Contacts of the helix formed by residues 241 - 251 (chain A) in PDB entry 2K0G
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 PRO 241 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A TRP* 6.3 0.2 - - + -
240A GLY* 1.4 83.3 - - - +
242A ALA* 1.3 62.2 + - + +
243A VAL* 5.5 0.7 - - + -
244A LEU* 4.0 2.4 - - + +
245A VAL* 2.6 43.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 242 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A PRO* 1.3 82.1 - - + +
243A VAL* 1.3 64.0 + - + +
245A VAL* 3.8 5.5 - - - +
246A GLU* 2.9 38.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 243 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A LEU* 3.4 31.2 - - + -
240A GLY* 3.6 20.0 - - - +
241A PRO* 3.2 0.8 - - + -
242A ALA* 1.3 79.3 - - + +
244A LEU* 1.3 55.5 + - - +
245A VAL 3.1 1.6 - - - -
246A GLU* 3.0 5.1 + - - +
247A ILE* 2.6 39.1 + - + +
329A MET* 4.1 21.3 - - + -
330A LEU* 4.6 0.7 - - + -
333A SER* 3.4 25.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 244 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A TRP* 3.1 25.8 - - + -
230A VAL* 3.4 11.4 - - + -
236A PHE 3.3 20.0 - - - +
237A GLN* 3.3 32.8 - - - +
239A LEU* 3.8 10.3 - - + +
240A GLY 2.8 23.6 + - - +
241A PRO* 4.3 3.4 - - + +
243A VAL* 1.3 74.0 - - - +
245A VAL* 1.3 52.1 + - - +
247A ILE* 3.9 10.3 - - + -
248A VAL* 2.6 46.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 245 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A PHE* 5.5 8.6 - - + -
227A TRP* 3.6 27.8 - - + -
241A PRO* 2.6 30.2 + - + +
242A ALA* 4.0 5.6 - - - +
244A LEU* 1.3 78.0 - - - +
246A GLU* 1.3 61.3 + - + +
248A VAL* 3.5 3.8 + - - +
249A ARG* 3.2 44.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 246 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A ALA* 2.9 27.4 + - + +
243A VAL* 3.0 6.0 + - - +
245A VAL* 1.3 78.6 - - + +
247A ILE* 1.3 61.0 + - - +
249A ARG* 3.6 9.0 + - - +
250A ALA* 3.2 26.7 + - - +
326A ASP* 3.8 2.1 - - - +
329A MET* 4.7 15.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 247 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A PHE* 5.0 6.7 - - + -
239A LEU* 4.1 13.7 - - + -
243A VAL* 2.6 17.8 + - + +
244A LEU* 3.3 23.1 - - + +
246A GLU* 1.3 71.4 - - - +
248A VAL* 1.3 59.8 + - - +
250A ALA 3.6 0.3 - - - -
251A LEU* 2.7 50.3 + - + +
322A LEU* 3.6 15.0 - - + -
326A ASP* 2.7 41.7 - - - +
329A MET* 3.3 27.6 - - + -
330A LEU* 3.4 20.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 248 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A PHE* 4.4 26.8 - - + +
226A ASN* 4.2 26.1 + - + -
227A TRP* 4.0 17.5 - - + -
230A VAL* 3.9 17.0 - - + -
244A LEU* 2.6 48.3 + - + +
245A VAL* 3.8 6.5 - - - +
246A GLU 3.3 0.2 - - - -
247A ILE* 1.3 76.2 - - + +
249A ARG* 1.3 55.2 + - - +
250A ALA 3.1 4.5 - - - -
251A LEU* 2.7 32.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 249 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A ARG* 5.3 13.8 - - - +
223A PHE* 4.5 25.6 - - + -
245A VAL* 3.2 31.6 + - - +
246A GLU* 3.6 10.5 + - - +
247A ILE 3.3 0.2 - - - -
248A VAL* 1.3 76.9 - - - +
250A ALA* 1.3 58.3 + - - +
251A LEU 4.3 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 250 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A GLU 3.2 11.0 + - - +
247A ILE 3.7 0.2 - - - +
248A VAL 3.1 0.2 - - - -
249A ARG* 1.3 81.6 - - - +
251A LEU* 1.3 59.1 + - - +
252A ARG* 4.0 2.1 + - - +
321A SER* 4.3 2.1 + - - +
322A LEU* 5.2 1.1 - - - -
323A HIS* 4.8 15.3 + - + +
326A ASP* 2.7 46.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 251 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A ASN* 3.3 29.1 + - - +
230A VAL* 3.5 25.4 - - + -
236A PHE* 4.8 10.5 - - + -
247A ILE* 2.7 31.7 + - + +
248A VAL* 2.7 28.5 - - - +
249A ARG 4.3 1.2 - - - -
250A ALA* 1.3 79.5 + - - +
252A ARG* 1.3 65.2 + - - +
320A LEU* 3.3 29.8 - - + -
321A SER 2.9 16.8 - - - +
322A LEU* 3.8 15.9 - - + +
----------------------------------------------------------
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