Contacts of the strand formed by residues 353 - 357 (chain A) in PDB entry 1OFD
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 ARG 353 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351A PRO* 5.6 3.6 - - + -
352A ALA* 1.3 77.0 - - - +
354A TYR* 1.3 61.5 + - - +
364A LEU* 3.3 2.9 - - - +
365A GLY 2.9 34.2 + - - +
366A SER 4.9 4.5 - - - +
367A GLU 4.6 2.0 - - - +
368A ALA* 3.6 48.9 - - + +
382A GLY 3.7 8.3 - - - -
383A ARG* 4.4 8.4 - - - +
1328A GLU* 4.4 6.5 + - - +
1329A ALA 2.3 31.8 + - - -
1330A ASN* 3.3 13.2 + - - +
1331A ASP* 4.6 2.6 + - - -
1358A VAL* 3.7 28.6 - - - +
1359A ILE* 4.1 8.7 + - - +
1360A ILE 3.9 4.9 - - - -
1361A GLY* 3.0 30.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 354 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353A ARG* 1.3 77.0 - - - +
355A CYS* 1.3 63.6 + - - +
356A ILE* 3.8 22.4 - - + -
362A ILE* 4.5 3.8 - - + -
363A VAL 3.1 13.2 - - - +
364A LEU* 3.9 22.7 - - + -
380A GLU* 3.1 27.6 + - + -
381A LYS* 3.5 5.2 - - - +
382A GLY* 2.8 49.3 + - - +
383A ARG* 3.2 35.5 + - - -
384A LEU* 4.5 7.2 - - + -
390A ILE* 3.7 29.1 - - + +
401A LYS* 3.5 12.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 355 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354A TYR* 1.3 75.2 - - - +
356A ILE* 1.3 62.9 + - - +
361A TYR 3.8 0.3 - - - +
362A ILE* 3.3 6.2 - - - +
363A VAL* 2.9 42.6 + - + +
368A ALA 5.8 3.8 - - - -
371A VAL 6.0 0.4 - - - -
373A LEU* 3.6 26.1 - - + +
378A ILE* 4.0 24.9 - - - -
380A GLU 3.6 4.9 - - - -
381A LYS* 4.8 9.6 - - - +
1328A GLU* 5.8 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 356 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354A TYR* 3.8 20.2 - - + -
355A CYS* 1.3 79.5 - - - +
357A THR* 1.3 68.9 + - - +
360A ASP* 3.9 8.5 - - - +
361A TYR 3.4 6.7 - - - +
362A ILE* 3.8 19.7 - - + -
378A ILE* 3.6 4.5 - - - +
379A VAL* 2.8 37.6 + - + -
380A GLU* 3.0 40.0 + - + +
399A ILE* 3.7 31.0 - - + -
401A LYS* 4.3 10.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 357 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A ILE* 1.3 83.9 - - - +
358A LYS* 1.3 60.5 + - - +
359A ASP* 3.0 16.7 + - - +
360A ASP* 2.9 18.9 + - - +
361A TYR* 2.9 41.2 + - + +
373A LEU* 4.2 29.6 - - + -
377A ASP* 3.2 26.5 - - - +
378A ILE* 4.2 4.0 - - + +
379A VAL* 4.0 7.4 - - - +
----------------------------------------------------------
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