Contacts of the strand formed by residues 433 - 438 (chain N) in PDB entry 2PPB
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 GLY 433 (chain N).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414N ARG* 3.5 4.1 - - - -
415N VAL* 2.8 40.2 + - - +
431N VAL 3.8 1.0 + - - -
432N TYR* 1.3 76.5 - - - +
434N ARG* 1.3 66.9 - - - +
446N VAL* 3.9 4.2 - - - +
447N VAL 2.8 12.6 - - - -
449N SER 3.0 13.9 - - - -
450N TYR* 3.6 5.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 434 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1156D LEU* 4.4 17.4 + - - +
1176D LYS* 4.0 9.1 - - - +
162N ARG* 3.3 49.3 + - - +
163N TYR* 4.0 32.7 - - - +
166N GLN* 5.8 0.6 - - - +
411N THR* 3.5 25.5 - - - +
412N GLY* 3.4 20.5 - - - +
413N ASP 3.4 4.7 - - - -
414N ARG* 4.6 0.2 - - - +
433N GLY* 1.3 77.6 - - - +
435N VAL* 1.3 82.4 + - - +
436N GLU* 4.0 14.6 + - - +
446N VAL* 3.4 4.5 - - - -
447N VAL* 3.1 36.8 + - + -
449N SER 3.0 6.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 435 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409N VAL* 3.7 21.1 - - + -
410N SER 3.6 14.6 - - - +
411N THR* 3.2 6.5 - - - +
412N GLY 2.9 21.3 + - - -
413N ASP 3.1 12.4 + - - +
415N VAL* 3.2 34.8 - - + -
421N LEU* 6.1 0.2 - - + -
434N ARG* 1.3 85.2 - - - +
436N GLU* 1.3 75.1 - - - +
437N VAL* 4.2 7.0 - - + -
444N VAL* 3.8 24.9 - - + -
445N ARG 3.8 2.9 - - - +
446N VAL* 4.7 5.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 436 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163N TYR 3.3 4.0 - - - +
166N GLN* 2.6 29.5 - - - +
204N LEU* 4.1 4.7 - - - +
394N LEU* 4.9 0.7 - - - +
411N THR* 3.6 8.7 - - + -
434N ARG* 4.0 20.5 + - - +
435N VAL* 1.3 83.9 - - - +
437N VAL* 1.3 61.2 + - - +
438N ASP 3.1 8.1 + - - -
444N VAL* 3.9 0.5 - - - -
445N ARG* 2.9 60.2 + - + +
447N VAL* 3.0 23.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 437 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403N PHE* 4.5 2.0 - - + -
407N VAL* 3.5 35.2 - - + -
409N VAL 3.6 22.9 - - - +
410N SER* 3.9 2.7 - - - -
411N THR* 2.8 33.7 + - - +
435N VAL* 4.2 8.5 - - + -
436N GLU* 1.3 70.5 - - - +
438N ASP* 1.3 59.3 + - - +
439N LEU* 3.2 19.9 + - + +
443N VAL 4.3 2.5 - - - -
444N VAL* 4.1 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 438 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204N LEU* 5.6 0.9 - - - +
403N PHE* 4.4 0.3 - - - -
436N GLU 3.1 8.1 + - - -
437N VAL* 1.3 69.3 - - - +
439N LEU* 1.3 58.9 + - - +
440N VAL* 3.0 45.7 + - - +
441N ARG* 3.6 20.3 + - - -
442N ASN* 3.5 1.0 + - - -
443N VAL* 2.9 35.7 + - + +
445N ARG* 3.1 37.0 + - - +
----------------------------------------------------------
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