Contacts of the strand formed by residues 348 - 353 (chain D) in PDB entry 3RL8
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 348 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333D ILE* 3.7 39.7 - - + -
334D ALA 3.4 3.4 - - - +
335D GLY 3.8 5.8 - - - +
336D GLY* 3.6 29.4 - - - +
346D ASN 4.5 0.7 - - - +
347D SER* 1.3 73.6 - - - +
349D TYR* 1.3 61.4 + - - +
370D LYS* 3.3 7.8 - - - +
371D LEU* 2.9 50.1 + - + +
379D LEU* 3.5 24.4 + - + +
382D VAL* 4.2 6.7 - - + -
383D THR 4.4 2.0 - - - +
384D HIS* 4.6 1.8 - - - -
387D ALA* 3.7 26.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 349 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397C PHE* 5.8 1.4 - - - -
333D ILE* 3.2 7.9 - - - +
334D ALA 2.9 33.5 + - - +
341D HIS* 3.4 44.4 - + + +
342D ILE* 3.7 19.4 - - + +
345D ASP* 2.7 32.6 + - - -
347D SER* 3.6 24.2 - - - -
348D ILE* 1.3 72.5 - - - +
350D VAL* 1.3 67.9 + - - +
351D THR* 3.9 0.6 - - + +
368D GLY* 3.4 28.3 - - - -
369D ASP 3.3 7.4 - - - -
370D LYS* 3.9 21.8 - - + +
371D LEU* 5.2 0.4 - - - -
405D PRO* 6.1 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 350 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377C VAL* 5.1 1.0 - - - +
331D PHE* 4.2 9.2 - - + -
332D SER 3.6 9.6 - - - +
333D ILE* 4.6 0.9 - - + -
349D TYR* 1.3 73.2 - - - +
351D THR* 1.3 61.5 + - - +
352D LYS 4.0 6.1 - - - +
353D ILE* 3.8 26.2 - - + -
365D LEU* 3.9 20.4 - - + -
366D GLN 3.6 20.6 - - - +
367D ILE* 3.5 5.4 - - - +
368D GLY* 2.7 30.3 + - - -
369D ASP* 2.8 17.8 + - + +
371D LEU* 3.7 28.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 351 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376C ASN 5.5 1.3 - - - +
377C VAL* 3.9 21.1 - - + +
332D SER* 3.0 24.8 + - - -
333D ILE 3.9 3.6 + - - -
334D ALA* 3.6 32.0 - - + +
341D HIS* 4.0 19.5 - - + +
349D TYR 3.9 2.2 - - - +
350D VAL* 1.3 76.9 - - - +
352D LYS* 1.3 64.7 + - - +
367D ILE* 3.8 21.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 352 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381C GLU 5.7 3.0 + - - -
382C VAL* 6.4 1.6 - - - -
386C GLU* 3.9 20.4 - - - +
331D PHE* 3.2 9.1 - - - +
332D SER* 2.9 46.3 + - - +
350D VAL* 3.8 2.4 - - - +
351D THR* 1.3 82.6 + - - +
353D ILE* 1.3 78.7 + - - +
354D ILE* 4.6 10.9 - - + +
367D ILE* 4.1 6.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 353 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386C GLU* 4.4 7.9 + - - +
330D GLY 3.9 3.4 - - - +
331D PHE* 4.0 4.0 - - + -
350D VAL* 3.8 23.8 - - + -
352D LYS* 1.3 81.4 - - - +
354D ILE* 1.3 65.1 + - - +
355D GLU 3.6 2.1 + - - -
359D ALA* 4.2 3.1 - - + +
360D HIS* 3.6 44.7 - - + +
365D LEU* 3.8 44.4 - - + +
366D GLN* 4.5 0.4 - - - -
367D ILE* 4.3 20.7 - - + +
----------------------------------------------------------
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