Contacts of the helix formed by residues 213 - 224 (chain C) in PDB entry 4D2W
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 THR 213 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B ALA* 4.3 5.4 - - - -
211C ASP* 3.7 6.7 + - - +
212C ASP* 1.3 86.9 - - + +
214C ALA* 1.3 59.4 + - - +
215C ALA* 4.4 6.4 - - - +
216C ALA* 3.3 23.0 + - - +
217C LEU* 3.2 27.1 + - - +
97D TYR* 6.4 1.1 - - - -
101D GLN* 5.1 13.9 + - - +
108D GLU* 4.8 2.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 214 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B ASN* 5.8 4.0 - - - +
79B ALA* 4.5 10.4 - - + +
80B ASN* 5.7 3.4 - - - +
172C LEU* 3.6 21.7 - - + +
213C THR* 1.3 68.5 - - - +
215C ALA* 1.3 60.3 + - - +
217C LEU* 3.3 2.9 + - - -
218C VAL* 3.0 35.4 + - + +
144D HIS* 5.6 13.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 215 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213C THR* 3.4 4.8 + - - +
214C ALA* 1.3 78.1 - - - +
216C ALA* 1.4 60.5 + - - +
218C VAL* 3.7 7.4 + - - +
219C ALA* 3.2 22.0 + - - +
97D TYR* 3.0 39.7 - - + +
108D GLU* 3.7 8.5 - - - +
111D VAL* 5.4 2.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 216 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211C ASP* 3.4 28.3 - - - +
213C THR* 3.3 20.2 + - - +
214C ALA 3.4 0.6 - - - -
215C ALA* 1.4 75.9 - - - +
217C LEU* 1.4 64.5 + - - +
219C ALA* 3.5 3.7 + - - +
220C LYS* 3.1 27.4 + - - +
108D GLU* 3.8 24.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 217 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B ASN* 5.0 14.1 - - - +
172C LEU* 3.8 27.4 - - + -
173C ALA* 3.9 21.5 - - + +
209C PHE* 3.3 36.1 - - + +
210C ASP* 3.8 5.4 - - - +
211C ASP* 3.8 20.7 - - + +
213C THR 3.2 14.5 + - - +
214C ALA* 3.3 9.6 + - - +
216C ALA* 1.4 72.0 - - - +
218C VAL* 1.3 65.3 + - - +
220C LYS* 3.2 5.8 + - + +
221C ILE* 3.0 35.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 218 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172C LEU* 3.6 28.7 - - + +
180C ILE* 3.9 25.6 - - + -
181C GLN* 5.3 0.9 - - - +
214C ALA 3.0 22.6 + - - +
215C ALA* 3.8 7.9 - - - +
216C ALA 3.5 0.2 - - - -
217C LEU* 1.3 74.0 - - - +
219C ALA* 1.3 62.2 + - - +
221C ILE* 3.3 9.7 + - - +
222C MET* 3.0 29.1 + - + +
111D VAL* 4.2 27.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 219 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215C ALA 3.2 13.1 + - - +
216C ALA* 3.6 9.2 - - - +
218C VAL* 1.3 78.9 - - - +
220C LYS* 1.3 62.3 + - + +
222C MET* 3.5 3.0 + - - +
223C ARG* 3.0 25.1 + - - +
105D SER* 4.9 0.9 - - - +
107D GLU* 3.8 18.6 - - + +
108D GLU* 3.6 33.4 - - + +
111D VAL* 4.2 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 220 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B LYS* 5.6 3.4 - - - +
209C PHE* 3.5 25.2 - - + -
210C ASP 2.9 36.6 + - - +
211C ASP* 3.1 21.7 + - + +
216C ALA 3.1 12.6 + - - +
217C LEU* 3.2 8.5 + - - +
219C ALA* 1.3 77.1 - - + +
221C ILE* 1.3 56.2 + - - +
223C ARG* 3.4 7.3 + - - +
224C GLY 2.9 24.3 + - - -
225C LYS 4.1 4.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 221 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172C LEU* 3.3 36.3 - - + +
173C ALA* 4.3 5.6 - - - +
175C ALA 3.6 21.1 - - - +
177C PRO* 3.9 17.8 - - + +
180C ILE* 5.0 6.1 - - + -
193C TRP* 3.9 16.1 - - + +
209C PHE* 3.8 27.8 - - + -
217C LEU* 3.0 35.2 + - + +
218C VAL* 3.3 8.3 + - - +
220C LYS* 1.3 72.2 - - - +
222C MET* 1.3 66.4 + - - +
224C GLY* 3.2 14.7 + - - -
246C VAL* 3.6 8.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 222 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177C PRO* 3.7 32.8 - - + +
180C ILE* 4.8 7.9 - - - -
181C GLN* 3.1 35.2 - - + +
218C VAL* 3.0 29.3 + - + +
219C ALA* 3.7 6.3 - - - +
221C ILE* 1.3 76.9 - - - +
223C ARG* 1.4 61.3 + - - +
246C VAL* 3.7 16.9 - - + +
111D VAL* 4.5 3.4 - - + -
266D ASP* 3.8 20.7 - - + +
267D TYR* 3.7 48.0 - - + +
269D TYR* 5.0 2.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 223 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219C ALA 3.0 18.4 + - - +
220C LYS* 3.7 6.7 - - - +
221C ILE 3.3 0.2 - - - -
222C MET* 1.4 76.6 - - - +
224C GLY* 1.3 60.9 + - - +
225C LYS* 3.2 60.2 + - + +
246C VAL* 4.2 4.4 - - - +
107D GLU* 3.8 33.7 + - + -
266D ASP* 3.8 32.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 224 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193C TRP* 4.9 0.7 - - - -
209C PHE* 3.6 16.9 - - - -
220C LYS 2.9 7.7 + - - -
221C ILE 3.2 13.5 + - - -
223C ARG* 1.3 76.6 - - - +
225C LYS* 1.4 62.4 + - - +
226C TYR* 3.6 17.5 - - - -
244C LEU 5.0 4.6 - - - +
246C VAL* 3.7 13.7 - - - -
----------------------------------------------------------
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