Contacts of the strand formed by residues 240 - 246 (chain D) in PDB entry 6NRB
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 240 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238D ILE* 3.1 17.9 - - - +
239D THR* 1.3 81.5 - - + +
241D VAL* 1.3 61.8 + - - +
242D GLU* 4.1 9.7 + - - +
323D MET* 3.8 0.2 - - - -
361D LEU* 3.4 35.0 - - + +
362D ALA 3.5 4.3 - - - -
363D GLU* 3.4 43.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 241 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238D ILE* 3.7 26.7 - - + -
240D ARG* 1.3 75.4 - - - +
242D GLU* 1.3 63.8 + - - +
244D ALA* 3.5 15.6 - - + +
296D ASN* 3.3 51.8 - - + +
321D LYS 4.6 2.2 - - - +
323D MET* 3.6 21.8 - - + -
361D LEU* 3.4 4.4 - - - +
362D ALA 2.7 38.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 242 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240D ARG* 4.1 13.0 + - - +
241D VAL* 1.3 72.7 - - - +
243D LYS* 1.3 74.0 + - + +
244D ALA* 3.0 5.6 + - - -
296D ASN* 3.3 13.7 + - - +
360D GLU 3.6 14.2 - - - +
361D LEU* 3.2 25.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 243 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242D GLU* 1.3 72.7 + - + +
244D ALA* 1.3 57.5 + - - +
245D LYS* 3.2 4.9 + - - +
296D ASN* 2.8 17.2 - - - +
358D SER* 3.7 28.8 + - - -
359D ALA 3.0 8.0 + - - +
360D GLU* 3.4 27.8 + - + +
380D ALA* 5.8 4.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 244 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241D VAL* 3.5 21.8 - - + +
242D GLU 3.4 0.7 - - - -
243D LYS* 1.3 68.8 - - - +
245D LYS* 1.3 63.1 + - - +
246D ILE 3.2 0.2 + - - -
296D ASN* 3.2 12.1 - - + -
297D VAL* 3.4 25.4 - - + -
358D SER* 4.0 1.1 - - - -
359D ALA* 2.2 60.9 + - + +
362D ALA* 3.5 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 245 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243D LYS 3.2 3.9 + - - +
244D ALA* 1.3 69.1 - - - +
246D ILE* 1.3 57.1 + - - +
291D LYS* 5.2 2.9 - - - +
293D THR 3.2 21.8 + - - +
294D GLY* 3.2 28.9 - - - +
295D CYS* 3.7 6.7 - - - +
296D ASN* 3.1 26.6 + - - +
297D VAL* 2.4 38.2 + - - +
353D ALA* 4.5 11.6 - - + +
356D LEU* 3.7 13.5 - - + -
357D GLY 3.1 6.7 - - - +
358D SER* 4.2 9.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 246 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244D ALA 3.5 10.3 - - - +
245D LYS* 1.3 64.2 - - - +
247D GLY* 1.3 61.0 + - - +
297D VAL* 3.6 7.4 - - + -
299D LEU* 3.5 30.3 - - + -
336D ILE* 4.1 3.4 - - + -
340D ILE* 3.7 22.9 - - + -
342D THR* 3.2 34.7 - - + +
356D LEU* 3.1 23.1 - - - +
357D GLY* 2.2 36.9 + - - +
359D ALA* 3.6 23.8 - - + +
376D ILE* 3.8 9.4 - - + -
379D CYS* 3.9 7.6 - - - -
----------------------------------------------------------
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