Contacts of the strand formed by residues 528 - 532 (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 ILE 528 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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521R TYR 3.8 1.2 - - - +
522R ARG* 5.2 0.2 - - - -
523R MET* 3.2 31.4 + - + +
526R PRO* 3.4 38.3 + - + +
527R LYS* 1.3 91.2 - - - +
529R VAL* 1.3 74.2 + - - +
530R LEU* 3.6 18.0 - - + +
540R LEU* 3.6 20.4 - - + -
541R THR 3.1 16.2 - - - +
542R GLY* 3.8 5.4 - - - +
543R ALA* 3.5 20.0 - - + -
548R GLU* 3.9 23.3 - - + +
552R ALA* 5.2 4.3 - - + -
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Residues in contact with VAL 529 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520R ILE* 4.9 5.2 - - + -
521R TYR 3.4 9.4 - - - +
522R ARG* 3.6 25.6 - - - +
527R LYS* 6.5 0.7 - - + -
528R ILE* 1.3 74.6 - - - +
530R LEU* 1.3 68.1 + - - +
531R LEU* 3.9 21.7 - - + +
541R THR* 2.7 44.6 + - + +
542R GLY* 4.7 1.5 - - - -
14X T 3.8 18.6 - - - +
15X T 3.3 31.2 - - - +
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Residues in contact with LEU 530 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490R CYS* 6.4 0.2 - - - -
519R LEU 3.9 0.3 - - - +
520R ILE* 3.5 3.5 - - - -
521R TYR* 2.9 48.8 + - + +
523R MET* 5.4 3.1 - - + -
528R ILE* 3.6 25.8 - - + +
529R VAL* 1.3 81.4 - - - +
531R LEU* 1.3 65.7 + - - +
532R ILE* 4.3 8.2 - - + +
538R ILE* 4.2 17.0 - - + -
539R VAL 3.1 12.3 - - - +
540R LEU* 3.6 24.7 - - + -
552R ALA* 4.8 11.0 - - + +
553R PHE* 5.4 4.5 - - + -
556R ILE* 4.2 28.7 - - + -
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Residues in contact with LEU 531 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516R PHE* 4.1 13.7 - - + -
519R LEU 3.5 2.5 - - - +
520R ILE* 4.2 15.7 - - + -
529R VAL* 3.9 14.1 - - + +
530R LEU* 1.3 79.7 - - - +
532R ILE* 1.3 69.7 + - - +
533R PHE* 4.3 7.2 - - + -
537R LYS 4.8 0.4 - - - -
538R ILE* 3.3 4.5 - - - +
539R VAL* 2.9 49.5 + - + +
541R THR* 5.5 2.9 - - + +
13X A 3.4 37.5 - - + +
14X T 3.8 28.9 - - - +
56Y A 6.0 0.2 - - + -
57Y T 4.8 7.6 - - - +
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Residues in contact with ILE 532 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496R ILE* 4.4 9.4 - - + -
498R LEU* 3.6 28.7 - - + +
501R LEU* 5.4 4.5 - - + -
518R GLY* 3.0 10.6 - - - -
519R LEU* 2.8 61.9 + - + +
521R TYR* 4.9 5.6 - - + -
530R LEU* 4.3 10.5 - - + +
531R LEU* 1.3 89.3 - - - +
533R PHE* 1.3 69.7 + - - +
534R VAL 4.4 0.3 + - - -
538R ILE* 3.5 31.4 - - + -
556R ILE* 5.6 7.0 - - + -
560R LEU* 5.3 8.3 - - + -
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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
------------------------------------------------------------
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