Contacts of the strand formed by residues 526 - 532 (chain A) in PDB entry 3CB4
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 526 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487A ILE* 4.4 19.1 - - + -
488A ASN* 3.6 12.8 - - - +
519A ILE* 3.5 17.7 - - + -
520A PRO 4.8 0.9 - - - +
522A GLN* 3.3 42.0 - - + +
524A PHE* 3.8 11.4 - - + +
525A ASP* 1.3 77.8 - - - +
527A ALA* 1.3 60.5 + - - +
528A ILE* 3.6 19.6 + - + +
540A SER 4.0 0.3 - - - +
541A THR* 3.4 3.5 - - - -
542A VAL* 2.8 45.4 + - + +
550B LEU* 3.8 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 527 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486A LEU 3.6 2.3 - - - +
487A ILE* 3.1 5.9 - - - -
488A ASN* 3.0 35.4 + - - +
489A GLY 4.6 2.4 + - - +
525A ASP* 4.0 2.2 - - + +
526A ILE* 1.3 70.4 - - - +
528A ILE* 1.3 61.3 + - - +
529A GLN* 5.3 1.7 - - + +
539A ARG* 5.8 9.0 - - + +
540A SER 4.0 3.8 - - - -
541A THR* 4.3 11.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 528 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485A VAL* 4.5 5.2 - - + -
486A LEU 3.8 2.2 - - - -
487A ILE* 3.7 23.8 - - + -
512A VAL* 4.1 22.6 - - + +
515A MET* 4.2 32.5 - - + -
516A LYS* 4.3 11.9 - - + +
519A ILE* 4.3 10.5 - - + -
526A ILE* 4.0 9.6 - - + +
527A ALA* 1.3 76.5 - - - +
529A GLN* 1.3 67.3 + - - +
539A ARG* 3.4 2.8 - - - +
540A SER 2.8 41.0 + - - +
542A VAL* 3.6 31.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 529 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484A ASP 3.8 0.7 - - - +
485A VAL* 3.4 7.3 - - - +
486A LEU* 2.9 73.0 + - + +
512A VAL* 4.3 4.5 - - - -
527A ALA* 5.3 2.5 - - + +
528A ILE* 1.3 77.8 - - - +
530A ALA* 1.3 60.8 + - - +
531A ALA* 4.2 4.5 - - - +
536A ILE* 3.2 31.9 - - + +
538A ALA 3.2 12.1 - - - +
539A ARG* 3.1 37.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 530 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483A VAL* 3.8 20.9 - - + -
484A ASP 3.4 5.2 - - - +
485A VAL* 4.6 3.1 - - + +
508A GLY* 3.8 23.8 - - - +
511A LEU* 5.2 4.5 - - + -
512A VAL* 3.9 6.8 - - + +
529A GLN* 1.3 75.3 - - - +
531A ALA* 1.3 62.6 + - - +
536A ILE* 3.7 4.2 - - - +
537A ILE* 3.0 30.5 + - + -
538A ALA 2.8 12.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 531 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483A VAL* 3.4 6.4 - - - -
484A ASP* 2.9 36.6 + - + +
486A LEU* 4.8 5.4 - - + -
529A GLN* 4.2 6.3 - - - +
530A ALA* 1.3 76.6 - - - +
532A ILE* 1.3 64.1 + - - +
533A GLY 3.9 14.7 + - - +
534A THR 4.7 1.3 - - - -
535A HIS 3.4 15.0 - - - +
536A ILE* 3.9 15.5 - - + -
537A ILE* 3.9 4.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 532 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481A VAL* 4.5 23.1 - - + -
482A ARG 4.0 17.3 - - - +
483A VAL* 4.3 5.2 - - + -
501A ARG* 5.4 6.7 - - - +
504A SER* 3.6 31.0 - - - +
531A ALA* 1.3 74.3 - - - +
533A GLY* 1.3 61.8 + - - +
534A THR 2.8 10.4 + - - -
535A HIS* 2.8 26.7 + - + +
537A ILE* 4.2 22.7 - - + -
165C THR* 5.0 10.5 - - + -
167C VAL* 6.5 1.3 - - + -
----------------------------------------------------------
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