Contacts of the strand formed by residues 395 - 397 (chain E) in PDB entry 1I43
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 ILE 395 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267E ASN* 4.1 22.4 - - - +
383E PRO* 3.9 0.9 - - - -
384E TYR* 3.2 21.3 - - + +
386E ALA* 3.0 33.9 - - + +
387E PRO 3.8 15.3 - - - +
388E SER* 3.9 17.0 - - - +
389E PHE* 4.4 7.2 - - - +
390E GLY 5.5 0.2 - - - +
391E GLY 5.6 0.2 - - - +
393E GLU 3.8 7.6 - - - +
394E SER* 1.3 80.5 - - - +
396E VAL* 1.3 65.1 + - - +
423E ARG* 3.9 1.5 - - - +
424E PHE* 3.7 4.0 - - - -
425E SER* 2.8 47.8 + - - +
77H ILE* 4.6 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 396 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377E VAL* 4.9 8.1 - - + +
380E LEU* 3.8 18.8 - - + -
383E PRO* 3.3 36.1 - - + +
384E TYR 2.9 10.5 + - - +
385E ILE* 3.4 13.4 - - + -
386E ALA 3.2 21.0 + - - +
395E ILE* 1.3 71.9 - - - +
397E ASP* 1.3 69.0 + - - +
422E VAL* 4.1 14.1 - - + -
423E ARG* 3.6 9.9 - - - +
424E PHE* 3.3 33.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 397 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377E VAL* 5.6 5.3 - - - +
385E ILE* 4.8 8.5 - - + -
386E ALA 3.7 10.2 - - - +
396E VAL* 1.3 82.8 - - - +
398E GLN* 1.3 62.3 + - - +
399E PRO* 3.1 9.5 - - - +
402E MET* 3.2 35.0 - - + +
422E VAL* 3.6 5.8 - - - +
423E ARG* 3.1 57.7 + - - +
604E PMC 3.3 15.8 + - - +
----------------------------------------------------------
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