Contacts of the strand formed by residues 498 - 508 (chain A) in PDB entry 2R8K
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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398A ASN* 3.1 29.2 - - - +
399A LYS 3.5 10.5 - - - +
400A ASN* 3.9 22.1 - - - +
401A LEU* 4.1 3.0 - - - +
446A SER* 6.5 0.9 - - - -
447A LEU* 2.8 16.8 - - - +
448A LYS* 2.7 74.4 + - + +
496A LEU* 3.6 2.9 - - - -
497A THR* 1.3 82.8 - - - +
499A LEU* 1.3 55.6 + - - +
500A SER* 4.5 5.4 - - - +
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Residues in contact with LEU 499 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398A ASN* 3.6 0.9 - - - +
399A LYS* 3.1 26.4 + - + +
401A LEU* 4.2 14.8 - - + +
406A CYS* 4.8 2.7 - - - -
412A CYS* 3.6 47.1 - - + +
415A TRP* 4.0 14.1 - - + -
416A LEU* 4.2 6.3 - - + -
419A PHE* 3.5 18.2 - - + -
445A ILE* 3.9 18.6 - - + -
446A SER 3.5 12.1 - - - +
447A LEU* 4.0 13.0 - - + -
481A VAL* 4.4 7.9 - - + -
496A LEU* 4.9 5.6 - - + -
498A LYS* 1.3 74.1 - - - +
500A SER* 1.3 74.0 + - - +
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Residues in contact with SER 500 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396A MET* 4.4 13.3 - - - -
397A SER 3.5 5.8 - - - -
398A ASN* 3.4 30.4 + - - -
416A LEU* 5.6 0.2 - - - -
419A PHE* 4.0 4.3 - - - -
445A ILE* 3.4 6.6 - - - +
446A SER* 3.0 48.8 + - - +
498A LYS* 4.5 7.1 - - - +
499A LEU* 1.3 82.5 - - - +
501A MET* 1.3 61.1 + - - +
502A THR* 4.2 0.4 + - - -
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Residues in contact with MET 501 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396A MET* 3.5 1.2 - - - -
397A SER 2.9 31.3 + - - -
416A LEU* 4.3 14.6 - - + +
419A PHE* 4.0 18.7 - - + -
420A CYS* 3.9 25.4 - - - -
423A LEU* 3.6 21.4 - - + +
443A VAL* 3.9 15.0 - - + -
444A SER 3.6 4.9 - - - +
445A ILE* 4.0 11.9 - - + -
473A LEU* 3.6 31.0 - - + +
474A LEU* 4.8 0.7 - - - -
477A GLY* 3.7 30.3 - - - -
500A SER* 1.3 74.3 - - - +
502A THR* 1.3 64.4 + - - +
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Residues in contact with THR 502 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394A SER* 4.6 5.8 - - - -
395A MET 3.3 4.7 - - - +
396A MET* 3.4 33.3 - - - +
443A VAL* 3.5 5.0 - - - +
444A SER* 3.0 49.3 + - - +
446A SER* 6.1 0.9 - - - -
500A SER 4.2 0.6 + - - -
501A MET* 1.3 73.1 - - - +
503A ILE* 1.3 69.1 + - - +
504A THR* 3.8 24.0 - - + +
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Residues in contact with ILE 503 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394A SER* 3.2 2.8 - - - -
395A MET* 3.0 51.0 + - + +
423A LEU* 4.3 22.9 - - + -
427A ILE* 3.6 24.5 - - + -
440A PRO* 3.9 18.4 - - + -
442A THR 3.6 2.9 - - - -
443A VAL* 3.9 24.7 - - + -
469A GLN* 5.1 1.6 - - - +
473A LEU* 4.5 9.2 - - + -
502A THR* 1.3 81.2 - - - +
504A THR* 1.3 66.6 + - - +
506A PHE* 3.5 23.6 - - + -
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Residues in contact with THR 504 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393A LYS 3.6 10.8 - - - +
394A SER* 3.3 22.2 - - - -
440A PRO* 4.0 5.4 - - - +
441A ARG 3.8 2.8 + - - -
442A THR* 2.8 39.3 + - - +
502A THR* 3.8 14.9 - - + +
503A ILE* 1.3 81.4 - - - +
505A ASN* 1.3 80.8 + - - +
506A PHE* 3.3 6.4 + - - -
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Residues in contact with ASN 505 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393A LYS 4.3 3.2 + - - -
441A ARG* 2.9 28.1 + - + +
442A THR* 2.9 34.0 + - + +
504A THR* 1.3 83.4 + - - +
506A PHE* 1.3 62.9 + - - +
507A ASP* 5.1 0.3 - - - +
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Residues in contact with PHE 506 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391A VAL* 5.7 3.6 - - + -
392A VAL* 3.6 29.8 - - + +
393A LYS 3.9 8.3 + - - -
394A SER* 3.9 9.9 - - - -
395A MET* 3.3 30.3 - - + -
427A ILE* 3.4 22.9 - - + -
438A VAL* 3.7 22.4 - - + -
439A ILE 3.9 0.9 - - - -
440A PRO* 3.7 25.4 - - + -
503A ILE* 3.5 33.9 - - + -
504A THR* 4.4 2.0 - - - -
505A ASN* 1.3 78.4 - - - +
507A ASP* 1.3 67.6 + - - +
508A ILE* 5.4 5.4 - - + -
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Residues in contact with ASP 507 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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437A ILE 3.6 1.0 - - - +
438A VAL* 3.4 7.5 - - - +
439A ILE* 3.2 47.8 + - + +
441A ARG* 3.6 28.6 + - - +
505A ASN 5.1 0.3 - - - +
506A PHE* 1.3 81.0 - - - +
508A ILE* 1.3 62.8 + - - +
509A ILE* 3.7 12.9 + - + +
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Residues in contact with ILE 508 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391A VAL* 4.6 26.5 - - + -
434A TYR* 4.8 3.6 - - + -
436A LYS* 3.3 37.8 + - + +
437A ILE 3.6 5.4 - - - -
438A VAL* 4.0 16.2 - - + -
506A PHE* 5.4 4.3 - - + -
507A ASP* 1.3 76.3 - - - +
509A ILE* 1.3 63.8 + - - +
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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