Contacts of the helix formed by residues 246 - 258 (chain A) in PDB entry 3RSG
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 GLY 246 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A TYR* 3.4 1.2 - - - +
245A SER* 1.3 76.9 + - - +
247A ALA* 1.3 66.4 + - - +
248A PRO* 3.2 3.8 - - - -
249A VAL* 3.1 25.3 + - - +
250A LEU* 3.4 14.3 + - - +
274A ILE* 5.1 2.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 247 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A TYR* 4.3 5.2 + - + +
246A GLY* 1.3 75.2 - - - +
248A PRO* 1.3 67.6 - - + +
250A LEU* 3.2 5.3 + - - +
251A SER* 3.1 25.8 + - - -
316A PRO* 3.7 32.8 - - + +
317A GLY* 3.8 9.4 - - - +
431A ASP* 3.4 25.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 248 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A ILE* 4.9 1.1 - - + -
239A ALA* 3.8 12.5 - - + -
240A GLY* 3.7 26.2 - - - +
244A TYR 4.0 3.6 - - - +
245A SER 3.2 17.3 - - - +
246A GLY 3.2 5.8 - - - -
247A ALA* 1.3 93.9 - - + +
249A VAL* 1.3 55.7 + - + +
251A SER* 3.9 3.6 - - - -
252A GLY 2.9 23.6 + - - -
265A LEU* 3.5 22.6 - - + +
267A VAL* 3.6 34.3 - - + -
275A ALA* 5.6 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 249 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A SER 3.9 15.0 - - - +
246A GLY* 3.1 13.4 + - - +
248A PRO* 1.3 73.1 - - + +
250A LEU* 1.3 64.2 + - + +
253A MET* 3.0 31.8 + - - +
265A LEU* 4.6 0.7 - - - -
274A ILE* 4.0 12.6 - - + -
275A ALA* 3.8 33.4 - - + +
278A ARG* 4.3 10.1 - - + -
279A PHE* 3.8 29.8 - - + -
282A LEU* 4.2 9.5 - - + +
478A LEU* 5.5 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 250 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A GLY* 3.4 12.5 + - - +
247A ALA 3.2 5.9 + - - +
249A VAL* 1.3 80.2 - - + +
251A SER* 1.3 62.4 + - - +
253A MET 4.0 0.3 - - - -
254A GLY* 3.0 20.4 + - - -
279A PHE* 6.2 0.7 - - + -
428A GLY* 3.7 32.8 - - - +
431A ASP* 3.9 18.2 - - + +
432A VAL* 3.8 12.1 - - + -
474A ALA* 3.7 21.5 - - + -
475A SER* 4.3 12.8 - - - +
478A LEU* 3.9 26.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 251 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A ILE* 3.5 27.0 - - - +
247A ALA 3.1 16.5 + - - -
248A PRO* 4.0 2.9 - - - -
250A LEU* 1.3 76.7 - - - +
252A GLY* 1.3 63.0 + - - +
254A GLY 3.2 1.4 + - - -
255A SER 3.1 6.6 + - - -
316A PRO* 3.6 19.7 - - - +
431A ASP* 2.8 28.1 + - - -
434A THR* 4.2 4.1 - - - -
435A GLY* 3.1 27.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 252 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A ILE* 3.3 16.9 - - - +
248A PRO 2.9 18.2 + - - -
249A VAL 4.0 0.4 - - - -
250A LEU 3.4 0.2 - - - -
251A SER* 1.3 75.2 - - - +
253A MET* 1.3 61.1 + - - +
255A SER* 3.2 6.9 + - - -
256A LEU* 3.1 22.3 + - - +
263A VAL* 4.0 2.5 - - - +
265A LEU* 3.7 10.5 - - - -
282A LEU* 3.8 13.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 253 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A VAL 3.0 18.0 + - - +
252A GLY* 1.3 71.2 - - - +
254A GLY* 1.3 60.1 + - - +
256A LEU* 3.7 30.1 - - + +
257A LYS* 2.8 56.9 + - + +
279A PHE* 3.2 60.3 - - + -
281A GLU* 5.1 7.6 - - - +
282A LEU* 3.9 7.6 - - + +
478A LEU* 3.6 22.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 254 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A LEU 3.0 14.2 + - - -
251A SER 3.2 4.9 + - - -
253A MET* 1.3 78.7 - - - +
255A SER* 1.3 61.5 + - - +
257A LYS* 3.6 1.6 + - - +
258A VAL* 3.5 26.0 + - - +
432A VAL* 3.9 14.8 - - - -
435A GLY 3.8 6.5 - - - -
436A MET* 3.7 6.3 - - - +
478A LEU* 3.4 14.3 - - - +
481A ILE* 4.9 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 255 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A VAL* 3.8 18.9 - - - +
237A ILE* 3.9 2.3 - - - +
251A SER 3.1 7.0 + - - -
252A GLY 3.2 8.5 + - - -
254A GLY* 1.3 76.2 - - - +
256A LEU* 1.3 62.6 + - - +
258A VAL* 3.2 11.4 - - - +
260A THR* 2.7 31.2 + - - -
263A VAL* 3.5 19.3 - - - -
435A GLY* 2.8 31.4 + - - -
439A GLY* 4.1 2.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 256 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A GLY 3.1 9.2 + - - +
253A MET* 3.1 37.6 + - + +
255A SER* 1.3 76.9 - - - +
257A LYS* 1.3 64.7 + - + +
259A GLY* 3.1 14.6 + - - -
260A THR 3.9 19.1 + - - +
261A GLY 4.7 5.8 - - - +
262A LEU* 5.0 0.2 - - - -
263A VAL* 3.5 31.9 - - + +
281A GLU* 4.1 25.8 - - + +
282A LEU* 3.7 15.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 257 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A MET* 2.8 45.1 + - + +
254A GLY 4.2 2.9 - - - +
255A SER 3.4 0.2 - - - -
256A LEU* 1.3 72.2 - - + +
258A VAL* 1.3 59.0 + - - +
259A GLY* 3.3 1.5 + - - -
279A PHE* 6.0 2.9 - - - -
478A LEU* 3.4 35.5 + - + +
479A ARG* 4.1 13.4 + - - +
481A ILE* 3.7 28.6 - - + +
482A PRO* 4.0 27.9 - - + +
485A ILE* 3.8 7.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 258 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A ARG* 4.9 0.5 + - - -
254A GLY 3.6 13.9 - - - +
255A SER* 3.2 17.3 - - - +
257A LYS* 1.3 78.1 - - - +
259A GLY* 1.3 57.0 + - - +
260A THR* 3.9 8.3 - - - +
436A MET* 3.8 44.6 - - + +
439A GLY* 4.1 2.5 - - - -
440A PHE* 3.6 34.8 - - + -
443A GLN* 3.0 21.1 + - - +
457A LEU* 5.2 0.7 - - + -
481A ILE* 4.0 9.2 - - + -
485A ILE* 4.1 12.8 - - + +
----------------------------------------------------------
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