Contacts of the strand formed by residues 244 - 249 (chain A) in PDB entry 6N8Q
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 LEU 244 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A TRP 4.1 0.2 - - - +
238A TRP* 3.6 6.8 - - - -
239A GLN* 3.0 60.3 + - - +
242A GLY 3.4 1.0 + - - -
243A ARG* 1.3 81.0 - - - +
245A LEU* 1.3 67.3 + - - +
246A VAL* 4.5 10.0 - - + +
256A GLN* 4.4 11.7 - - + +
257A TRP 3.3 23.1 - - - +
258A PRO* 4.2 2.7 - - + -
259A VAL* 4.3 0.4 - - - -
269A LEU* 3.7 28.3 - - + -
288A TRP* 3.7 26.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 245 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A LEU* 3.6 31.6 - - + -
213A VAL* 4.9 0.2 - - + -
215A ILE* 4.5 3.1 - - + -
225A TYR* 4.0 20.6 - - + +
227A PHE* 4.2 12.3 - - + -
236A ILE* 4.0 9.0 - - + -
237A TRP 3.5 9.9 - - - +
238A TRP* 3.4 34.1 - - + -
244A LEU* 1.3 72.6 - - - +
246A VAL* 1.3 64.0 + - - +
256A GLN* 3.2 4.3 - - - +
257A TRP* 2.6 53.1 + - + +
259A VAL* 3.7 24.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 246 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A ILE* 3.3 5.6 - - - +
237A TRP* 2.8 44.0 + - + +
244A LEU* 4.5 6.7 - - + -
245A LEU* 1.3 78.8 - - - +
247A SER* 1.3 62.3 + - - +
254A TYR* 4.1 11.2 - - + -
255A CYS 3.2 10.8 - - - +
256A GLN* 3.9 21.8 - - + +
286A ILE* 3.9 36.4 - - + +
288A TRP* 3.8 33.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 247 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A PHE* 5.1 2.9 - - - -
233A LEU* 3.7 8.3 - - - -
235A ASN 3.5 4.7 - - - -
236A ILE* 3.5 20.9 - - - -
245A LEU 4.2 0.6 - - - -
246A VAL* 1.3 75.0 - - - +
248A CYS* 1.3 60.1 + - - +
249A HIS* 2.6 28.9 + - - -
254A TYR* 3.0 6.8 - - - +
255A CYS* 2.8 33.1 + - - +
257A TRP* 2.9 26.7 + - - -
286A ILE* 4.6 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 248 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A LEU* 3.6 2.6 - - - +
234A GLU* 2.9 22.0 + - - -
235A ASN* 3.1 43.5 + - - +
247A SER* 1.3 72.0 - - - +
249A HIS* 1.3 66.2 + - - +
253A SER 3.4 8.3 - - - +
254A TYR* 4.2 3.1 - - + -
283A ILE* 3.2 39.7 - - + +
285A ARG 3.9 10.3 - - - -
286A ILE* 3.7 20.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 249 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A SER* 3.4 31.4 - - - -
231A GLN* 3.2 20.6 + - + +
232A GLN 3.1 20.1 + - - +
233A LEU* 4.0 7.4 - - + -
234A GLU* 3.5 6.7 - - - -
247A SER* 2.6 40.0 + - - -
248A CYS* 1.3 80.9 + - - +
250A SER* 1.3 64.3 + - - +
251A ASP* 3.3 16.6 - - - +
252A GLY* 3.3 6.3 + - - -
253A SER* 2.9 17.0 + - - +
255A CYS* 3.6 20.1 - - - -
282A ALA* 3.6 0.2 - - - -
283A ILE 3.2 24.1 + - - +
----------------------------------------------------------
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