ILE* 3.6 29.6 - - + -
111A LEU* 4.5 12.8 - - + -
115A VAL* 4.0 24.9 - - + -
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Residues in contact with PRO 88 (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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69A VAL* 5.8 0.2 - - - +
72A PHE* 3.5 34.2 - - + -
73A LYS 3.2 28.7 - - - +
74A TYR* 3.7 14.6 + - + -
86A LYS* 3.5 9.6 - - + +
87A TRP* 1.3 93.3 + - - +
89A ILE* 1.3 60.7 + - - +
95A LEU* 4.0 15.5 - - + -
96A GLU 3.3 8.1 - - - +
97A THR* 4.2 10.3 - - - +
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Residues in contact with ILE 89 (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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64A LEU* 4.6 0.4 - - + -
66A THR* 3.7 31.9 - - + +
72A PHE* 4.1 5.2 - - - -
87A TRP* 3.9 7.6 - - + +
88A PRO* 1.3 77.7 - - - +
90A ILE* 1.3 76.1 + - - +
91A THR* 3.5 7.9 + - + -
95A LEU* 3.5 4.0 - - - +
96A GLU* 2.7 50.8 + - + +
98A PHE* 3.8 45.3 - - + -
300A GOL 3.7 28.7 - - - -
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Residues in contact with ILE 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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72A PHE* 4.2 24.8 - - + -
89A ILE* 1.3 81.9 - - - +
91A THR* 1.3 61.1 + - - +
92A ASP* 4.2 14.3 - - - +
93A GLY 4.4 9.9 - - - +
94A LYS 3.4 22.2 - - - +
95A LEU* 4.4 11.0 - - + +
300A GOL 4.9 5.5 - - - -
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Residues in contact with THR 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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89A ILE* 3.5 14.5 + - + -
90A ILE* 1.3 75.1 - - - +
92A ASP* 1.3 69.2 + - - +
93A GLY 3.8 0.4 - - - -
94A LYS* 3.1 21.5 + - - +
96A GLU* 3.4 30.1 + - - +
98A PHE* 4.1 23.8 - - + -
300A GOL 4.8 12.6 - - - +
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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