Contacts of the strand formed by residues 528 - 535 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263G VAL* 3.9 31.6 - - + -
305G CYS* 4.7 3.8 - - - -
491G LEU 3.8 13.7 - - - +
492G THR* 3.2 5.4 - - - +
493G LEU* 3.0 54.1 + - + +
498G ARG* 3.7 26.2 - - + -
501G LEU* 4.6 7.9 - - + -
503G ILE* 4.6 1.6 - - + -
516G LEU* 3.5 35.4 - - + -
519G ARG* 5.5 1.1 - - - -
526G ASP 4.9 2.2 - - - -
527G GLY* 1.3 78.1 - - - -
529G ASN* 1.3 60.9 + - - +
530G ASP 3.9 0.4 - - - -
531G TRP* 3.9 18.2 - + + -
533G PHE* 3.7 27.6 - + + -
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Residues in contact with ASN 529 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268F ARG* 4.9 6.4 + - - -
492G THR* 4.0 14.8 + - - +
526G ASP 6.1 0.2 - - - +
528G PHE* 1.3 72.7 - - - +
530G ASP* 1.3 78.3 + - - +
531G TRP* 3.2 7.1 + - - +
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Residues in contact with ASP 530 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233F ASP* 4.4 5.6 - - - +
267F ALA* 5.9 0.3 - - - +
268F ARG* 3.4 34.0 + - - +
269F LEU* 5.4 0.6 - - - +
490G ARG* 2.8 50.2 + - - +
491G LEU 3.1 7.3 + - - -
492G THR* 2.9 23.7 + - - +
529G ASN* 1.3 79.6 - - - +
531G TRP* 1.3 62.6 + - - +
532G ALA 3.5 2.6 + - - -
565G LYS* 4.2 21.5 + - - +
567G THR* 5.6 0.2 + - - -
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Residues in contact with TRP 531 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268F ARG* 5.3 12.6 - - - -
263G VAL* 3.9 21.7 - - + +
264G ASP* 3.6 30.3 - - - -
265G GLY* 4.2 2.9 - - - -
304G ASN 2.7 29.4 + - - -
305G CYS* 3.8 10.6 - - - +
307G GLY* 3.7 25.4 - - - -
310G ASN* 4.2 9.1 - - - +
489G ALA 3.3 0.5 - - - +
490G ARG* 4.1 0.4 - - - -
491G LEU 3.0 26.8 + - - +
528G PHE* 3.9 28.7 - + + -
529G ASN 3.1 6.6 - - - +
530G ASP* 1.3 77.1 - - - +
532G ALA* 1.3 61.1 + - - +
533G PHE* 3.3 42.1 + + + -
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Residues in contact with ALA 532 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310G ASN* 2.6 30.6 + - - +
488G GLN* 3.8 31.8 + - + +
489G ALA 3.9 4.3 - - - -
490G ARG* 4.0 27.8 - - + +
530G ASP 3.5 2.4 + - - -
531G TRP* 1.3 76.1 - - - +
533G PHE* 1.3 59.0 + - - +
534G MET* 3.1 3.6 + - - +
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Residues in contact with PHE 533 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304G ASN* 4.2 9.9 - - + +
305G CYS* 5.1 1.3 - - - -
310G ASN* 4.0 5.8 - - - +
487G VAL 3.7 0.5 - - - +
488G GLN* 3.2 1.4 - - - -
489G ALA* 2.7 46.3 + - - +
491G LEU* 3.7 31.0 - - + -
503G ILE* 4.2 6.5 - - + -
515G LEU* 3.4 45.7 - - + +
516G LEU* 3.9 21.5 - - + -
528G PHE* 3.7 34.1 - + - -
531G TRP* 3.5 35.9 - + + -
532G ALA* 1.3 70.2 - - - +
534G MET* 1.3 58.7 + - - +
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Residues in contact with MET 534 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304G ASN* 3.5 2.7 + - - +
309G THR 4.6 1.1 - - - +
310G ASN* 3.0 43.2 + - - +
311G SER 3.7 16.2 - - - +
312G ILE* 3.9 17.0 - - + -
314G THR 5.5 2.0 - - - +
334G SER* 2.8 15.6 + - - -
335G SER* 3.4 35.2 + - - +
486G HIS* 4.1 18.8 - - + -
487G VAL 3.2 13.2 - - - +
488G GLN* 4.4 5.6 - - + +
515G LEU* 4.8 0.9 - - - -
532G ALA 4.0 3.6 - - - +
533G PHE* 1.3 75.0 - - - +
535G THR* 1.3 78.3 + - - +
536G THR* 3.6 19.3 - - + -
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Residues in contact with THR 535 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334G SER* 3.3 16.0 - - - -
485G GLU 4.3 1.4 - - - +
486G HIS* 4.1 1.9 - - - -
487G VAL* 2.8 57.9 + - + +
505G LEU* 4.5 10.8 - - + -
513G SER* 2.7 32.6 + - - +
515G LEU* 4.3 4.5 - - + -
534G MET* 1.3 79.9 - - - +
536G THR* 1.3 61.9 + - - +
537G HIS* 3.1 11.8 + - - +
538G SER* 4.5 7.4 + - - +
547G TRP* 5.7 1.1 - - + -
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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
------------------------------------------------------------
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