Contacts of the strand formed by residues 469 - 475 (chain B) in PDB entry 3PSB
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 GLY 469 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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465B SER* 3.8 5.7 - - - -
466B GLY 2.7 31.3 + - - +
468B PHE* 1.3 78.6 - - - +
470B THR* 1.3 63.0 + - - -
483B LYS* 4.2 6.1 - - - -
484B MET 3.1 14.4 - - - -
485B LEU* 4.6 6.7 - - - +
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Residues in contact with THR 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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462B ARG* 3.5 38.8 - - + +
464B GLY 3.2 18.4 - - - +
465B SER* 4.2 3.0 - - - +
469B GLY* 1.3 75.5 - - - -
471B VAL* 1.3 61.5 + - - +
472B TYR* 3.6 16.1 - - + +
482B VAL 3.5 1.9 - - - +
483B LYS* 3.2 0.9 - - - -
484B MET 2.8 32.3 + - - -
486B ASN* 2.9 26.3 + - - +
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Residues in contact with VAL 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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2B SM6 3.6 50.5 - - + +
462B ARG* 3.9 2.8 - - - +
463B ILE* 2.9 44.2 + - + -
464B GLY 2.9 19.8 + - - +
465B SER 3.7 4.0 - - - +
466B GLY* 3.4 26.5 - - - +
470B THR* 1.3 75.0 - - - +
472B TYR* 1.3 71.1 + - - +
481B ALA* 5.0 0.9 - - + -
482B VAL 3.4 9.2 - - - +
483B LYS* 4.2 8.5 - - + -
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Residues in contact with TYR 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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459B VAL* 3.5 33.0 - - + -
460B GLY 3.8 4.9 - - - -
461B GLN 3.2 9.4 - - - +
462B ARG* 3.5 37.1 - - + +
463B ILE* 3.8 6.5 - - - -
470B THR* 3.6 28.3 - - + +
471B VAL* 1.3 76.4 - - - +
473B LYS* 1.3 62.3 + - - +
481B ALA* 3.6 3.8 - - - +
482B VAL* 2.7 52.3 + - + +
484B MET* 3.7 26.2 - - + -
486B ASN* 3.9 23.0 + - - +
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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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460B GLY* 3.0 28.4 + - - -
461B GLN* 3.1 18.3 + - + +
463B ILE* 3.8 11.7 - - + +
472B TYR* 1.3 73.1 - - - +
474B GLY* 1.3 63.5 + - - +
479B ASP* 3.6 32.0 + - - -
480B VAL 3.8 4.7 - - - +
531B TRP* 3.6 53.5 - - + +
533B GLU* 4.4 7.3 + - - -
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Residues in contact with GLY 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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458B THR 3.2 12.8 - - - -
459B VAL* 4.7 0.4 - - - -
460B GLY* 4.2 1.8 - - - -
472B TYR 3.8 1.6 + - - -
473B LYS* 1.3 78.1 - - - +
475B LYS* 1.3 68.9 + - - +
479B ASP* 3.5 6.4 - - - +
480B VAL* 2.9 40.4 + - - +
482B VAL* 4.5 7.6 - - - +
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Residues in contact with LYS 475 (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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715A GLU* 4.0 23.2 + - - -
456B GLN 4.0 3.6 - - - +
457B ILE* 5.4 0.2 - - - +
458B THR* 3.0 49.9 + - + +
474B GLY* 1.3 78.7 - - - +
476B TRP* 1.3 60.3 + - - +
477B HIS 4.3 0.2 - - - -
478B GLY* 3.6 11.3 - - - +
479B ASP* 3.3 29.3 + - - +
480B VAL* 3.8 1.7 - - - +
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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