Contacts of the strand formed by residues 438 - 448 (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 VAL 438 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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392A VAL* 6.3 0.2 - - + -
427A ILE* 3.7 25.2 - - + +
430A LEU* 5.0 9.2 - - + -
431A GLU* 2.7 29.7 + - + +
434A TYR* 4.4 12.1 - - + -
436A LYS* 3.4 16.2 - - + +
437A ILE* 1.3 79.8 - - - +
439A ILE* 1.3 73.8 + - - +
506A PHE* 3.7 32.8 - - + -
507A ASP 3.4 11.2 - - - +
508A ILE* 4.0 19.3 - - + -
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Residues in contact with ILE 439 (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* 4.3 14.8 - - + +
438A VAL* 1.3 83.9 - - - +
440A PRO* 1.3 69.7 - - + +
441A ARG* 3.4 31.2 + - - +
463A TYR* 4.1 16.4 - - + +
466A ILE 5.2 9.2 - - - +
467A ASN* 5.4 6.5 - - - -
468A PHE 5.2 7.9 - - - +
506A PHE* 3.9 4.0 - - - -
507A ASP* 3.2 46.9 + - + +
509A ILE* 4.7 10.3 - - + -
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Residues in contact with PRO 440 (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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427A ILE* 4.5 1.3 - - + -
439A ILE* 1.3 82.5 - - + +
441A ARG* 1.3 61.5 + - - +
442A THR 3.3 3.6 - - - +
443A VAL* 5.1 4.7 - - + -
461A VAL* 3.0 10.0 - - - +
463A TYR* 2.9 38.7 + - - +
469A GLN* 3.7 27.1 - - + +
473A LEU* 5.2 4.7 - - + -
503A ILE* 3.9 29.2 - - + -
504A THR 4.0 5.8 - - - +
505A ASN 4.0 0.4 - - - +
506A PHE* 3.7 29.2 - - + -
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Residues in contact with ARG 441 (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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439A ILE* 3.4 41.8 - - - +
440A PRO* 1.3 73.2 - - - +
442A THR* 1.3 59.1 + - - +
460A PRO* 3.5 9.4 - - - +
461A VAL* 3.3 26.5 + - - +
463A TYR* 4.0 20.3 - - - -
505A ASN* 2.9 23.2 + - + +
507A ASP* 3.6 26.8 + - - +
509A ILE* 5.9 2.4 - - - +
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Residues in contact with THR 442 (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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440A PRO* 3.3 2.6 + - - +
441A ARG* 1.3 80.7 - - - +
443A VAL* 1.3 67.6 + - - +
458A SER* 3.9 12.9 + - - +
459A GLY* 2.7 25.5 + - - -
460A PRO* 4.2 1.7 - - - +
461A VAL* 4.4 0.7 - - - -
503A ILE* 3.6 4.3 - - - +
504A THR* 2.8 51.7 + - - +
505A ASN* 2.9 26.7 + - + +
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Residues in contact with VAL 443 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440A PRO* 5.1 3.4 - - + -
442A THR* 1.3 81.9 + - - +
444A SER* 1.3 66.7 + - - +
445A ILE* 4.8 3.1 - - + -
458A SER* 4.4 0.9 - - - -
459A GLY 2.9 28.5 + - - +
460A PRO* 5.0 1.0 - - - +
461A VAL* 4.3 20.6 - - + -
473A LEU* 3.5 36.8 - - + -
476A VAL* 5.3 9.4 - - + +
477A GLY* 5.1 6.1 - - - -
480A PHE* 3.5 10.7 - - + -
501A MET* 3.9 20.4 - - + -
502A THR 3.5 10.5 - - - +
503A ILE* 3.9 8.5 - - + -
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Residues in contact with SER 444 (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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443A VAL* 1.3 74.2 - - - +
445A ILE* 1.3 70.3 + - - +
446A SER* 5.0 1.6 + - - -
456A ARG* 4.6 14.3 - - - -
457A LYS 3.2 7.0 - - - -
458A SER* 3.4 28.9 - - - -
480A PHE* 4.6 0.4 - - - -
501A MET* 3.6 0.3 - - - -
502A THR* 3.0 49.6 + - - +
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Residues in contact with ILE 445 (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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416A LEU* 3.9 19.5 - - + -
443A VAL* 4.8 2.0 - - + -
444A SER* 1.3 78.6 - - - +
446A SER* 1.3 62.8 + - - +
447A LEU* 5.2 0.2 - - + -
456A ARG* 3.3 4.1 - - - -
457A LYS 3.0 28.5 + - - -
477A GLY* 2.9 45.3 - - - +
480A PHE* 4.2 13.9 - - + -
481A VAL* 4.1 11.4 - - + +
484A LEU* 3.7 14.3 - - + +
499A LEU* 3.9 22.4 - - + -
500A SER 3.4 9.4 - - - +
501A MET* 4.0 15.3 - - + -
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Residues in contact with SER 446 (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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444A SER* 4.3 2.3 + - - -
445A ILE* 1.3 73.6 - - - +
447A LEU* 1.3 66.6 + - - +
454A VAL* 5.3 2.2 - - - -
455A TYR 3.3 6.3 - - - -
456A ARG* 2.8 43.9 + - - -
498A LYS* 6.5 0.9 - - - -
499A LEU* 3.5 4.0 - - - +
500A SER* 3.0 42.5 + - - +
502A THR* 6.1 0.7 - - - -
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Residues in contact with LEU 447 (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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412A CYS* 6.4 0.2 - - - -
445A ILE* 5.2 0.7 - - + -
446A SER* 1.3 78.6 - - - +
448A LYS* 1.3 68.1 + - - +
449A THR* 4.1 3.6 - - + -
454A VAL* 3.3 7.6 - - - +
455A TYR* 2.9 42.6 + - + -
481A VAL* 5.6 4.0 - - + +
484A LEU* 3.5 28.9 - - + -
493A TYR* 3.2 42.6 - - + +
496A LEU* 3.8 26.5 - - + -
498A LYS* 2.8 14.1 - - - +
499A LEU* 4.0 15.5 - - + -
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Residues in contact with LYS 448 (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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447A LEU* 1.3 75.3 - - - +
449A THR* 1.3 57.1 + - - +
452A TYR* 4.4 23.8 - - + +
453A GLU 3.1 14.6 - - - +
454A VAL* 3.6 20.5 - - + +
496A LEU* 3.4 6.8 - - - +
497A THR* 2.7 45.0 + - - +
498A LYS* 2.7 55.7 + - + +
7Q G 5.7 10.7 + - - +
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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