Contacts of the strand formed by residues 69 - 74 (chain D) in PDB entry 1OVM
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 ALA 69 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20D ALA* 4.6 3.8 - - - -
24D PHE* 5.4 0.9 - - + -
59D ALA* 3.0 37.9 - - + +
62D TYR* 3.8 15.3 - - + -
63D ALA* 3.6 6.3 - - + -
68D PHE* 1.3 91.9 - - - +
70D ALA* 1.3 63.0 + - - +
95D PRO 3.2 5.1 + - - -
96D VAL* 3.5 5.8 - - + -
97D LEU 2.8 22.7 + - - -
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Residues in contact with ALA 70 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D LEU* 3.8 25.4 - - + -
20D ALA* 5.1 1.8 - - + -
22D HIS 4.6 9.5 + - - +
23D LEU* 3.5 21.0 - - + +
24D PHE* 3.2 30.7 + - - -
59D ALA* 4.2 3.0 - - - +
68D PHE* 4.9 1.3 - - + -
69D ALA* 1.3 78.0 - - - +
71D LEU* 1.3 60.6 + - - +
97D LEU* 3.3 16.2 - - + +
99D ILE* 4.7 1.8 - - + -
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Residues in contact with LEU 71 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D LEU* 4.2 1.3 - - - -
24D PHE* 3.3 8.7 - - + +
25D GLY* 4.1 0.9 - - - -
52D GLU 4.6 0.9 - - - +
55D ALA* 3.5 34.1 - - + -
56D SER* 3.8 27.1 - - - +
59D ALA* 4.5 4.5 - - + -
70D ALA* 1.3 76.2 - - - +
72D LEU* 1.3 63.2 + - - +
73D THR* 3.9 11.9 - - + -
82D ALA* 3.9 10.3 - - + -
86D ILE* 4.0 12.6 - - + -
96D VAL* 4.3 8.7 - - + -
97D LEU 2.7 13.8 + - - +
98D HIS* 3.8 25.4 - - + +
99D ILE* 2.7 35.2 + - - +
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Residues in contact with LEU 72 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D LEU* 3.9 17.0 - - + -
24D PHE 2.6 14.7 + - - +
25D GLY* 3.1 21.8 - - - -
26D VAL 3.4 7.6 + - - +
31D ASN* 4.2 18.4 - - + +
34D PHE* 3.4 35.7 - - + -
35D LEU* 3.5 25.1 - - + -
46D TRP* 4.1 5.4 - - + -
71D LEU* 1.3 74.9 - - - +
73D THR* 1.3 69.1 + - - +
99D ILE* 3.1 38.1 - - + +
101D GLY* 4.4 5.6 - - - +
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Residues in contact with THR 73 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25D GLY* 5.4 0.4 - - - -
26D VAL 4.4 4.9 - - - -
31D ASN* 3.3 12.3 + - - +
52D GLU* 3.9 19.1 - - + +
71D LEU* 3.9 15.0 - - + -
72D LEU* 1.3 80.3 - - - +
74D THR* 1.3 59.9 + - - +
78D GLY* 3.6 24.2 - - - +
79D GLU* 3.4 11.6 + - - +
82D ALA* 4.5 0.9 - - + -
98D HIS* 2.7 33.0 + - + +
99D ILE 2.9 4.7 + - - +
100D VAL* 3.3 5.5 - - - +
101D GLY 3.0 23.2 + - - -
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Residues in contact with THR 74 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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600C TPP 3.9 21.3 - - + -
26D VAL 4.6 1.8 + - - +
27D PRO 4.7 0.9 - - - +
28D GLY* 3.9 16.3 - - - -
30D TYR* 3.8 22.0 + - - +
31D ASN* 3.8 13.4 - - - +
52D GLU* 5.1 0.2 - - - +
73D THR* 1.3 77.6 - - - +
75D PHE* 1.3 71.3 + - - +
77D VAL* 3.6 27.1 - - + -
78D GLY* 3.0 23.3 + - - +
79D GLU* 3.1 9.0 + - - +
100D VAL* 3.9 2.9 - - - -
101D GLY 4.0 2.7 - - - -
116D HIS* 4.4 4.8 - - + -
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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