Contacts of the strand formed by residues 392 - 401 (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 392 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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389R ILE* 6.1 1.3 - - + -
390R VAL* 4.2 9.4 - - + +
391R PRO* 1.3 73.5 - - - +
393R LEU* 1.3 67.9 + - - +
394R GLN* 3.3 13.6 + - - +
488R GLY* 3.5 1.1 - - - -
489R SER* 2.9 41.5 + - - +
490R CYS* 4.7 1.6 - - - +
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Residues in contact with LEU 393 (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 3.6 1.0 + - - +
392R THR* 1.3 75.6 - - - +
394R GLN* 1.3 72.1 + - - +
396R ILE* 5.0 8.3 - - + -
453R LYS* 4.4 26.0 - - + +
454R SER* 5.9 0.7 - - - -
455R GLU* 5.1 0.4 - - - +
486R ILE* 4.2 11.9 - - + -
487R VAL 3.8 3.8 - - - +
488R GLY* 5.2 1.8 - - - -
546R ARG* 3.4 43.7 - - + +
549R ILE* 3.9 28.5 - - + -
550R TYR* 3.8 19.3 - - + +
585R LEU* 6.2 2.0 - - + -
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Residues in contact with GLN 394 (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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392R THR* 3.3 16.1 + - - -
393R LEU* 1.3 91.1 - - - +
395R ASN* 1.3 62.1 + - + +
453R LYS* 3.4 30.4 - - - +
487R VAL* 2.9 29.5 + - + -
488R GLY* 4.0 2.5 - - - -
489R SER* 3.2 31.6 + - - +
55Y A 4.7 5.6 - - - +
56Y A 2.6 53.7 + - - +
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Residues in contact with ASN 395 (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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394R GLN* 1.3 81.2 - - - +
396R ILE* 1.3 68.6 + - - +
397R VAL* 3.9 11.9 - - - +
451R GLY* 3.4 12.7 - - - +
452R ALA 2.8 40.8 + - - +
487R VAL* 2.5 47.1 + - + +
54Y T 2.4 43.2 + - - +
55Y A 3.8 19.7 - - - -
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Residues in contact with ILE 396 (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* 5.0 12.1 - - + -
395R ASN* 1.3 83.8 + - - +
397R VAL* 1.3 71.6 + - - +
398R ALA* 5.4 0.2 - - + -
449R VAL* 3.8 2.1 - - - +
450R THR* 4.2 0.3 - - - -
452R ALA* 2.4 60.6 + - + +
453R LYS* 3.3 25.8 - - - +
454R SER* 3.6 10.5 - - - +
455R GLU* 5.0 6.7 - - + +
458R SER* 5.2 4.7 - - - +
483R ILE* 3.7 41.1 - - + -
485R ASN 3.8 3.6 - - - +
486R ILE* 3.7 24.7 - - + -
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Residues in contact with VAL 397 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395R ASN* 3.9 4.0 - - - +
396R ILE* 1.3 81.1 - - - +
398R ALA* 1.3 61.2 + - - +
448R VAL* 5.2 0.2 - - + -
449R VAL* 2.9 13.5 - - - +
450R THR* 3.7 19.1 - - + -
483R ILE* 3.3 3.6 - - - +
484R GLN* 2.9 50.5 + - + +
485R ASN* 3.1 24.4 + - + +
487R VAL* 6.0 4.3 - - + -
16X A 3.5 19.5 - - + +
17X G 5.2 0.7 - - - +
54Y T 3.9 21.1 - - + +
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Residues in contact with ALA 398 (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* 5.4 0.4 - - + -
397R VAL* 1.3 73.6 - - - +
399R THR* 1.3 63.6 + - - +
448R VAL* 3.7 10.0 - - - +
449R VAL* 2.9 44.1 + - + +
458R SER* 4.6 1.3 - - - +
481R PHE* 4.3 10.3 - - + -
482R LYS 3.2 20.2 - - - +
483R ILE* 3.6 17.3 - - + +
484R GLN* 3.7 10.0 - - - +
17X G 5.9 0.5 - - - +
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Residues in contact with THR 399 (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* 1.3 77.0 - - - +
400R VAL* 1.3 75.9 + - - +
401R THR* 5.1 1.4 + - - +
446R LYS* 5.3 3.1 - - - +
447R MET 3.1 14.1 + - - -
448R VAL* 5.1 0.7 - - - -
449R VAL* 4.0 1.3 - - - -
480R ASP* 2.7 28.1 - - + +
481R PHE* 3.2 12.1 - - - -
482R LYS* 3.0 23.2 + - + +
484R GLN* 5.5 3.1 - - + -
17X G 4.2 29.1 + - - +
18X T 4.5 8.1 + - - +
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Residues in contact with VAL 400 (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* 1.3 84.1 + - - +
401R THR* 1.3 72.2 + - - +
402R LEU 4.3 0.2 - - - -
446R LYS* 3.5 4.5 - - - +
447R MET* 2.9 63.0 + - + +
449R VAL* 3.5 19.1 - - + -
462R SER* 4.4 5.4 - - - +
477R LYS 5.2 0.7 - - - +
478R PHE* 3.7 30.3 - - + -
479R THR 3.6 6.7 - - - +
480R ASP 3.2 5.6 - - - -
481R PHE* 3.5 19.5 - - + -
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Residues in contact with THR 401 (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* 5.1 1.6 + - - +
400R VAL* 1.3 76.6 - - - +
402R LEU* 1.3 60.2 + - - +
403R GLY* 3.4 18.2 - - - +
445R GLY 4.1 0.4 - - - +
446R LYS* 3.2 35.0 - - + +
477R LYS 3.6 0.9 - - - +
479R THR* 2.3 61.7 + - - +
480R ASP* 3.0 29.0 + - - +
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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