Contacts of the strand formed by residues 80 - 87 (chain A) in PDB entry 2O8L
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 80 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63A LEU 3.7 0.3 - - - +
64A LYS* 3.2 7.6 - - - +
65A ALA 2.8 40.7 + - - +
66A PHE* 5.0 0.2 - - - -
67A PRO* 3.7 20.2 - - + -
77A ASN 3.3 22.0 - - - -
79A GLY* 1.3 76.5 - - - -
81A THR* 1.3 63.3 + - - +
99A PHE* 3.6 20.8 - - + -
100A SER 4.1 9.2 - - - -
102A ASN* 3.4 29.6 - - + -
106A LYS* 3.2 25.1 - - + -
107A HIS 3.5 0.2 - - - -
108A ILE* 3.3 28.7 - - + -
111A VAL* 3.6 30.5 - - + -
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Residues in contact with THR 81 (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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61A HIS* 3.3 47.8 - - + +
63A LEU 3.6 3.1 - - - -
64A LYS* 3.7 15.2 - - + +
80A PHE* 1.3 76.4 - - - +
82A ALA* 1.3 67.0 + - - +
83A GLU* 5.7 0.2 - - + -
99A PHE* 3.4 3.8 - - - -
100A SER* 3.3 34.2 + - - +
102A ASN* 5.4 2.2 - - - +
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Residues in contact with ALA 82 (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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60A PRO* 3.1 28.3 - - + +
61A HIS* 3.2 21.5 + - - -
63A LEU* 2.9 23.0 + - + +
81A THR* 1.3 76.4 - - - +
83A GLU* 1.3 59.9 + - - +
84A GLN 4.8 0.7 - - - +
85A ILE* 4.8 1.6 - - + -
97A VAL* 3.4 28.9 - - + -
98A LYS 3.6 0.9 - - - -
99A PHE* 3.4 11.5 - - + -
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Residues in contact with GLU 83 (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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60A PRO* 3.5 19.4 - - - +
61A HIS* 2.8 33.6 - - - -
81A THR* 4.1 0.4 - - - +
82A ALA* 1.3 76.2 - - - +
84A GLN* 1.3 61.2 + - + +
98A LYS* 2.8 13.6 + - + +
99A PHE 4.4 1.6 - - - -
100A SER* 3.2 41.6 + - - +
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Residues in contact with GLN 84 (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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60A PRO* 4.2 1.7 - - - +
82A ALA 3.9 0.2 - - - -
83A GLU* 1.3 83.4 - - + +
85A ILE* 1.3 74.0 + - - +
86A THR* 4.2 10.4 + - - +
96A ILE 3.9 0.3 - - - +
97A VAL* 3.6 0.5 - - - +
98A LYS* 2.8 67.1 + - + +
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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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53A VAL* 3.6 49.8 - - + -
56A THR* 4.2 17.0 - - + +
60A PRO* 3.9 30.9 - - + +
63A LEU* 4.7 5.4 - - + -
82A ALA* 4.8 1.3 - - + -
84A GLN* 1.3 84.4 - - - +
86A THR* 1.3 73.1 + - - +
87A LYS* 4.1 5.1 + - + +
95A ALA* 4.4 1.1 - - + -
96A ILE 3.3 6.7 - - - +
97A VAL* 4.3 10.3 - - + -
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Residues in contact with THR 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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84A GLN* 4.2 15.8 + - - +
85A ILE* 1.3 76.0 + - - +
87A LYS* 1.3 73.8 + - - +
88A TYR 3.7 0.3 + - - -
96A ILE* 2.8 51.8 + - - +
98A LYS* 5.7 1.9 - - - +
205A PHE* 4.3 10.8 - - + -
209A ASN* 3.9 22.5 + - - +
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Residues in contact with LYS 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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50A LYS* 4.1 24.3 - - + +
53A VAL* 3.9 20.0 - - + -
54A ASP* 2.5 40.3 + - - -
85A ILE* 4.1 4.7 + - + -
86A THR* 1.3 84.3 - - - +
88A TYR* 1.3 72.1 + - - +
89A SER* 3.4 3.1 + - - -
94A LEU 3.9 4.3 - - - -
95A ALA* 4.2 1.3 - - - +
205A PHE* 3.9 2.6 - - - -
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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