Contacts of the strand formed by residues 274 - 279 (chain 0) in PDB entry 1POV
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 CYS 274 (chain 0).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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940 THR* 4.2 3.8 - - - -
960 GLU* 2.7 50.4 + - - +
990 ASN* 3.4 17.2 + - - +
1780 HIS* 3.6 27.8 - - + +
1790 VAL 3.2 14.1 - - - +
1800 GLN* 4.3 6.1 - - + -
2670 ILE* 4.1 7.4 - - - +
2720 ASN* 3.6 2.7 + - - +
2730 ASN* 1.3 84.8 - - - +
2750 ALA* 1.3 60.9 + - - +
2760 THR* 5.2 1.1 - - - -
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Residues in contact with ALA 275 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
990 ASN* 3.7 5.2 - - - +
1770 VAL 3.5 1.4 - - - +
1780 HIS* 3.4 4.4 + - - -
1790 VAL* 2.8 41.5 + - + +
1930 VAL* 4.6 4.7 - - + -
2650 GLN* 3.5 28.5 - - + -
2670 ILE* 3.8 20.6 - - + +
2740 CYS* 1.3 74.7 - - - +
2760 THR* 1.3 62.7 + - - +
2770 LEU* 4.2 5.8 - - + -
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Residues in contact with THR 276 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
730 ILE* 4.8 11.7 - - + -
920 ILE* 5.6 2.9 - - + -
940 THR* 5.4 3.8 + - - +
960 GLU 5.5 2.3 + - - -
990 ASN 3.3 8.1 + - - +
1000 SER* 3.0 17.6 - - - -
1010 VAL* 2.8 27.2 + - - +
1760 THR* 3.9 26.9 - - + -
1770 VAL 3.3 3.4 - - - +
1780 HIS* 2.9 28.4 + - + +
2650 GLN* 5.5 0.2 - - - -
2740 CYS* 5.2 1.7 - - - -
2750 ALA* 1.3 74.3 - - - +
2770 LEU* 1.3 65.0 + - - +
2780 VAL* 4.0 3.2 + - + +
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Residues in contact with LEU 277 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1010 VAL* 3.5 19.7 - - + -
1760 THR* 3.5 1.7 - - - -
1770 VAL* 2.8 57.7 + - + +
1790 VAL* 4.7 1.8 - - + -
1930 VAL* 3.7 42.0 - - + +
1950 ALA* 3.9 26.0 - - + +
2630 PRO* 4.1 7.6 - - + +
2640 HIS* 4.2 6.3 - - - -
2650 GLN* 4.4 9.0 - - + -
2750 ALA* 4.5 4.3 - - + +
2760 THR* 1.3 80.3 - - - +
2780 VAL* 1.3 61.6 + - - +
2790 LEU* 3.6 13.6 + - + +
2980 ILE* 5.6 2.0 - - + -
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Residues in contact with VAL 278 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
730 ILE* 4.4 17.5 - - + -
1010 VAL 2.7 15.2 + - - +
1020 VAL* 3.6 8.7 - - + +
1030 ALA 2.9 27.9 + - - -
1070 TRP* 4.1 34.5 - - + -
1080 PRO* 3.5 33.7 - - + -
1750 TYR 3.6 5.2 - - - +
1760 THR* 4.1 20.2 - - + +
2760 THR* 4.8 3.1 - - + +
2770 LEU* 1.3 71.1 - - - +
2790 LEU* 1.3 59.4 + - - +
2800 PRO* 3.5 3.5 - - - +
3250 MET* 4.7 0.4 - - - -
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Residues in contact with LEU 279 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1030 ALA* 3.9 16.8 - - + +
1080 PRO* 4.1 7.1 - - - +
1510 LEU* 4.5 1.8 - - + -
1740 GLY* 3.3 2.6 - - - -
1750 TYR* 2.7 51.6 + - + +
1770 VAL* 4.1 20.9 - - + -
1950 ALA* 3.6 22.7 - - + -
2630 PRO* 5.0 0.4 - - + -
2770 LEU* 4.2 17.0 - - + +
2780 VAL* 1.3 75.6 - - - +
2800 PRO* 1.3 66.5 - - + +
2960 TRP* 3.9 38.4 - - + +
2980 ILE* 4.1 15.5 - - + -
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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