Contacts of the helix formed by residues 223 - 229 (chain C) in PDB entry 6DWM
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 ASN 223 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221C ASN 3.6 5.4 + - - +
222C ASN* 1.3 73.2 - - - +
224C PHE* 1.3 66.0 + - - +
225C GLY 3.3 2.7 - - - -
226C GLU* 3.1 28.2 + - + +
227C VAL* 3.0 26.9 + - - +
247C SER* 2.9 46.3 + - - +
250C ALA* 4.1 14.1 - - - +
251C PHE* 4.1 16.3 + - - -
254C LEU* 4.3 3.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 224 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115C ILE* 4.0 22.0 - - + -
123C PHE* 4.3 4.7 - + - -
222C ASN* 3.3 3.6 - - + -
223C ASN* 1.3 79.4 + - - +
225C GLY* 1.3 68.5 + - - +
227C VAL* 3.2 0.9 + - - +
228C VAL* 3.0 35.8 + - + +
251C PHE* 3.5 32.3 - + - -
254C LEU* 3.9 8.6 - - + +
255C ASN* 4.2 5.4 - - - -
320C ASP* 5.5 3.8 - - - +
496C LEU* 4.5 13.2 - - + -
602C HJJ 3.4 93.3 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 225 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222C ASN 5.1 1.4 + - - -
223C ASN 3.3 0.8 - - - -
224C PHE* 1.3 82.4 - - - +
226C GLU* 1.3 60.9 + - - +
229C GLY 3.1 8.8 + - - -
320C ASP* 5.5 1.8 + - - -
495C GLY* 3.1 5.0 - - - -
496C LEU* 2.7 42.6 + - - -
497C THR* 4.3 16.8 + - - -
499C LYS* 6.1 2.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 226 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223C ASN* 3.1 29.6 + - + +
225C GLY* 1.3 79.7 - - - +
227C VAL* 1.3 61.4 + - + +
229C GLY* 4.1 5.7 + - - +
232C ASN* 4.6 3.6 + - - +
247C SER* 5.3 4.0 + - - +
493C ILE* 4.1 17.8 - - + +
494C TYR* 3.9 19.9 - - - +
495C GLY* 4.2 7.4 - - - -
497C THR 6.1 0.2 - - - +
499C LYS* 4.4 20.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 227 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111C THR* 3.8 20.7 + - + +
223C ASN* 3.0 34.5 + - + +
226C GLU* 1.3 79.3 - - + +
228C VAL* 1.3 62.2 + - - +
232C ASN* 2.6 44.4 + - - +
235C ASP* 4.8 0.2 - - - +
247C SER* 3.5 21.5 - - - +
248C LEU* 4.2 8.5 - - + +
251C PHE* 3.7 35.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 228 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111C THR* 5.0 7.2 - - - -
112C PHE* 3.9 17.4 - - + -
115C ILE* 4.2 7.0 - - + -
123C PHE* 3.7 27.1 - - + -
224C PHE* 3.0 31.3 + - + +
227C VAL* 1.3 73.3 - - + +
229C GLY* 1.3 68.8 + - - +
230C SER* 3.3 3.1 + - - -
235C ASP* 5.8 0.8 - - - +
251C PHE* 3.6 31.2 - - + -
386C ILE* 5.7 0.7 - - + -
387C PRO* 4.9 5.3 - - + +
496C LEU* 3.8 22.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 229 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225C GLY 3.1 11.1 + - - -
226C GLU 4.1 3.1 + - - +
227C VAL 3.3 2.2 - - - +
228C VAL* 1.3 77.6 - - - +
230C SER* 1.3 68.9 + - - +
231C GLY 3.2 2.6 + - - -
232C ASN* 3.3 16.6 + - - +
494C TYR* 3.6 11.0 - - - -
495C GLY 4.0 3.8 - - - -
496C LEU* 3.5 26.6 - - - +
----------------------------------------------------------
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