Contacts of the helix formed by residues 223 - 232 (chain A) in PDB entry 3C6G
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 SER 223 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A UNX 3.4 5.2 - - - -
219A GLU 3.9 2.2 + - - -
220A LEU* 2.9 28.1 + - - -
222A ALA* 1.3 77.5 - - - +
224A ALA* 1.3 65.5 + - - +
225A SER* 3.2 14.0 + - - -
226A VAL* 3.0 16.0 + - - +
227A PHE* 3.1 16.7 + - - -
242A LYS* 3.3 32.0 + - - +
485A LEU* 5.0 7.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 224 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A UNX 3.8 12.8 - - - -
52A ILE* 4.7 12.5 - - + +
56A ALA* 5.1 13.7 - - + -
222A ALA 3.7 1.8 + - - -
223A SER* 1.3 72.5 + - - +
225A SER* 1.3 63.9 + - - +
226A VAL 3.1 0.2 + - - -
227A PHE* 3.1 10.6 + - - +
228A LEU* 3.0 33.8 + - + +
485A LEU* 5.5 3.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 225 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A UNX 3.7 11.1 - - - -
223A SER* 3.1 13.0 + - - -
224A ALA* 1.3 78.4 - - - +
226A VAL* 1.3 58.2 + - - +
228A LEU* 3.6 10.4 + - - +
229A TYR* 2.9 25.3 + - - +
235A ILE* 5.1 3.3 - - - +
242A LYS* 3.8 29.1 + - - +
243A HIS* 4.7 11.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 226 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A LEU* 3.8 20.4 - - + -
220A LEU* 3.1 26.9 - - + +
221A ALA 3.6 17.5 - - - +
223A SER* 3.0 8.4 + - - +
225A SER* 1.3 78.0 - - - +
227A PHE* 1.3 66.6 + - + +
228A LEU 3.1 1.8 - - - -
229A TYR* 3.6 7.2 - - + +
230A ASN* 2.9 39.3 + - - +
242A LYS* 5.4 1.1 - - + +
243A HIS* 5.1 13.9 - - + +
246A LEU* 3.8 22.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 227 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A ILE* 3.7 23.2 - - + +
55A LEU* 4.8 15.0 - - + -
62A PRO* 6.2 5.4 - - + -
81A LEU* 3.6 44.0 - - + +
84A ILE* 5.1 0.7 - - - +
221A ALA 4.6 4.5 - - - -
222A ALA* 3.5 27.1 - - - -
223A SER 3.1 25.1 + - - -
224A ALA* 3.1 9.5 + - - +
226A VAL* 1.3 77.0 - - + +
228A LEU* 1.3 57.4 + - - +
230A ASN* 3.6 8.5 + - - +
231A ALA* 3.1 26.0 + - - +
377A LEU* 6.3 2.0 - - + -
380A PHE* 4.1 29.8 - + - -
401A ILE* 5.7 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 228 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A ILE* 4.4 13.2 - - + -
52A ILE* 3.9 27.1 - - + -
224A ALA* 3.0 26.1 + - + +
225A SER* 3.7 7.9 - - - +
227A PHE* 1.3 73.6 - - - +
229A TYR* 1.3 55.8 + - - +
231A ALA* 3.0 5.7 + - - +
232A PHE* 2.6 58.9 + - + -
235A ILE* 3.8 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 229 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A PRO* 3.8 23.4 + - + +
114A LEU* 3.9 17.5 - - + -
117A LYS* 4.0 15.0 + - + +
225A SER 2.9 21.7 + - - +
226A VAL* 3.2 10.7 + - + +
228A LEU* 1.3 72.1 - - - +
230A ASN* 1.3 68.5 + - - +
232A PHE 4.1 4.7 - - - -
233A PRO* 3.0 61.8 + - + +
235A ILE* 4.0 8.0 - - + +
236A GLY* 4.0 13.7 - - - -
243A HIS* 4.1 25.1 - + + -
247A PHE* 3.5 35.0 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 230 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A ILE* 3.6 21.1 - - + +
112A LEU* 3.7 26.4 - - + +
113A PRO* 3.4 27.9 - - + +
114A LEU* 2.8 38.3 + - - +
115A PHE* 6.0 1.2 - - - -
226A VAL* 2.9 37.6 + - - +
227A PHE* 3.8 8.7 - - - +
229A TYR* 1.3 71.9 - - - +
231A ALA* 1.3 66.7 + - - +
233A PRO* 4.0 2.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 231 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A ILE* 4.3 1.1 - - + -
81A LEU 4.1 2.9 - - - +
82A GLY* 3.5 34.0 - - - +
84A ILE* 3.9 10.0 - - - +
227A PHE 3.1 14.2 + - - +
228A LEU* 3.0 9.1 + - - +
230A ASN* 1.3 79.9 - - - +
232A PHE* 1.3 82.3 + - + +
233A PRO* 3.5 6.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 232 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A PHE* 2.9 75.8 - + - -
49A ILE* 4.1 2.7 - - + -
82A GLY* 3.7 16.2 - - - -
228A LEU* 2.6 43.3 + - + +
229A TYR 3.1 4.5 - - - +
231A ALA* 1.3 90.3 - - + +
233A PRO* 1.3 58.9 - - - +
234A TRP* 3.1 32.5 - + + +
235A ILE* 2.9 36.6 + - + +
----------------------------------------------------------
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