Contacts of the strand formed by residues 528 - 535 (chain H) in PDB entry 1P8J
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 PHE 528 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263H VAL* 3.8 31.2 - - + -
305H CYS* 4.6 5.6 - - - -
491H LEU 3.8 14.4 - - - +
492H THR* 3.2 5.0 - - - +
493H LEU* 2.9 55.3 + - + +
498H ARG* 3.6 27.8 - - + -
501H LEU* 4.7 5.4 - - + -
503H ILE* 4.6 4.3 - - + -
516H LEU* 3.5 32.5 - - + -
519H ARG* 5.5 0.9 - - - -
526H ASP 4.9 2.2 - - - -
527H GLY* 1.3 77.9 - - - -
529H ASN* 1.3 60.5 + - - +
530H ASP 3.9 0.7 - - - -
531H TRP* 4.0 16.8 - + + -
533H PHE* 3.7 28.5 - + + -
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Residues in contact with ASN 529 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268E ARG* 3.8 19.0 + - - +
492H THR* 4.1 14.3 + - - +
526H ASP 6.0 0.4 - - - +
528H PHE* 1.3 73.5 - - - +
530H ASP* 1.3 74.1 + - - +
531H TRP* 3.2 6.8 + - - +
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Residues in contact with ASP 530 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233E ASP* 4.4 7.0 - - - +
267E ALA* 5.9 0.5 - - - +
268E ARG* 3.6 34.9 + - - +
269E LEU* 5.5 0.5 - - - +
490H ARG* 2.8 41.8 + - - +
491H LEU 3.1 5.5 + - - +
492H THR* 2.9 22.7 + - - +
529H ASN* 1.3 77.4 - - - +
531H TRP* 1.3 63.3 + - - +
532H ALA* 3.5 2.4 + - - +
565H LYS* 3.1 25.4 + - - +
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Residues in contact with TRP 531 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268E ARG* 6.1 3.8 - - - -
263H VAL* 3.9 21.7 - - + +
264H ASP* 3.5 31.0 - - - -
265H GLY* 4.4 3.6 - - - -
304H ASN 2.7 29.3 + - - -
305H CYS* 3.7 17.3 - - - +
307H GLY* 3.7 18.2 - - - -
310H ASN* 4.3 9.9 - - - +
489H ALA 3.3 0.5 - - - +
490H ARG* 3.3 1.1 - - - -
491H LEU 2.9 26.5 + - - -
528H PHE* 4.0 28.4 - + + -
529H ASN 3.2 6.0 - - - +
530H ASP* 1.3 77.8 - - - +
532H ALA* 1.3 60.6 + - - +
533H PHE* 3.3 42.3 + + + -
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Residues in contact with ALA 532 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310H ASN* 2.5 29.8 + - - +
488H GLN* 3.6 33.0 + - + +
489H ALA 3.9 4.3 - - - -
490H ARG* 4.0 25.8 - - + +
530H ASP 3.5 2.2 + - - -
531H TRP* 1.3 77.3 - - - +
533H PHE* 1.3 59.7 + - - +
534H MET* 3.2 4.0 + - - +
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Residues in contact with PHE 533 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304H ASN* 3.9 13.7 - - + +
305H CYS* 5.1 1.8 - - - -
310H ASN* 3.9 4.0 - - - +
487H VAL 3.8 0.3 - - - +
488H GLN* 3.2 1.2 - - - -
489H ALA* 2.7 47.8 + - - +
491H LEU* 3.7 30.7 - - + -
503H ILE* 4.3 6.3 - - + -
515H LEU* 3.4 45.2 - - + +
516H LEU* 4.0 20.6 - - + -
528H PHE* 3.7 35.2 - + - -
531H TRP* 3.5 36.1 - + + -
532H ALA* 1.3 72.0 - - - +
534H MET* 1.3 58.3 + - - +
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Residues in contact with MET 534 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304H ASN* 3.3 6.3 + - - +
309H THR 4.6 0.2 - - - +
310H ASN* 3.1 41.8 + - - +
311H SER 3.7 17.0 - - - +
312H ILE* 4.0 16.6 - - + -
314H THR 5.5 1.8 - - - +
334H SER* 2.8 16.4 + - - -
335H SER* 3.3 31.5 + - - +
486H HIS* 4.1 17.3 - - + -
487H VAL 3.2 14.4 - - - +
488H GLN* 4.4 5.8 - - + +
515H LEU* 4.8 1.1 - - - -
532H ALA 3.2 4.0 + - - +
533H PHE* 1.3 74.4 - - - +
535H THR* 1.3 69.3 + - - +
536H THR* 3.5 30.1 - - + -
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Residues in contact with THR 535 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334H SER* 3.3 16.0 - - - -
485H GLU 4.3 1.2 - - - +
486H HIS* 4.1 1.9 - - - -
487H VAL* 2.9 54.7 + - + +
505H LEU* 4.5 10.5 - - + -
513H SER* 2.8 33.8 + - - +
515H LEU* 4.4 4.0 - - + -
534H MET* 1.3 82.0 - - - +
536H THR* 1.3 61.7 + - - +
537H HIS* 3.1 12.6 + - - +
538H SER* 4.9 7.8 + - - +
547H TRP* 5.8 0.9 - - + -
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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