Contacts of the strand formed by residues 68 - 72 (chain A) in PDB entry 3O7O
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 GLU 68 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22A MET* 3.6 2.4 - - - -
23A GLU* 2.8 45.1 + - + +
25A ASN* 2.6 30.3 + - - -
38A MET* 3.7 9.4 - - - +
66A TYR* 3.3 17.7 - - + +
67A PRO* 1.3 73.9 - - - +
69A PHE* 1.3 60.3 + - - +
70A TYR* 3.7 10.8 - - + -
74A LYS* 2.8 13.4 + - - -
228A GLU* 2.6 36.9 - - - +
229A ILE 3.2 17.5 - - - +
230A GLY* 3.9 5.8 - - - -
245A TRP* 4.2 5.6 - - - -
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Residues in contact with PHE 69 (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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13A PHE* 4.1 6.7 - + + -
15A TRP* 3.9 12.6 - + - -
20A LEU* 4.0 20.6 - - + -
21A SER 3.2 12.3 - - - +
22A MET* 4.1 1.1 - - - +
45A ILE* 3.7 28.5 - - + -
68A GLU* 1.3 75.1 - - - +
70A TYR* 1.3 66.5 + - - +
100A VAL* 4.8 1.3 - - + -
227A TRP 4.1 0.2 - - - +
228A GLU* 3.6 0.7 - - - -
229A ILE* 2.7 70.0 + - + +
245A TRP* 4.9 0.2 - + - -
247A PHE* 3.4 36.3 - + + -
250A PHE* 3.8 38.8 - + - -
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Residues in contact with TYR 70 (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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10A THR* 4.0 5.2 - - - +
20A LEU* 3.5 11.6 - - - +
21A SER* 2.7 60.5 + - - -
23A GLU* 4.2 18.9 + - + -
68A GLU* 3.7 17.7 - - + -
69A PHE* 1.3 80.3 - - - +
71A TYR* 1.3 59.5 + - - +
72A GLY 3.5 18.1 + - - -
74A LYS* 3.7 36.8 - - + +
77A GLU* 4.5 4.2 - - - +
79A HIS* 3.2 31.6 - - - +
226A VAL* 3.5 20.6 - - + -
227A TRP 3.2 13.2 - - - +
228A GLU* 3.6 10.5 - - + -
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Residues in contact with TYR 71 (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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18A ILE* 3.6 21.8 - - + -
19A PRO* 3.3 30.1 - - + +
20A LEU* 3.6 9.4 - - + +
70A TYR* 1.3 72.3 - - - +
72A GLY* 1.3 59.5 + - - +
83A GLY 4.6 1.4 + - - -
84A SER* 3.7 14.1 - - - -
85A LYS* 2.8 43.5 + - + +
86A LEU* 3.7 30.2 - - + +
96A PHE* 4.1 15.5 - + + -
226A VAL* 3.3 5.3 - - - +
227A TRP* 2.9 39.9 + - + +
250A PHE* 5.1 8.3 - - + -
252A ILE* 3.9 20.7 - - + +
254A LEU* 5.6 2.0 - - + +
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Residues in contact with GLY 72 (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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19A PRO 5.1 0.8 + - - -
21A SER* 4.8 0.3 + - - -
70A TYR* 3.5 20.0 + - - -
71A TYR* 1.3 79.0 - - - +
73A TYR* 1.3 59.7 + - - -
80A THR* 3.2 18.5 + - - -
81A ALA* 4.4 2.9 + - - +
84A SER* 3.2 26.6 + - - -
86A LEU* 4.1 5.4 - - - -
225A THR 3.8 5.8 - - - -
226A VAL* 4.0 1.8 - - - -
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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