Contacts of the strand formed by residues 479 - 491 (chain R) in PDB entry 6CNB
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 479 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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400R VAL* 3.4 4.0 - - - +
401R THR* 2.3 77.4 + - - +
402R LEU 3.9 4.5 - - - +
403R GLY* 4.0 2.7 + - - -
477R LYS* 4.6 10.1 - - + -
478R PHE* 1.3 86.9 - - - +
480R ASP* 1.3 66.6 + - - +
481R PHE* 3.5 3.1 - - - -
599R PRO* 5.2 3.1 - - + -
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Residues in contact with ASP 480 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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399R THR* 2.7 32.1 - - + +
400R VAL* 3.2 4.3 - - - -
401R THR* 3.0 29.9 + - - +
446R LYS* 5.4 0.2 - - - +
479R THR* 1.3 80.7 - - - +
481R PHE* 1.3 52.7 + - - +
482R LYS* 3.8 1.6 - - - -
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Residues in contact with PHE 481 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398R ALA* 4.3 13.5 - - + -
399R THR 3.2 6.1 - - - -
400R VAL* 3.5 14.4 - - + -
449R VAL* 4.4 0.7 - - + -
458R SER* 3.3 27.8 - - - -
459R LYS* 3.0 42.6 - - + +
462R SER* 3.9 14.8 - - - -
478R PHE* 3.4 27.4 - + + -
480R ASP* 1.3 73.3 - - - +
482R LYS* 1.3 62.3 + - - +
483R ILE* 5.0 10.1 - - + -
592R LEU* 3.6 31.4 - - + -
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Residues in contact with LYS 482 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398R ALA* 3.2 3.8 - - - -
399R THR* 3.0 38.6 + - + +
480R ASP 3.7 3.0 + - - -
481R PHE* 1.3 77.8 - - - +
483R ILE* 1.3 71.7 + - - +
484R GLN* 3.3 1.6 + - - +
544R LYS* 3.4 38.3 - - - +
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Residues in contact with ILE 483 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396R ILE* 3.7 20.6 - - + -
397R VAL 3.3 7.0 - - - +
398R ALA* 3.6 9.9 - - + -
455R GLU* 4.0 24.7 - - + -
458R SER* 5.4 1.3 - - - +
481R PHE* 5.0 11.2 - - + -
482R LYS* 1.3 77.9 - - - +
484R GLN* 1.3 57.3 + - - +
485R ASN* 3.2 29.6 - - - +
486R ILE* 3.6 22.0 - - + -
544R LYS* 3.1 35.7 - - + +
588R THR* 4.3 13.2 - - + -
592R LEU* 5.1 7.0 - - + -
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Residues in contact with GLN 484 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397R VAL* 2.9 29.5 + - + +
398R ALA* 4.2 10.9 - - - +
399R THR* 5.5 2.6 - - + -
448R VAL* 4.9 3.0 - - - +
482R LYS* 3.3 5.8 + - - +
483R ILE* 1.3 73.9 - - - +
485R ASN* 1.3 64.1 + - - +
542R GLY 5.5 0.7 - - - -
543R ALA 4.8 0.5 - - - -
544R LYS* 3.2 29.2 - - - +
16X A 2.7 73.4 + - - +
17X G 2.9 43.9 + - - +
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Residues in contact with ASN 485 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397R VAL* 3.1 40.0 + - + +
483R ILE* 3.2 7.4 - - - +
484R GLN* 1.3 83.9 - - - +
486R ILE* 1.3 94.4 + - - +
487R VAL* 5.5 1.3 - - - -
541R THR* 2.8 16.1 + - - -
542R GLY* 2.8 20.7 + - - +
543R ALA 3.0 12.4 + - - -
15X T 2.4 45.4 + - - +
16X A 4.2 7.6 - - - +
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Residues in contact with ILE 486 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393R LEU* 4.2 9.6 - - + -
395R ASN 3.6 3.6 - - - -
396R ILE* 3.7 23.1 - - + -
455R GLU* 4.6 9.6 - - - +
483R ILE* 3.6 20.6 - - + -
485R ASN* 1.3 107.2 + - - +
487R VAL* 1.3 74.6 + - - +
540R LEU* 3.8 2.3 - - - +
541R THR* 3.2 14.2 + - - -
543R ALA* 2.5 13.8 + - - +
544R LYS 3.5 28.5 - - - +
545R GLN 3.9 12.3 - - - +
546R ARG* 4.2 5.2 - - + +
549R ILE* 3.8 20.0 - - + -
588R THR* 5.1 1.3 - - - +
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Residues in contact with VAL 487 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393R LEU* 3.8 3.1 - - - +
394R GLN* 2.9 38.9 + - + -
395R ASN* 2.5 38.0 + - + +
396R ILE* 5.5 0.2 - - - -
397R VAL* 6.0 4.5 - - + -
485R ASN* 5.5 1.6 - - - -
486R ILE* 1.3 84.9 - - - +
488R GLY* 1.3 64.6 + - - +
539R VAL* 5.0 2.5 - - + -
540R LEU 3.5 5.2 - - - +
541R THR* 3.9 15.3 - - - +
549R ILE* 5.7 0.4 - - - -
15X T 4.6 1.3 - - - +
16X A 6.0 0.9 - - + +
54Y T 5.0 0.9 - - - +
55Y A 4.0 29.6 - - + +
56Y A 4.5 18.8 - - + +
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Residues in contact with GLY 488 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391R PRO* 5.6 1.3 - - - -
392R THR 3.5 10.8 - - - -
393R LEU* 4.4 5.2 - - - -
394R GLN* 4.0 4.9 - - - -
487R VAL* 1.3 76.1 - - - +
489R SER* 1.3 58.8 + - - -
539R VAL* 3.3 5.9 - - - +
540R LEU* 2.4 55.4 + - - +
549R ILE* 5.6 5.4 - - - -
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Residues in contact with SER 489 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391R PRO* 3.5 4.7 - - - +
392R THR* 2.9 39.1 + - - +
394R GLN* 3.2 30.7 + - - -
488R GLY* 1.3 74.6 - - - -
490R CYS* 1.3 64.5 + - - +
538R ILE 3.2 10.5 - - - -
539R VAL* 3.9 15.7 - - - +
540R LEU* 4.3 0.7 - - - +
56Y A 4.5 12.5 + - - -
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Residues in contact with CYS 490 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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389R ILE* 5.6 4.3 - - + +
390R VAL 5.0 1.8 - - - +
391R PRO* 3.6 22.9 - - + -
392R THR* 4.9 1.8 - - - +
489R SER* 1.3 79.0 - - - +
491R ASP* 1.3 60.6 + - - +
492R VAL* 5.7 0.4 - - - -
530R LEU* 6.4 0.4 - - - -
537R LYS* 3.3 7.0 - - - +
538R ILE* 2.5 65.0 + - - -
540R LEU* 6.4 2.0 - - - -
553R PHE* 3.4 36.3 - - + -
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Residues in contact with ASP 491 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290R PHE* 6.0 0.7 - - - +
293R ASN* 4.5 8.5 + - - -
389R ILE* 4.8 19.0 - - - +
490R CYS* 1.3 79.2 - - - +
492R VAL* 1.3 65.7 + - - +
493R LYS* 3.1 39.9 + - - +
535R SER* 3.3 10.7 + - - +
536R GLY 2.9 6.6 - - - -
537R LYS* 2.8 51.0 + - + +
553R PHE* 6.1 0.7 - - - -
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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