Contacts of the strand formed by residues 552 - 556 (chain B) in PDB entry 2J0M
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 552 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506B GLU* 3.8 4.3 - - - +
507B LEU* 3.0 48.5 + - + -
530B LEU* 3.7 42.2 - - + -
547B ILE* 5.9 0.2 - - + -
548B ALA 3.4 18.4 - - - +
549B ALA* 2.7 21.2 + - - +
550B ARG 3.4 0.6 - - - +
551B ASN* 1.3 74.6 - - - +
553B LEU* 1.3 65.1 + - - +
560B VAL* 3.8 14.4 - - + -
561B LYS 3.5 11.7 - - - +
562B LEU* 4.6 6.7 - - + -
611B CYS* 4.7 2.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 553 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484B VAL* 4.2 15.5 - - + -
502B CYS* 3.5 19.5 - - + -
505B GLY 3.5 12.3 - - - +
506B GLU* 4.4 5.8 - - + -
550B ARG 5.4 0.4 - - - +
551B ASN 5.0 0.4 - - - +
552B VAL* 1.3 81.0 - - - +
554B VAL* 1.3 63.3 + - - +
555B SER 3.8 0.3 + - - -
560B VAL* 3.4 4.3 - - - +
561B LYS* 2.8 33.9 + - - +
563B GLY* 4.6 4.5 - - - -
1687B 4ST 3.3 95.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 554 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502B CYS* 3.6 6.6 - - - -
504B LEU* 3.1 38.0 + - + +
505B GLY 2.7 24.3 + - - +
507B LEU* 3.8 30.7 - - + -
510B PHE* 3.8 33.0 - - + -
553B LEU* 1.3 75.5 - - - +
555B SER* 1.3 58.2 + - - +
556B SER 3.0 30.3 - - - +
557B ASN 5.1 0.7 - - - +
559B CYS 3.7 4.5 - - - +
560B VAL* 3.9 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 555 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500B GLU* 4.9 2.1 + - - -
501B LEU 5.4 1.2 + - - -
502B CYS* 4.3 12.9 - - - +
503B THR* 4.7 8.3 + - - -
504B LEU* 4.5 8.0 + - - +
553B LEU 3.8 2.2 + - - -
554B VAL* 1.3 74.2 - - - +
556B SER* 1.3 63.2 + - - +
559B CYS* 2.8 21.0 + - - +
561B LYS* 3.4 40.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 556 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504B LEU* 4.0 13.0 - - - -
554B VAL* 3.0 20.1 - - - +
555B SER* 1.3 78.3 - - - +
557B ASN* 1.3 73.4 + - - +
558B ASP* 3.2 19.3 + - - -
559B CYS* 3.0 18.4 + - - -
----------------------------------------------------------
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