Contacts of the strand formed by residues 442 - 447 (chain R) in PDB entry 5A31
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 442 (chain R).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399R CYS* 3.6 8.9 - - - +
413R SER* 2.8 39.6 + - - -
414R HIS 3.0 10.1 + - - +
419R TYR 3.6 29.8 - - - +
420R ASN 3.9 7.9 - - - +
421R LEU* 3.4 23.6 - - + -
438R HIS* 3.6 26.5 - - + +
440R PHE 4.1 0.4 - - - +
441R ARG* 1.3 67.9 - - - +
443R LEU* 1.3 59.5 + - - +
444R HIS 4.2 1.8 - - - +
456R SER* 3.6 19.7 - - - -
457R GLY 3.8 9.0 - - - +
458R ALA* 4.3 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 443 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185R ALA 4.1 5.6 - - - +
186R ASP* 3.6 20.2 - - - +
187R ASP 3.4 38.6 - - - +
188R PHE* 3.8 16.6 - - - +
190R TYR 3.8 7.3 - - - +
355R LYS* 3.1 13.4 + - - +
399R CYS* 3.6 25.1 - - + -
400R ASN* 2.8 28.6 + - - +
441R ARG* 3.0 39.4 + - + +
442R VAL* 1.3 74.3 - - - +
444R HIS* 1.3 68.8 + - + +
457R GLY 3.2 3.0 + - - -
459R GLY 5.3 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 444 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184R LEU* 3.5 24.9 - - + +
185R ALA* 3.0 30.3 + - - +
187R ASP 5.0 0.2 + - - -
190R TYR* 3.7 18.1 + - - +
191R SER* 4.7 0.7 - - - +
192R LEU* 3.3 38.0 - - + +
193R ILE* 3.3 24.7 - - + -
400R ASN* 4.1 2.0 - - - +
442R VAL* 4.2 2.1 - - - +
443R LEU* 1.3 91.7 - - + +
445R LEU* 1.3 62.6 + - - +
456R SER* 3.3 6.2 - - - -
457R GLY* 2.7 51.8 + - - +
458R ALA* 4.3 4.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 445 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191R SER* 4.8 3.7 + - - -
193R ILE* 3.2 13.6 - - - +
400R ASN* 3.8 24.9 + - + +
401R MET* 3.6 34.8 - - - +
402R VAL* 4.2 10.5 - - + +
411R VAL* 3.9 15.0 - - + +
412R THR 4.7 0.4 - - - -
413R SER* 3.8 24.2 - - - +
421R LEU* 4.3 7.2 - - + -
444R HIS* 1.3 72.1 - - - +
446R THR* 1.3 65.2 + - - +
454R VAL* 3.5 27.1 - - + -
455R VAL 3.3 9.2 - - - +
456R SER* 3.7 18.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 446 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193R ILE* 3.7 17.9 - - + +
194R ASP* 3.4 9.5 + - - -
195R TRP* 3.2 35.4 + - + +
201R LEU* 3.8 21.1 - - + -
402R VAL* 4.3 9.4 - - - -
445R LEU* 1.3 80.1 - - - +
447R LEU* 1.3 63.0 + - - +
448R SER 4.1 0.3 + - - -
454R VAL* 3.4 5.2 - - - +
455R VAL* 2.9 45.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 447 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195R TRP* 3.5 18.0 - - - +
402R VAL* 3.8 23.3 - - + +
403R TRP 3.7 22.7 - - - +
404R SER* 4.9 1.3 - - - -
405R LYS* 3.8 37.4 + - + +
446R THR* 1.3 76.1 + - - +
448R SER* 1.3 71.9 + - - +
449R ASN* 3.8 0.3 + - - -
451R GLY* 4.0 18.6 - - - +
453R THR 3.6 13.7 - - - +
454R VAL* 4.0 17.7 - - + +
469R PHE* 4.0 9.9 - - + -
----------------------------------------------------------
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