Contacts of the helix formed by residues 238 - 247 (chain A) in PDB entry 3GA5
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 238 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ASN* 3.7 28.9 - - + +
16A PHE* 4.0 35.4 - - + +
19A VAL* 4.4 12.6 - - + -
212A ASP* 2.9 31.2 + - + +
213A ALA 4.0 5.2 - - - +
216A MET* 4.0 17.5 - - - -
236A ASP* 3.4 8.4 - - + +
237A ALA* 1.3 78.0 - - - +
239A PRO* 1.3 74.5 - - + +
240A GLU* 3.8 12.1 - - - +
241A ALA* 2.8 16.6 + - - +
242A LEU* 2.9 11.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 239 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A VAL* 5.1 11.4 - - + -
237A ALA 3.6 3.1 - - - +
238A LEU* 1.3 89.6 - - + +
240A GLU* 1.3 71.7 + - - +
242A LEU* 3.2 15.2 + - + +
243A ALA* 3.1 22.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 240 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ASN* 5.1 6.1 + - - -
216A MET* 3.8 31.9 - - + -
238A LEU* 3.8 10.4 - - + +
239A PRO* 1.3 92.0 - - - +
241A ALA* 1.3 61.3 + - - +
243A ALA* 3.5 8.6 + - - +
244A LEU* 3.2 27.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 241 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A ASP* 3.2 44.4 - - + +
216A MET* 4.6 3.5 - - - -
237A ALA 4.8 0.4 - - - -
238A LEU* 2.8 9.1 + - + +
240A GLU* 1.3 77.1 - - - +
242A LEU* 1.3 62.1 + - - +
244A LEU* 3.0 5.2 + - - +
245A VAL* 2.8 33.0 + - - +
250A MET* 3.9 20.0 - - + +
253A THR* 4.8 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 242 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A ALA* 3.8 33.2 - - + +
238A LEU 2.9 13.6 + - - +
239A PRO* 3.5 13.9 - - + +
241A ALA* 1.3 76.6 - - - +
243A ALA* 1.3 56.8 + - - +
245A VAL* 3.4 6.0 + - + +
246A LYS* 3.0 27.3 + - - +
253A THR* 4.5 5.2 - - + -
255A LEU* 6.4 0.2 - - + -
298A VAL* 3.8 29.8 - - + -
303A LEU* 3.9 17.7 - - + +
306A PHE* 4.2 18.4 - - + +
307A THR* 4.2 25.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 243 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A PRO 3.1 12.0 + - - +
240A GLU* 3.6 12.3 - - - +
241A ALA 3.2 0.2 - - - -
242A LEU* 1.3 77.9 - - - +
244A LEU* 1.3 58.5 + - + +
246A LYS* 3.4 13.9 + - - +
247A SER* 3.0 26.3 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
216A MET* 3.9 20.6 - - + -
219A VAL* 4.3 19.5 - - + -
240A GLU* 3.2 14.6 + - + +
241A ALA 3.0 7.9 + - - +
243A ALA* 1.3 76.6 - - + +
245A VAL* 1.3 60.5 + - - +
247A SER* 3.2 6.2 + - - +
248A GLY 2.9 7.4 + - - -
249A ALA* 2.8 44.7 + - + -
250A MET* 3.0 36.8 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
241A ALA 2.8 21.3 + - - +
242A LEU* 3.5 11.0 - - + +
244A LEU* 1.3 75.9 - - - +
246A LYS* 1.3 64.6 + - - +
248A GLY* 3.1 11.6 + - - -
250A MET* 3.5 25.7 - - + +
251A ALA 5.0 2.7 - - - +
252A GLY* 4.5 9.0 - - - +
253A THR* 4.2 21.5 - - + +
298A VAL* 5.0 1.1 - - + +
299A ASP* 3.8 12.1 - - + -
300A LYS* 3.7 40.1 - - + +
303A LEU* 4.1 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 246 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A LEU 3.0 12.1 + - - +
243A ALA* 3.6 14.1 - - - +
244A LEU 3.3 0.2 - - - -
245A VAL* 1.3 77.6 - - - +
247A SER* 1.3 57.8 + - - +
248A GLY 3.2 0.2 - - - -
300A LYS* 3.1 23.2 + - - +
303A LEU* 3.6 24.2 - - + +
307A THR* 5.0 13.1 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
243A ALA 3.0 12.7 + - - -
244A LEU* 3.2 19.0 + - - +
245A VAL 3.2 0.2 - - - -
246A LYS* 1.3 77.5 - - - +
248A GLY* 1.3 58.8 + - - +
249A ALA* 3.2 17.2 + - - +
300A LYS* 5.3 0.9 - - - -
----------------------------------------------------------
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