Contacts of the strand formed by residues 456 - 462 (chain D) in PDB entry 3GXM
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 ALA 456 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69D LEU* 4.4 11.0 - - + -
449D LEU 3.6 6.3 - - - +
450D MET* 4.5 2.0 - - + -
451D HIS* 4.9 1.5 + - - -
455D SER* 1.3 76.0 + - - +
457D VAL* 1.3 62.1 + - - +
492D TYR 4.4 0.4 - - - -
493D LEU* 3.4 6.6 - - - +
494D TRP* 3.0 72.3 + - + +
496D ARG* 4.1 13.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 457 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426D PHE* 3.9 15.7 - - + +
427D ILE* 4.5 10.8 - - + -
447D VAL 3.9 0.5 - - - +
448D ALA* 3.2 4.0 - - - +
449D LEU* 2.9 63.6 + - + +
451D HIS* 3.7 27.8 - - + +
456D ALA* 1.3 75.9 - - - +
458D VAL* 1.3 68.2 + - - +
459D VAL* 4.8 4.0 - - + -
491D THR* 3.6 27.4 - - + -
492D TYR 3.2 5.4 - - - +
493D LEU* 4.0 4.7 - - + -
494D TRP* 5.1 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 458 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67D LEU* 5.0 0.4 - - + -
69D LEU* 4.6 3.1 - - + -
436D LEU* 3.9 18.6 - - + -
446D ALA* 4.9 0.2 - - + -
447D VAL 3.2 8.7 - - - +
448D ALA* 3.6 19.5 - - + -
456D ALA* 5.5 0.2 - - + -
457D VAL* 1.3 81.3 - - - +
459D VAL* 1.3 73.4 + - - +
460D VAL* 3.9 17.0 - - + -
472D ILE* 4.3 15.9 - - + -
490D HIS 3.7 0.9 - - - +
491D THR* 3.3 2.3 - - - -
492D TYR* 2.8 43.0 + - + +
494D TRP* 3.6 29.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 459 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368D ILE* 4.8 3.3 - - + +
422D HIS* 3.7 19.7 - - + +
423D PHE* 3.7 42.2 - - + -
427D ILE* 4.8 4.9 - - + -
445D ASP 3.6 1.0 - - - +
446D ALA* 3.2 6.2 - - - +
447D VAL* 3.0 38.0 + - + +
449D LEU* 5.6 0.9 - - + -
457D VAL* 4.8 6.3 - - + -
458D VAL* 1.3 77.1 - - - +
460D VAL* 1.3 65.0 + - - +
489D ILE* 3.8 20.2 - - + -
490D HIS 3.1 11.7 - - - +
491D THR* 4.1 10.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 460 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67D LEU* 4.5 14.8 - - + -
444D LEU* 4.3 11.2 - - + -
445D ASP 3.2 6.7 - - - +
446D ALA* 4.5 2.0 - - + -
458D VAL* 3.9 18.2 - - + -
459D VAL* 1.3 79.7 - - - +
461D LEU* 1.3 66.8 + - - +
470D LEU* 4.2 13.5 - - + -
472D ILE* 4.9 2.7 - - + -
484D SER* 3.6 28.8 + - - +
488D SER 4.2 0.2 - - - +
489D ILE* 3.3 6.3 - - - +
490D HIS* 2.8 41.5 + - + +
492D TYR* 4.1 22.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 461 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361D MET* 4.0 14.1 - - + +
364D SER* 3.6 26.0 - - - +
365D HIS* 3.7 22.4 - - + +
368D ILE* 4.0 6.9 - - + +
419D HIS* 3.8 16.6 - - + -
444D LEU* 3.6 10.8 - - - +
445D ASP* 2.8 49.8 + - + +
460D VAL* 1.3 74.4 - - - +
462D ASN* 1.3 68.9 - - - +
463D ARG* 3.7 25.8 + - + -
488D SER 3.6 12.1 - - - +
489D ILE* 4.0 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 462 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361D MET* 4.4 2.3 - - - +
443D ASP* 4.9 2.1 - - - +
444D LEU* 3.5 15.9 - - + +
461D LEU* 1.3 74.1 - - - +
463D ARG* 1.3 59.3 + - - +
464D SER* 2.7 25.1 + - - -
466D LYS 2.7 25.3 + - - -
468D VAL* 3.9 4.8 - - - +
484D SER* 3.0 32.5 + - - +
485D PRO 3.1 20.6 + - - +
486D GLY* 3.2 4.9 - - - -
487D TYR* 2.9 31.0 + - - -
488D SER* 3.0 13.5 + - - +
----------------------------------------------------------
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