Contacts of the strand formed by residues 515 - 524 (chain A) in PDB entry 2A8B
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 515 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477A TRP* 4.1 21.5 - - + +
478A GLN* 4.3 9.9 - - - +
481A TRP* 3.7 21.1 - - + -
511A ILE* 3.6 3.3 - - - -
512A TYR* 2.7 43.4 + - - +
513A GLY 3.2 0.4 - - - -
514A LYS* 1.3 80.4 - - - +
516A GLU* 1.3 61.9 + - - +
517A VAL* 4.0 2.2 + - + +
535A LEU* 3.8 38.6 - - + -
536A LYS 3.8 5.6 - - - +
537A GLN* 3.5 22.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 516 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509A ARG* 3.1 37.0 + - - +
510A GLY 3.5 9.4 - - - +
511A ILE* 4.4 9.2 - - + +
514A LYS 4.0 0.6 + - - -
515A VAL* 1.3 72.7 - - - +
517A VAL* 1.3 60.9 + - - +
518A LEU* 3.1 26.8 - - + +
534A VAL 3.6 1.0 - - - +
535A LEU* 3.2 4.3 - - - -
536A LYS* 2.8 64.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 517 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477A TRP* 3.9 24.7 - - + -
506A PRO* 3.5 24.5 - - + -
509A ARG* 3.2 5.0 - - - -
510A GLY 2.8 32.2 + - - +
512A TYR* 3.2 33.0 - - + -
515A VAL* 4.7 2.9 - - + +
516A GLU* 1.3 74.4 - - - +
518A LEU* 1.3 64.3 + - - +
533A LEU* 4.2 28.0 - - + -
534A VAL 3.4 5.8 - - - +
535A LEU* 4.1 11.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 518 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
508A LYS 3.5 9.2 - - - +
509A ARG* 3.6 19.5 - - + -
516A GLU* 3.1 37.9 - - + +
517A VAL* 1.3 81.5 - - - +
519A VAL* 1.3 64.9 + - - +
520A ILE* 3.5 9.3 + - + -
533A LEU* 3.2 6.2 - - - +
534A VAL* 2.8 53.3 + - + -
536A LYS* 4.9 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 519 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505A TRP* 5.4 0.2 - - + -
506A PRO* 3.2 25.1 - - + +
507A GLU 3.2 30.5 - - - +
508A LYS* 2.7 20.0 + - - +
518A LEU* 1.3 72.4 - - - +
520A ILE* 1.3 65.5 + - - +
521A SER* 3.6 23.1 - - - +
522A VAL* 4.2 13.0 - - + -
531A ARG* 4.4 13.2 - - + -
532A ASN 3.9 3.4 - - - +
533A LEU* 3.9 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 520 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518A LEU* 4.3 10.8 - - + -
519A VAL* 1.3 77.1 - - - +
521A SER* 1.3 64.5 + - - +
532A ASN* 2.7 23.9 + - + +
533A LEU 4.2 0.7 - - - -
534A VAL* 3.7 45.5 - - + +
543A HIS* 5.5 3.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 521 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519A VAL* 3.6 8.2 - - - +
520A ILE* 1.3 84.7 - - - +
522A VAL* 1.3 67.7 + - - +
523A ASN* 3.4 5.1 + - - -
531A ARG* 3.5 3.8 - - - -
532A ASN* 2.7 57.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 522 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507A GLU 5.8 0.9 - - - +
519A VAL* 4.2 13.9 - - + -
521A SER* 1.3 80.6 - - - +
523A ASN* 1.3 78.4 + - - +
524A GLU* 4.3 1.8 - - + +
529A THR* 5.0 5.6 - - + -
530A ILE 3.2 13.9 - - - +
531A ARG* 4.5 17.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 523 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521A SER* 3.4 5.9 + - - -
522A VAL* 1.3 82.1 + - - +
524A GLU* 1.3 61.4 + - - +
525A CYS* 5.4 1.6 - - - -
529A THR* 3.4 2.9 - - - -
530A ILE* 2.6 57.5 + - + +
532A ASN* 2.4 35.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 524 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522A VAL* 4.3 2.0 - - + -
523A ASN* 1.3 72.5 - - - +
525A CYS* 1.3 74.3 + - - +
528A TYR 4.3 0.9 - - - -
529A THR* 4.2 18.8 - - + -
----------------------------------------------------------
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