Contacts of the strand formed by residues 555 - 557 (chain B) 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 VAL 555 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533B CYS* 4.1 20.0 - - - -
538B VAL* 4.5 15.0 - - + -
554B GLY* 1.3 73.4 - - - -
556B TYR* 1.3 66.7 + - - +
557B LEU* 3.8 1.4 + - + +
560B THR 3.5 0.9 - - - +
561B LEU* 5.4 0.4 - - - +
562B ILE* 3.1 28.9 + - + +
563B GLY* 3.1 28.2 - - - +
564B SER* 3.6 9.1 - - - +
565B ILE* 4.7 3.8 - - + +
571B PHE* 4.5 5.4 - - + -
599B VAL* 3.1 21.3 - - + +
601B ILE* 4.2 19.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 556 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B ILE* 6.5 1.1 - - + -
351B MET* 3.1 36.9 - - + +
553B TYR 4.7 5.6 + - - -
554B GLY* 4.9 5.6 - - - -
555B VAL* 1.3 76.5 - - - +
557B LEU* 1.3 60.2 - - - +
558B ASN 3.5 1.6 + - - -
559B GLY* 4.1 6.1 - - - -
560B THR* 3.2 12.8 - - - +
561B LEU* 3.4 47.8 - - + +
596B GLN* 5.0 7.0 - - - -
597B MET 4.8 2.7 + - - -
598B ALA* 3.7 24.2 - - + -
599B VAL 2.8 9.3 + - - -
600B HIS* 3.2 39.2 + + + +
601B ILE* 2.9 27.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 557 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526B GLU* 3.4 35.7 - - + +
529B ILE* 4.4 15.3 - - + -
530B LYS* 4.8 9.4 - - + -
555B VAL* 3.8 4.0 + - + +
556B TYR* 1.3 68.4 - - - +
558B ASN* 1.3 84.1 + - - +
559B GLY 3.0 0.7 - - - -
560B THR* 2.8 40.0 + - - +
562B ILE* 4.5 16.8 - - + +
601B ILE* 3.2 31.4 - - + +
603B THR* 4.1 9.9 - - + -
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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