Contacts of the strand formed by residues 495 - 500 (chain D) in PDB entry 5I94
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 MET 495 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220D ILE* 4.7 1.8 - - - -
226D PHE* 3.8 28.9 - - + -
264D VAL* 3.6 25.6 - - + -
265D CYS 3.3 15.3 - - - +
266D THR* 3.7 7.6 - - - +
267D ALA 4.3 1.3 - - - +
434D ALA* 3.4 13.0 - - - +
490D VAL 3.7 0.3 - - - -
491D VAL* 2.8 62.5 + - + +
494D VAL* 1.3 91.4 - - + +
496D GLY* 1.3 62.4 + - - +
497D MET* 4.1 20.0 - - + -
520D LEU* 4.1 9.6 - - + -
526D PHE* 4.0 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 496 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264D VAL* 3.6 0.5 - - - -
265D CYS 2.8 28.9 + - - -
427D SER 4.0 5.4 - - - -
430D ALA* 3.6 17.3 - - - -
431D ALA* 3.6 12.7 - - - +
489D LEU 3.4 8.1 - - - -
495D MET* 1.3 76.0 - - - +
497D MET* 1.3 71.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 497 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230D ILE* 5.4 0.7 - - - -
262D VAL* 4.5 5.2 - - + -
263D SER 3.2 7.4 - - - +
264D VAL* 3.4 29.4 - - + -
427D SER* 4.2 6.1 - - - -
430D ALA* 3.4 8.7 - - - +
487D ILE 3.6 0.6 - - - +
488D LEU* 3.6 3.5 - - - +
489D LEU* 2.7 65.1 + - + +
491D VAL* 5.9 0.7 - - + -
495D MET* 4.1 11.2 - - + -
496D GLY* 1.3 81.5 - - - +
498D MET* 1.3 59.2 + - - +
499D CYS* 3.5 22.2 - - - -
516D PHE* 3.3 35.7 - - + -
520D LEU* 4.1 10.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 498 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262D VAL* 3.6 2.4 - - - -
263D SER 3.1 29.7 + - - -
281D PHE* 3.9 23.1 - - + -
283D LEU* 4.4 11.7 - - + -
286D CYS* 4.2 14.1 - - - -
423D CYS* 3.6 29.8 - - - +
426D ALA* 3.6 28.9 - - + -
427D SER* 4.0 2.6 - - - +
486D GLY* 4.0 4.9 - - - -
487D ILE 3.4 32.1 - - - +
488D LEU* 3.8 22.4 - - + -
497D MET* 1.3 75.2 - - - +
499D CYS* 1.3 66.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 499 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260D TRP* 3.8 16.8 - - + -
261D GLY 3.3 5.4 - - - -
262D VAL* 4.4 5.4 - - - +
485D GLY 3.7 1.5 - - - +
486D GLY* 3.2 4.0 - - - -
487D ILE* 2.9 42.5 + - + +
489D LEU* 5.5 0.9 - - - -
497D MET* 3.5 29.6 - - - -
498D MET* 1.3 75.0 - - - +
500D TRP* 1.3 62.6 + - - +
513D GLY* 4.2 13.7 - - - -
516D PHE* 3.9 19.3 - - - -
517D CYS* 4.9 6.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 500 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255D PHE* 3.4 42.6 - + - -
259D LEU* 3.7 25.1 - - + -
260D TRP* 2.9 22.2 + - - -
261D GLY 2.8 22.1 + - - -
276D ASP* 3.7 20.0 - - + -
279D VAL* 3.6 32.1 - - + -
281D PHE* 3.4 48.3 - + + +
423D CYS* 3.5 16.8 - - - -
484D ALA 2.9 25.8 + - - -
485D GLY 3.5 11.0 - - - -
499D CYS* 1.3 78.1 - - - +
501D SER* 1.3 66.5 + - - +
502D PRO* 3.9 11.1 - - + +
510D SER* 4.8 0.2 - - - -
----------------------------------------------------------
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