Contacts of the strand formed by residues 506 - 514 (chain D) in PDB entry 3E20
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 GLN 506 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500D LEU* 3.4 4.4 - - - +
501D VAL* 2.6 39.9 + - + +
504D ILE* 3.1 31.3 + - + +
505D ASN* 1.3 78.5 - - - +
507D THR* 1.3 70.1 + - - +
508D LEU* 4.1 7.6 - - + -
537D ASP* 3.1 50.1 + - - +
538D ASP* 4.8 1.4 - - - +
540D ASP* 4.4 11.5 - - - +
541D VAL* 4.9 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 507 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498D ASN* 4.5 15.9 - - + +
499D VAL 3.6 11.9 - - - +
500D LEU* 3.7 11.5 - - - +
505D ASN* 3.8 3.5 + - - -
506D GLN* 1.3 82.7 + - - +
508D LEU* 1.3 77.6 + - - +
535D ARG 4.8 0.7 - - - +
536D GLY* 5.1 2.4 - - - -
537D ASP 5.3 0.7 + - - -
550D THR* 4.4 16.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 508 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484D LEU* 3.9 23.3 - - + -
498D ASN* 3.5 8.5 - - - +
499D VAL* 3.0 42.4 + - + +
501D VAL* 3.6 28.5 - - + -
506D GLN* 4.1 2.4 + - + -
507D THR* 1.3 83.6 - - - +
509D GLU* 1.3 60.6 + - - +
534D VAL* 4.0 18.6 - - + -
535D ARG 3.6 6.5 - - - +
536D GLY 3.8 18.6 - - - +
537D ASP 3.2 27.6 - - - +
538D ASP* 4.3 3.6 - - + -
541D VAL* 4.2 8.3 - - + -
547D LEU* 4.9 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 509 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496D ASN* 4.0 17.1 - - - +
497D SER 3.5 10.1 - - - +
498D ASN* 3.5 12.1 - - - +
508D LEU* 1.3 74.5 - - - +
510D VAL* 1.3 67.1 + - - +
511D THR* 3.6 22.3 + - + +
534D VAL* 3.1 7.6 - - - +
535D ARG* 2.7 64.4 + - + +
495J LYS* 5.5 1.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 510 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493D ILE* 4.5 6.7 - - + -
494D LYS 4.6 2.9 - - - +
496D ASN* 2.7 37.2 + - - -
497D SER 2.8 17.8 + - - +
499D VAL* 3.5 39.7 - - + -
509D GLU* 1.3 75.0 - - - +
511D THR* 1.3 55.5 + - - +
512D ALA 3.9 20.0 - - - +
513D ILE* 4.1 16.6 - - + -
532D LEU* 4.1 24.7 - - + -
533D ARG 3.7 5.4 - - - +
534D VAL* 4.5 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 511 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495D LYS* 4.6 4.8 - - - +
496D ASN* 4.0 10.6 - - - +
509D GLU* 3.6 32.8 - - + +
510D VAL* 1.3 73.7 - - - +
512D ALA* 1.3 62.1 + - - +
533D ARG* 2.9 34.7 + - - +
534D VAL* 4.8 0.9 - - - -
535D ARG* 4.0 30.8 + - + +
511J THR* 6.0 3.4 - - - -
535J ARG* 3.4 20.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 512 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495D LYS* 5.1 2.0 - - - -
510D VAL* 3.5 5.9 + - - +
511D THR* 1.3 84.6 + - - +
513D ILE* 1.3 70.3 + - - +
514D TYR* 3.6 33.0 - - + +
520D GLU* 3.9 14.4 - - - +
531D ARG 3.9 0.2 - - - +
532D LEU* 3.6 5.0 - - - -
533D ARG* 3.2 33.7 + - + -
535J ARG* 4.9 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 513 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493D ILE* 4.3 14.6 - - + +
494D LYS 3.9 5.6 - - - -
495D LYS* 3.6 34.5 - - + +
510D VAL* 4.1 7.6 - - + -
512D ALA* 1.3 77.9 - - - +
514D TYR* 1.3 66.2 + - - +
520D GLU* 3.2 7.9 + - - +
521D ILE* 2.8 60.7 + - + +
522D SER 4.2 3.1 - - - +
523D SER* 5.1 0.4 - - - +
524D SER* 3.6 17.5 - - - +
530D VAL* 3.8 18.4 - - + -
531D ARG 3.7 2.5 - - - -
532D LEU* 3.5 20.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 514 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483D ILE* 5.1 1.1 - - + -
512D ALA* 3.6 25.9 - - + +
513D ILE* 1.3 77.7 - - - +
515D ASP* 1.3 66.5 + - - +
518D ASP* 4.4 6.1 - - - -
519D GLU 3.4 5.6 - - - +
520D GLU* 3.6 40.0 + - + -
530D VAL* 3.6 3.6 - - - -
531D ARG* 3.0 47.7 + - + +
533D ARG* 3.0 34.0 + - + -
480J LEU* 3.1 57.8 + - + -
481J GLY* 3.6 10.7 - - - -
533J ARG* 4.8 4.7 - - - -
----------------------------------------------------------
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