Contacts of the strand formed by residues 498 - 509 (chain B) in PDB entry 2R8J
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 LYS 498 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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398B ASN* 3.5 25.4 - - - +
399B LYS 3.8 5.2 - - - +
400B ASN* 3.4 23.9 + - - +
401B LEU* 4.1 3.1 - - - +
447B LEU* 2.9 9.5 - - - +
448B LYS* 2.6 68.9 + - + +
496B LEU* 3.6 2.8 - - - +
497B THR* 1.3 81.2 - - - +
499B LEU* 1.3 60.3 + - - +
500B SER* 6.1 0.2 - - - -
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Residues in contact with LEU 499 (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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398B ASN* 3.2 2.2 + - - -
399B LYS 3.0 31.9 + - - +
401B LEU* 3.9 12.3 - - + -
406B CYS* 4.5 6.7 - - - -
412B CYS* 3.9 12.6 - - + +
415B TRP* 3.7 26.7 - - + -
416B LEU* 3.5 28.0 - - + -
419B PHE* 3.6 12.9 - - + -
445B ILE* 4.2 13.5 - - + -
446B SER 3.5 4.3 - - - +
447B LEU* 3.8 28.5 - - + -
481B VAL* 4.7 4.3 - - + -
496B LEU* 4.4 5.8 - - + -
498B LYS* 1.3 76.2 - - - +
500B SER* 1.3 69.3 + - - +
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Residues in contact with SER 500 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396B MET* 4.7 13.3 - - - +
397B SER 3.4 7.0 - - - -
398B ASN* 3.6 24.7 - - - -
419B PHE* 4.2 5.6 - - - -
444B SER 3.6 0.3 + - - +
445B ILE* 3.3 11.4 - - - +
446B SER* 2.8 50.3 + - - +
499B LEU* 1.3 80.8 - - - +
501B MET* 1.3 59.4 + - - +
502B THR* 4.4 6.2 + - - -
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Residues in contact with MET 501 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396B MET* 3.7 0.9 - - - -
397B SER 3.0 28.7 + - - -
416B LEU* 3.4 31.4 - - + +
419B PHE* 4.0 17.2 - - + -
420B CYS* 4.3 15.0 - - - -
423B LEU* 3.8 23.0 - - + +
443B VAL* 4.0 12.8 - - + -
444B SER 3.6 3.1 - - - -
445B ILE* 3.7 15.9 - - + -
473B LEU* 3.7 34.8 - - + +
474B LEU* 4.7 7.0 - - - -
477B GLY* 3.9 14.4 - - - -
500B SER* 1.3 72.7 - - - +
502B THR* 1.3 63.5 + - - +
503B ILE* 4.8 0.9 - - + -
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Residues in contact with THR 502 (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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394B SER* 4.7 3.6 - - - +
395B MET 3.2 20.9 - - - +
396B MET* 3.4 37.1 - - + +
442B THR 4.1 0.3 - - - +
443B VAL* 3.6 1.9 - - - -
444B SER* 2.9 46.3 + - - -
500B SER* 4.4 4.3 + - - -
501B MET* 1.3 72.7 - - - +
503B ILE* 1.3 61.1 + - - +
504B THR* 4.1 19.1 + - + +
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Residues in contact with ILE 503 (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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394B SER* 3.6 0.7 - - - -
395B MET* 3.0 44.7 + - + +
423B LEU* 4.2 28.9 - - + -
427B ILE* 3.9 16.8 - - + -
440B PRO* 3.7 26.9 - - + -
442B THR 3.3 9.6 - - - +
443B VAL* 4.3 8.7 - - + -
473B LEU* 4.0 29.4 - - + -
501B MET* 4.2 1.1 + - + -
502B THR* 1.3 73.2 - - - +
504B THR* 1.3 66.0 + - - +
506B PHE* 3.8 20.3 - - + -
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Residues in contact with THR 504 (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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393B LYS 4.0 10.1 - - - -
394B SER* 3.3 21.1 - - - -
440B PRO* 4.0 2.1 - - - +
441B ARG 3.5 3.1 + - - -
442B THR* 3.0 30.1 + - - +
444B SER* 6.5 0.2 - - - -
502B THR* 4.1 14.1 + - + +
503B ILE* 1.3 81.3 - - - +
505B ASN* 1.3 90.6 + - - +
506B PHE* 3.6 6.5 - - - -
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Residues in contact with ASN 505 (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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393B LYS 3.9 6.9 + - - -
441B ARG* 3.1 26.2 + - + +
442B THR* 2.6 39.1 + - - +
504B THR* 1.3 89.6 + - - +
506B PHE* 1.3 64.3 + - - +
507B ASP* 4.9 0.6 - - - +
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Residues in contact with PHE 506 (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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391B VAL* 5.9 3.1 - - + -
392B VAL* 3.7 24.9 - - + +
393B LYS* 3.6 25.5 + - - -
394B SER* 3.6 14.8 - - - -
395B MET* 3.3 34.8 - - + -
427B ILE* 5.1 0.4 - - + -
438B VAL* 4.0 21.8 - - + -
439B ILE 3.6 2.5 - - - -
440B PRO* 3.5 36.8 - - + -
503B ILE* 3.8 22.4 - - + -
504B THR* 4.3 0.9 - - - -
505B ASN* 1.3 79.3 - - - +
507B ASP* 1.3 69.8 + - - +
508B ILE* 4.3 4.3 - - + -
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Residues in contact with ASP 507 (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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437B ILE 3.0 12.5 - - - +
438B VAL* 4.7 0.2 - - - -
439B ILE* 3.3 23.4 + - - +
441B ARG* 2.7 47.7 + - - +
505B ASN 4.9 0.3 - - - +
506B PHE* 1.3 80.4 - - - +
508B ILE* 1.3 63.9 + - - +
509B ILE* 3.3 6.4 + - + +
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Residues in contact with ILE 508 (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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391B VAL* 4.6 22.9 - - + -
434B TYR* 4.4 18.4 - - + -
436B LYS* 4.4 22.9 - - + +
437B ILE 3.2 5.4 - - - +
438B VAL* 4.1 23.1 - - + -
506B PHE* 5.6 2.9 - - + -
507B ASP* 1.3 70.8 + - - +
509B ILE* 1.3 63.9 + - - +
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Residues in contact with ILE 509 (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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7A LYS* 4.6 8.5 - - - -
436B LYS* 4.0 19.5 - - - +
437B ILE* 2.7 50.4 + - + +
439B ILE* 3.5 28.0 - - + -
441B ARG* 4.5 8.5 - - - +
466B ILE* 4.8 14.4 - - + -
507B ASP* 4.0 11.9 - - + +
508B ILE* 1.3 76.6 - - - +
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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