Contacts of the strand formed by residues 132 - 137 (chain 0) 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 LEU 132 (chain 0).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300 PHE* 4.7 2.9 - - + -
790 LEU 3.8 7.2 - - - +
800 TYR* 3.4 38.8 - - + -
810 PRO* 3.5 30.7 - - + -
930 LEU* 3.4 24.9 - - + +
940 PRO* 3.3 17.8 - - - +
1300 GLY 3.8 1.6 + - - +
1310 ASP* 1.3 87.2 + - - +
1330 CYS* 1.3 61.5 + - - +
1460 ILE* 3.6 16.8 - - + -
1470 GLY 3.3 16.8 - - - +
1480 VAL* 4.4 2.9 - - + +
1690 LEU* 3.7 7.0 - - + -
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Residues in contact with CYS 133 (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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930 LEU* 4.1 8.1 - - - +
940 PRO* 3.3 15.9 - - + +
960 PHE* 3.5 36.1 - - + -
1270 VAL* 5.5 1.3 - - + -
1310 ASP 4.6 3.8 - - - +
1320 LEU* 1.3 77.8 - - - +
1340 ALA* 1.3 60.0 + - - +
1350 ILE* 3.8 9.8 + - - -
1460 ILE* 3.7 4.7 - - - +
1470 GLY 2.9 55.2 + - - -
1480 VAL 4.6 0.2 - - - -
1660 PHE* 3.6 24.0 - - - -
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Residues in contact with ALA 134 (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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860 LEU* 3.4 32.3 - - + -
900 PRO 5.5 1.1 - - - +
930 LEU* 4.2 6.3 - - + +
940 PRO 2.9 13.2 + - - +
950 THR* 3.3 17.3 - - + -
960 PHE* 2.9 26.2 + - - +
1330 CYS* 1.3 70.7 - - - +
1350 ILE* 1.3 63.9 + - - +
1360 SER* 3.6 1.4 + - - +
1430 PRO* 4.0 10.3 - - + -
1450 ALA 3.6 5.2 - - - -
1460 ILE* 4.7 0.4 - - - -
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Residues in contact with ILE 135 (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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960 PHE* 3.6 12.1 - - + -
980 THR* 3.6 11.0 - - + -
1060 LEU* 3.6 31.9 - - + -
1120 LEU* 3.5 24.7 - - + -
1330 CYS* 4.2 24.0 - - - +
1340 ALA* 1.3 72.5 - - - +
1360 SER* 1.3 60.9 + - - +
1430 PRO* 3.3 4.0 - - - +
1440 VAL* 2.9 36.5 + - + +
1450 ALA* 3.0 33.9 + - + +
1470 GLY* 4.7 6.1 - - - +
1660 PHE* 4.4 8.3 - - + -
1680 VAL* 5.0 7.6 - - + -
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Residues in contact with SER 136 (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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950 THR* 4.1 16.1 - - - +
960 PHE 2.8 12.1 + - - +
970 THR* 3.1 13.1 - - - -
980 THR* 2.9 26.2 + - - +
1340 ALA 3.9 6.9 + - - -
1350 ILE* 1.3 75.3 + - - +
1370 LEU* 1.3 73.7 + - - +
1400 ASN 5.0 2.5 - - - -
1410 ARG 6.3 0.4 - - - -
1420 ALA 4.7 9.3 - - - -
1430 PRO* 4.3 12.5 - - - +
1440 VAL 4.9 0.4 - - - +
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Residues in contact with LEU 137 (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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970 THR* 3.8 11.4 + - - +
980 THR* 3.4 32.5 - - - +
990 TRP 4.7 1.3 - - - +
1000 PRO* 5.5 3.6 - - + -
1030 LEU* 3.5 56.3 - - + -
1060 LEU* 4.7 0.7 - - + -
1360 SER* 1.3 80.5 - - - +
1380 VAL* 1.3 62.1 + - - +
1390 GLY* 4.2 2.9 - - - +
1400 ASN* 2.8 53.8 + - + +
1420 ALA 5.1 0.8 + - - -
1440 VAL* 3.7 22.2 - - + -
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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