Contacts of the strand formed by residues 526 - 533 (chain B) in PDB entry 2O2C
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 SER 526 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102B ASP 4.3 2.1 - - - +
103B TYR* 4.8 0.2 - - - -
105B LYS* 3.0 39.1 + - - +
457B CYS* 3.2 12.8 - - - +
459B PHE* 4.1 11.7 - - - -
484B THR* 3.4 37.5 + - - +
487B LEU* 4.3 6.7 - - - -
524B ARG 4.1 1.1 + - - -
525B PRO* 1.3 77.0 - - - +
527B ASN* 1.3 67.0 + - - +
528B THR* 4.8 1.1 + - - -
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Residues in contact with ASN 527 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B LEU* 4.2 11.2 - - + -
102B ASP 3.4 5.6 - - - +
103B TYR* 3.4 27.9 - - - +
106B SER* 5.6 0.9 - - - -
373B LEU* 3.5 21.9 + - + +
376B VAL* 4.0 22.8 - - - +
389B HIS* 4.8 6.1 - - - -
456B PRO* 6.2 1.6 - - - +
457B CYS 2.8 6.7 + - - +
458B ASP* 3.0 27.3 + - - +
459B PHE* 2.8 30.0 + - - +
526B SER* 1.3 78.9 - - - +
528B THR* 1.3 62.9 + - - +
529B LEU* 5.4 1.8 - - + -
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Residues in contact with THR 528 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B PHE* 3.4 3.5 - - - +
101B LEU* 3.5 1.2 - - - +
102B ASP* 2.8 44.2 + - - +
105B LYS* 4.4 3.2 + - - -
459B PHE* 3.4 3.4 - - - +
480B PHE* 3.6 29.4 - - + +
484B THR* 3.5 28.1 + - + +
526B SER* 4.2 1.1 + - - -
527B ASN* 1.3 72.2 - - - +
529B LEU* 1.3 65.7 + - - +
530B LEU 4.7 0.7 - - - +
597C LEU* 3.7 41.1 - - + +
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Residues in contact with LEU 529 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B LEU* 4.0 17.9 - - + -
100B PHE 3.3 4.9 - - - +
101B LEU* 3.8 32.1 - - + -
373B LEU* 4.9 2.2 - - + -
458B ASP* 4.6 11.4 - - + +
459B PHE 2.7 13.0 + - - +
460B ILE* 3.3 24.4 - - + +
461B GLY 2.9 26.7 + - - +
480B PHE* 3.8 1.9 - - - -
527B ASN* 5.5 1.1 - - + -
528B THR* 1.3 73.9 - - - +
530B LEU* 1.3 60.3 + - - +
531B ILE* 5.5 0.2 - - - -
542B ILE* 6.1 0.7 - - + -
545B MET* 3.6 38.8 - - + -
546B TYR* 3.5 24.7 - - + +
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Residues in contact with LEU 530 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B PHE* 3.7 3.6 - - - -
99B LEU* 3.8 0.4 - - - +
100B PHE* 2.8 53.0 + - + +
461B GLY 3.5 20.9 - - - +
463B ILE* 3.9 31.2 - - + -
477B MET* 4.1 9.2 - - + -
480B PHE* 3.9 17.0 - - + -
481B PHE* 4.6 5.8 - - + -
528B THR* 4.0 1.8 - - + -
529B LEU* 1.3 73.4 - - - +
531B ILE* 1.3 60.9 + - - +
597C LEU* 4.0 36.8 - - + +
600C MET* 3.9 24.0 - - + -
601C PHE 4.9 0.2 - - - +
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Residues in contact with ILE 531 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B LEU* 5.8 0.4 - - + -
97B ASN* 4.2 4.0 - - - +
98B PHE* 3.3 24.7 - - - +
99B LEU* 3.7 23.1 - - + -
398B LEU* 6.1 1.3 - - + -
460B ILE* 5.6 3.4 - - + -
461B GLY 3.0 17.6 + - - +
462B ALA* 3.9 10.1 - - + -
463B ILE* 3.0 28.8 + - - +
529B LEU 5.5 1.1 - - - -
530B LEU* 1.3 77.8 - - - +
532B LYS* 1.3 57.7 + - - +
533B SER 3.6 23.1 - - - +
534B LEU* 3.8 24.0 - - + +
538B ALA* 4.0 13.5 - - + +
541B ALA* 6.4 0.4 - - + -
542B ILE* 4.0 17.5 - - + -
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Residues in contact with LYS 532 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B ASP* 2.8 31.8 + - + +
96B GLU* 4.0 21.6 + - - +
97B ASN* 3.1 22.1 + - + +
98B PHE* 3.9 14.6 + - + -
463B ILE* 3.3 9.5 + - + +
464B GLN* 2.8 66.4 + - + +
531B ILE* 1.3 71.5 - - - +
533B SER* 1.3 60.8 + - - +
604C LEU* 4.4 35.2 - - + +
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Residues in contact with SER 533 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B ASP* 4.4 4.0 + - - -
97B ASN* 3.0 25.8 + - - +
462B ALA* 4.1 3.1 - - - -
464B GLN* 3.8 25.8 + - - -
466B GLN* 3.8 16.3 + - - -
531B ILE* 3.4 6.9 - - - +
532B LYS* 1.3 82.7 - - - +
534B LEU* 1.3 58.9 - - - +
535B THR* 3.1 23.4 + - - +
538B ALA* 3.3 7.3 - - - +
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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