Contacts of the strand formed by residues 511 - 516 (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 THR 511 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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412G ALA* 6.4 1.8 - - + -
413G THR 5.5 1.8 - - - +
414G ASN* 3.3 13.1 - - + +
415G GLY* 3.3 12.0 + - - -
420G VAL* 5.2 3.1 - - + -
505G LEU 3.4 2.9 - - - +
506G ILE* 3.3 2.0 - - - -
507G SER* 2.9 37.1 + - - -
509G MET 3.4 0.4 - - - -
510G GLY* 1.3 74.5 - - - +
512G ARG* 1.3 62.5 + - - +
513G SER* 3.6 5.0 + - - +
537G HIS* 3.7 36.3 - - + +
538G SER* 3.8 6.7 + - - +
541G GLU* 2.4 26.0 + - - -
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Residues in contact with ARG 512 (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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422G HIS* 4.0 11.6 - - - -
504G HIS* 3.3 47.2 + - + -
505G LEU 3.5 2.7 - - - -
506G ILE* 3.8 28.0 - - + +
510G GLY 3.3 7.0 + - - +
511G THR* 1.3 74.6 - - - +
513G SER* 1.3 60.0 + - - +
514G THR* 4.0 1.9 + - - -
537G HIS* 5.0 1.2 + - - -
550G GLU* 2.9 30.3 + - - -
552G GLU* 4.7 6.7 + - - -
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Residues in contact with SER 513 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334G SER* 4.1 6.7 - - - -
422G HIS* 3.9 4.9 - - - -
504G HIS* 3.2 5.4 - - - -
505G LEU* 2.7 44.4 + - - -
511G THR* 3.6 5.4 + - - +
512G ARG* 1.3 73.5 - - - +
514G THR* 1.3 60.3 + - - +
515G LEU* 3.3 7.2 + - - +
535G THR* 2.7 41.4 + - - +
537G HIS* 3.5 14.8 - - - +
538G SER* 4.8 3.1 + - - -
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Residues in contact with THR 514 (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* 3.8 7.6 + - - -
333G CYS* 4.7 2.4 - - - -
334G SER* 3.8 10.4 + - - -
422G HIS* 2.9 32.7 + - + -
503G ILE 4.0 0.4 - - - +
504G HIS* 3.2 32.9 + - + +
512G ARG 5.0 0.7 + - - -
513G SER* 1.3 70.4 - - - +
515G LEU* 1.3 61.4 + - - +
516G LEU* 3.8 24.9 - - - +
517G ALA* 4.0 14.6 - - + +
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Residues in contact with LEU 515 (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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302G SER* 4.4 0.7 + - - -
304G ASN* 2.7 31.9 + - - +
334G SER* 3.9 14.6 - - - +
489G ALA* 3.3 30.1 - - + -
491G LEU* 4.9 0.4 - - + -
503G ILE* 2.8 29.6 + - + +
505G LEU* 3.9 33.2 - - + +
513G SER* 3.3 4.4 + - - +
514G THR* 1.3 73.4 - - - +
516G LEU* 1.3 62.2 + - - +
533G PHE* 3.4 35.7 - - + +
535G THR* 4.3 15.3 - - + -
549G LEU* 4.2 4.5 - - + -
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Residues in contact with LEU 516 (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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302G SER* 4.1 9.9 - - - +
304G ASN* 5.6 0.2 - - + -
305G CYS* 3.6 30.1 - - - -
498G ARG* 5.0 4.9 - - + +
501G LEU* 4.3 16.6 - - + +
502G ALA* 3.0 5.2 - - - +
503G ILE* 2.6 52.9 + - + +
514G THR* 3.3 7.7 - - - +
515G LEU* 1.3 81.4 - - - +
517G ALA* 1.3 74.3 + - - +
519G ARG* 4.1 11.7 - - - -
528G PHE* 3.5 33.4 - - + -
533G PHE* 3.9 9.6 - - + -
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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