Contacts of the strand formed by residues 402 - 405 (chain A) in PDB entry 2F61
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 402 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A LEU* 3.7 42.2 - - + +
107A SER* 4.6 0.9 - - - -
108A TYR* 3.5 36.7 + - + +
383A LEU 3.8 8.5 - - - +
384A ALA* 3.2 8.4 - - + +
385A LEU 3.1 22.5 + - - -
400A SER* 3.2 4.8 + - - -
401A PRO* 1.3 83.5 - - - +
403A ILE* 1.3 67.4 + - - +
404A VAL* 4.6 0.4 - - + -
411A PHE* 3.8 16.2 - - + -
412A TYR 3.1 7.6 - - - +
413A LYS* 3.9 26.7 - - + -
417A PHE* 4.2 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 403 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352A VAL* 3.5 24.2 - - + -
354A LEU* 3.6 33.4 - - + -
385A LEU* 3.1 9.2 - - + +
386A ASN 3.5 26.5 - - - +
387A PRO* 3.5 19.7 - - + -
399A ASP* 3.7 4.3 - - - +
400A SER* 3.7 23.1 - - - +
402A ILE* 1.3 76.4 - - - +
404A VAL* 1.3 65.2 + - - +
411A PHE* 3.2 3.3 - - - -
412A TYR* 2.7 42.3 + - + +
414A GLN* 3.8 10.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 404 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A ASN* 3.5 47.9 - - + +
95A ALA* 5.0 0.9 - - + -
96A LEU* 3.8 26.5 - - + -
104A LEU* 4.1 11.0 - - + -
384A ALA* 4.4 8.1 - - + -
385A LEU 2.8 10.5 + - - +
386A ASN* 3.5 7.1 - - - +
387A PRO* 3.3 20.7 - - - +
402A ILE* 4.6 0.4 - - + -
403A ILE* 1.3 74.8 - - - +
405A ASP* 1.3 63.3 + - - +
406A ILE* 3.5 20.1 + - + +
410A THR 3.9 2.9 - - - -
411A PHE* 4.0 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 405 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387A PRO* 4.6 14.8 - - + +
403A ILE 3.9 1.8 + - - -
404A VAL* 1.3 71.4 - - - +
406A ILE* 1.3 64.0 + - - +
407A THR* 2.9 26.9 + - - +
408A LYS* 3.1 36.9 + - + +
409A ASP* 3.4 9.0 + - - -
410A THR* 2.9 25.9 + - - +
412A TYR* 3.8 26.0 + - + -
----------------------------------------------------------
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