Contacts of the strand formed by residues 333 - 338 (chain D) in PDB entry 1I0E
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 333 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127D LEU* 3.3 31.4 - - + -
296D HIS* 4.5 5.4 - - + +
297D VAL 2.9 11.0 - - - +
298D LYS* 3.2 35.4 - - + -
322D THR* 3.8 41.1 + - + -
332D SER* 1.3 78.3 - - - +
334D PHE* 1.3 66.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 334 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295D VAL 3.1 3.5 - - - +
296D HIS* 3.2 6.2 - - - -
297D VAL* 2.7 43.9 + - + +
299D LEU* 4.3 11.0 - - + -
303D SER* 3.7 32.1 - - - -
308D PHE* 4.3 11.7 - + + -
319D LYS* 4.0 37.0 - - + -
320D ARG 4.3 14.8 - - - +
321D GLY* 6.0 0.9 - - - -
322D THR* 4.6 3.8 - - - -
332D SER* 3.3 27.4 - - - -
333D VAL* 1.3 80.2 - - - +
335D ASP* 1.3 61.3 + - - +
336D VAL* 3.5 3.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 335 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130D ARG* 5.0 4.9 + - - -
292D ARG* 3.0 32.9 + - - -
294D GLY* 4.6 1.7 - - - -
295D VAL 3.4 14.2 + - - +
296D HIS* 4.8 14.6 - - - +
319D LYS* 3.2 17.3 - - - -
320D ARG* 3.2 34.7 + - + +
322D THR* 3.9 15.9 + - - +
334D PHE* 1.3 72.0 - - - +
336D VAL* 1.3 63.6 + - - +
337D SER* 3.3 5.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 336 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294D GLY* 3.1 2.1 - - - -
295D VAL* 3.0 38.5 + - + +
297D VAL* 4.5 16.6 - - + -
312D LEU* 5.0 11.4 - - + -
317D LEU* 5.1 8.7 - - + -
318D GLN 3.0 15.3 - - - +
319D LYS* 4.2 3.7 - - + +
334D PHE* 3.5 3.5 - - + -
335D ASP* 1.3 73.2 - - - +
337D SER* 1.3 58.0 + - - +
353D VAL* 4.6 2.8 - - + +
357D VAL* 5.0 8.7 - - + -
360D MET* 5.0 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 337 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292D ARG* 3.9 29.9 + - - -
293D GLY 3.1 14.1 - - - -
294D GLY* 4.1 2.0 - - - -
317D LEU* 3.4 9.3 - - - -
318D GLN* 2.8 45.9 + - - +
320D ARG* 4.0 10.0 + - - -
335D ASP* 3.3 8.6 + - - -
336D VAL* 1.3 75.0 - - - +
338D ASN* 1.3 64.8 + - - +
353D VAL* 4.8 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 338 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291D LEU* 3.4 14.9 + - - +
292D ARG* 3.2 12.1 - - - +
293D GLY* 2.7 37.3 + - - +
316D ARG 4.1 0.4 - - - +
317D LEU* 3.9 11.1 - - + +
318D GLN* 3.8 8.0 - - - +
337D SER* 1.3 75.9 - - - +
339D ALA* 1.3 58.9 + - - +
340D ASP 3.0 23.1 - - - +
341D ARG* 3.4 10.9 + - - -
349D GLN* 3.4 22.7 - - + +
352D LEU* 5.4 3.1 - - + -
353D VAL* 3.8 19.6 - - + +
----------------------------------------------------------
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