Contacts of the strand formed by residues 500 - 506 (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 ASP 500 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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495G TYR* 4.6 2.2 - - + -
497G ARG* 3.0 49.1 + - - +
498G ARG 2.9 0.6 + - - -
499G GLY* 1.3 78.0 - - - +
501G LEU* 1.3 59.9 + - - +
520G PRO* 5.7 0.3 - - - +
552G GLU 3.6 0.4 - - - +
553G ASN* 3.6 13.7 - - - +
554G THR* 2.7 40.6 + - - -
555G SER* 3.2 24.5 + - - -
557G ALA* 4.3 2.9 - - - +
559G ASN* 2.9 24.0 + - - +
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Residues in contact with LEU 501 (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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461G ILE* 4.4 2.0 - - + -
493G LEU* 4.0 30.7 - - + -
495G TYR* 3.5 56.8 - - + +
498G ARG* 3.0 18.5 + - + +
499G GLY 4.0 0.9 - - - +
500G ASP* 1.3 81.1 - - - +
502G ALA* 1.3 58.6 + - - +
503G ILE* 4.8 5.6 - - + -
516G LEU* 4.2 13.7 - - + +
517G ALA 3.7 4.0 - - - +
518G ALA* 3.6 19.9 + - - -
528G PHE* 4.6 10.3 - - + -
551G ILE* 3.9 21.5 - - + -
552G GLU 3.5 7.9 - - - +
553G ASN* 4.9 0.2 - - - -
554G THR* 4.6 0.2 - - - -
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Residues in contact with ALA 502 (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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501G LEU* 1.3 74.9 - - - +
503G ILE* 1.3 62.9 + - - +
504G HIS* 4.4 14.5 + - + -
516G LEU 3.0 9.9 - - - +
517G ALA* 4.7 1.8 - - - -
518G ALA 4.6 5.8 - - - +
550G GLU 3.6 1.0 - - - +
551G ILE* 3.5 2.3 - - - -
552G GLU* 3.0 41.7 + - + +
554G THR* 3.4 25.4 - - + -
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Residues in contact with ILE 503 (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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491G LEU* 3.9 26.7 - - + -
493G LEU* 4.3 17.3 - - + -
501G LEU* 4.8 3.6 - - + -
502G ALA* 1.3 79.5 - - - +
504G HIS* 1.3 68.4 + - - +
514G THR* 3.6 2.1 - - - -
515G LEU* 2.8 33.6 + - + -
516G LEU* 2.6 48.5 + - + +
528G PHE* 4.6 1.6 - - + -
533G PHE* 4.2 8.5 - - + -
549G LEU* 3.9 22.2 - - + -
550G GLU 3.1 9.0 - - - +
551G ILE* 4.2 16.4 - - + -
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Residues in contact with HIS 504 (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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502G ALA* 4.4 20.8 + - + -
503G ILE* 1.3 80.9 + - - +
505G LEU* 1.3 59.5 + - - +
506G ILE* 4.3 0.7 - - + -
512G ARG* 3.3 49.6 + - + +
513G SER 3.2 6.5 - - - +
514G THR* 3.2 38.9 + - + +
515G LEU* 4.2 1.3 - - - +
548G VAL 3.7 0.5 - - - +
549G LEU* 3.5 8.5 - - - +
550G GLU* 2.7 56.3 + - + +
552G GLU* 4.7 10.7 + - - -
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Residues in contact with LEU 505 (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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487G VAL* 3.9 19.5 - - + +
489G ALA* 4.1 17.9 - - + -
504G HIS* 1.3 73.5 - - - +
506G ILE* 1.3 60.1 + - - +
507G SER 4.1 0.4 + - - -
511G THR 3.4 2.4 - - - +
512G ARG* 3.5 0.3 - - - -
513G SER* 2.7 41.1 + - - +
515G LEU* 3.9 20.1 - - + +
535G THR* 4.5 10.3 - - + -
547G TRP* 3.7 38.6 - - + -
548G VAL 3.4 19.7 - - - +
549G LEU* 4.4 4.9 - - + -
566G PHE* 4.2 21.8 - - + -
568G LEU* 4.1 3.6 - - + -
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Residues in contact with ILE 506 (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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505G LEU* 1.3 79.6 - - - +
507G SER* 1.3 74.9 + - - +
510G GLY* 4.0 16.8 - - - +
511G THR 3.3 7.9 - - - +
512G ARG* 3.8 31.0 - - + +
546G GLU 4.2 0.7 - - - +
547G TRP* 3.5 9.0 - - - -
548G VAL* 2.8 51.0 + - + +
550G GLU* 3.5 27.8 - - - +
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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