Contacts of the strand formed by residues 468 - 474 (chain B) in PDB entry 1OGS
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 VAL 468 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65B LEU* 4.3 11.9 - - + -
442B ASN* 5.5 2.9 - - + -
443B ASP* 5.7 7.6 - - + +
444B LEU* 3.8 33.9 - - + -
462B ASN* 3.6 9.4 - - - +
464B SER* 4.6 4.0 - - - +
466B LYS* 3.5 13.2 - - + +
467B ASP* 1.3 80.5 - - - +
469B PRO* 1.3 76.3 - - + +
470B LEU* 3.0 6.2 - - - +
483B ILE* 4.2 0.9 - - - -
484B SER 2.7 34.4 + - - +
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Residues in contact with PRO 469 (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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64B GLY* 6.1 4.7 - - - -
65B LEU* 4.0 13.0 + - - +
467B ASP* 3.8 8.1 - - + +
468B VAL* 1.3 93.7 - - + +
470B LEU* 1.3 61.1 + - - +
482B THR 3.8 7.0 - - - +
483B ILE* 4.1 20.8 - - + -
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Residues in contact with LEU 470 (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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65B LEU* 3.4 24.2 - - + +
67B LEU* 3.7 30.7 - - + -
444B LEU* 4.0 15.0 - - + -
460B VAL* 4.5 11.7 - - + -
468B VAL 3.0 24.2 - - - +
469B PRO* 1.3 74.5 - - - +
471B THR* 1.3 66.7 + - - +
472B ILE* 4.6 10.3 - - + -
481B GLU* 3.9 0.5 - - - -
482B THR* 2.9 52.0 + - + +
483B ILE 3.9 0.2 - - - -
484B SER* 3.5 24.0 - - - +
492B TYR* 5.6 0.9 - - + +
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Residues in contact with THR 471 (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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60B HIS* 3.0 41.3 + - + -
65B LEU 3.0 10.3 + - - -
66B LEU* 3.4 12.1 - - + +
67B LEU* 2.8 28.6 + - - +
470B LEU* 1.3 79.7 + - - +
472B ILE* 1.3 65.5 + - - +
479B PHE* 3.7 31.0 - - + -
480B LEU 3.2 12.1 - - - +
481B GLU* 4.3 6.3 - - + +
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Residues in contact with ILE 472 (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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67B LEU* 3.2 20.4 - - + +
69B LEU* 5.2 1.6 - - + +
436B LEU* 4.7 12.3 - - + -
458B VAL* 4.3 19.3 - - + -
460B VAL* 4.8 5.6 - - + -
470B LEU* 4.6 11.2 - - + -
471B THR* 1.3 78.8 - - - +
473B LYS* 1.3 67.3 + - - +
474B ASP 3.9 0.3 + - - -
478B GLY 3.8 0.7 - - - +
479B PHE* 3.4 2.9 - - - -
480B LEU* 2.8 52.5 + - + +
482B THR* 5.1 3.4 - - + -
492B TYR* 4.1 33.4 - - + -
494B TRP* 3.9 22.7 - - + -
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Residues in contact with LYS 473 (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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66B LEU* 3.7 24.5 - - + +
67B LEU 2.7 10.1 + - - -
68B THR* 3.6 24.6 - - + +
69B LEU* 2.8 33.9 + - - +
472B ILE* 1.3 73.6 - - - +
474B ASP* 1.3 62.0 + - - +
475B PRO* 3.9 19.3 - - - +
478B GLY 3.6 4.9 - - - +
479B PHE* 3.6 35.8 - - + -
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Residues in contact with ASP 474 (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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69B LEU* 3.5 12.6 - - + +
472B ILE 3.9 0.2 + - - -
473B LYS* 1.3 75.6 - - - +
475B PRO* 1.3 58.9 - - - +
476B ALA 2.7 17.8 + - - -
477B VAL* 2.9 20.8 + - + +
478B GLY* 2.8 35.6 + - - +
480B LEU* 5.3 1.8 - - + -
494B TRP* 2.7 38.1 + - + +
496B ARG* 2.9 39.8 + - - +
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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