Contacts of the strand formed by residues 67 - 73 (chain Q) in PDB entry 5OA3
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 ASP 67 (chain Q).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24Q HIS 3.3 1.9 - - - +
25Q CYS* 3.2 4.7 - - - -
26Q LYS* 2.9 58.3 + - + +
28Q GLY* 4.0 14.1 - - - +
29Q ASN* 4.4 5.7 + - - -
31Q LEU* 2.8 42.5 + - - +
65Q GLY 4.3 0.6 - - - -
66Q VAL* 1.3 71.4 - - - +
68Q ILE* 1.3 60.9 + - - +
69Q ARG* 3.0 43.2 + - - -
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Residues in contact with ILE 68 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23Q ALA* 4.0 17.3 - - + -
24Q HIS 3.2 8.3 - - - +
25Q CYS* 3.5 23.8 - - - -
31Q LEU 2.8 10.4 + - - +
32Q ILE* 3.3 30.7 - - + +
33Q LYS 3.0 28.4 + - - +
63Q PHE* 4.5 6.1 - - + -
66Q VAL* 3.6 14.8 + - + -
67Q ASP* 1.3 77.5 - - - +
69Q ARG* 1.3 66.4 + - - +
70Q VAL* 3.7 21.5 - - + -
88Q ILE* 4.5 17.9 - - + +
91Q ALA* 4.4 9.6 - - + -
92Q LEU* 5.2 1.6 - - + -
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Residues in contact with ARG 69 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14252 G 3.5 29.7 + - - -
14262 U 3.4 36.5 + - - +
22Q VAL 3.5 2.6 - - - +
24Q HIS* 2.9 45.9 + - + +
26Q LYS* 3.7 23.2 - - + +
31Q LEU* 3.8 22.8 + - - +
33Q LYS* 3.8 16.8 - - - +
67Q ASP* 3.0 35.4 + - - +
68Q ILE* 1.3 74.3 - - - +
70Q VAL* 1.3 61.4 + - - +
71Q ARG 4.2 0.2 + - - -
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Residues in contact with VAL 70 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22Q VAL 3.2 13.5 - - - +
23Q ALA* 4.4 3.8 - - + -
32Q ILE* 5.1 3.1 - - + -
33Q LYS 2.9 17.8 + - - +
34Q VAL* 3.6 13.4 - - + -
35Q ASN* 2.7 32.7 + - - -
68Q ILE* 3.7 22.7 - - + +
69Q ARG* 1.3 78.6 - - - +
71Q ARG* 1.3 61.4 + - - +
72Q VAL* 3.7 22.8 + - + -
84Q ILE* 4.6 8.1 - - + -
87Q SER* 3.6 22.4 - - - +
88Q ILE* 4.9 5.4 - - + -
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Residues in contact with ARG 71 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14062 G 3.5 24.4 + - - -
14072 U 3.5 28.3 + - - -
14282 G 2.3 35.4 + - - +
14432 C 4.3 11.5 + - - -
20Q THR 4.0 1.4 - - - +
21Q ALA* 3.6 1.6 - - - -
22Q VAL* 2.9 50.8 + - + +
35Q ASN* 4.4 12.3 - - - +
69Q ARG 4.2 0.2 + - - -
70Q VAL* 1.3 73.3 - - - +
72Q VAL* 1.3 62.2 + - - +
73Q LYS* 3.2 31.3 + - + +
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Residues in contact with VAL 72 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15442 C 4.9 3.6 + - - -
20Q THR 3.3 16.4 - - - +
21Q ALA* 3.5 18.6 - - + -
34Q VAL* 4.3 10.1 - - + -
35Q ASN* 4.5 15.7 + - + +
70Q VAL* 3.7 11.6 + - + -
71Q ARG* 1.3 78.4 - - - +
73Q LYS* 1.3 74.2 + - - +
80Q GLN* 3.7 41.6 + - + +
83Q ALA* 4.1 11.0 - - + -
84Q ILE* 3.6 22.7 - - + -
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Residues in contact with LYS 73 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14282 G 2.7 31.9 + - - -
15442 C 5.8 2.0 - - - +
15452 A 3.5 11.9 - - - +
15852 U 2.8 42.7 + - - +
18Q THR 4.3 0.2 - - - +
20Q THR* 2.9 35.1 + - - +
35Q ASN* 5.0 12.6 - - - +
71Q ARG* 3.2 31.3 + - + +
72Q VAL* 1.3 82.2 - - - +
74Q GLY* 1.3 64.6 + - - +
80Q GLN* 4.3 2.5 - - - +
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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