Contacts of the helix formed by residues 194 - 208 (chain C) in PDB entry 4I6N
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 TRP 194 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C ILE* 2.9 41.0 + - + +
48C GLY* 3.7 14.6 - - - -
49C PHE* 3.5 21.3 - + - -
165C TYR* 3.6 25.4 - - + -
166C VAL 4.1 0.7 - - - -
167C PRO* 3.5 44.7 - - + +
172C VAL* 3.8 16.9 - - + +
188C VAL* 3.8 18.4 - - + +
192C GLY 3.4 2.6 + - - +
193C ASP* 1.3 75.2 + - - +
195C THR* 1.3 80.9 + - + +
196C GLU 3.4 1.6 - - - -
197C VAL* 3.2 20.9 + - - +
198C ALA* 3.6 22.0 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 195 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C ILE* 4.0 13.3 - - + +
44C LYS* 4.3 9.1 - - + -
46C ILE* 4.0 26.5 - - + -
49C PHE* 4.0 14.4 - - + -
193C ASP* 2.7 21.4 + - - +
194C TRP* 1.3 113.3 - - + +
196C GLU* 1.3 64.4 + - - +
198C ALA* 3.2 3.6 + - - +
199C ILE* 3.0 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 196 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C LEU 5.7 0.2 - - - +
189C ALA* 5.9 4.7 - - + -
193C ASP* 3.0 18.9 + - - +
194C TRP 3.4 0.2 - - - -
195C THR* 1.3 76.6 + - - +
197C VAL* 1.3 58.8 + - + +
199C ILE* 3.9 17.8 - - - +
200C LYS* 2.9 44.7 + - + +
203C LYS* 4.8 8.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 197 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172C VAL* 3.8 25.6 - - + -
185C LEU* 3.9 21.4 - - + +
186C GLY* 4.3 10.3 - - - +
187C THR 3.4 23.6 - - - +
188C VAL* 4.5 5.2 - - - -
189C ALA* 4.7 7.4 - - + +
193C ASP 5.0 0.9 - - - +
194C TRP 3.2 10.9 + - - +
195C THR 3.2 1.0 - - - -
196C GLU* 1.3 80.1 - - + +
198C ALA* 1.3 61.7 + - - +
200C LYS* 3.5 14.2 + - - +
201C ALA* 3.2 21.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 198 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C PHE* 3.9 9.4 - - + -
165C TYR* 3.8 22.1 - - + -
172C VAL* 4.2 3.1 - - + +
185C LEU* 4.2 10.3 - - - -
194C TRP* 3.6 30.3 + - + -
195C THR 3.2 7.4 + - - +
197C VAL* 1.3 76.5 - - - +
199C ILE* 1.3 66.0 + - - +
201C ALA* 3.1 4.5 + - - +
202C ILE* 2.8 27.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 199 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C LEU* 4.8 6.1 - - + -
36C LEU* 4.0 22.7 - - + +
40C ILE* 5.3 5.6 - - + -
49C PHE* 4.0 25.8 - - + -
195C THR* 3.0 20.9 + - - +
196C GLU* 3.9 18.8 - - - +
198C ALA* 1.3 74.3 - - - +
200C LYS* 1.3 57.3 + - - +
202C ILE* 3.1 8.8 + - + +
203C LYS* 2.8 55.6 + - + +
218C LEU* 4.1 22.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 200 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185C LEU 5.6 4.2 + - - -
196C GLU* 2.9 26.4 + - + +
197C VAL* 3.6 14.1 - - - +
199C ILE* 1.3 78.0 - - - +
201C ALA* 1.3 59.8 + - - +
203C LYS* 3.3 9.0 + - - +
204C GLU* 2.9 47.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 201 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165C TYR* 4.2 9.2 - - + -
174C GLU* 4.8 2.7 - - - +
185C LEU* 3.6 41.3 - - + -
197C VAL 3.2 4.7 + - - +
198C ALA 3.1 9.0 + - - +
200C LYS* 1.3 81.4 - - - +
202C ILE* 1.3 62.9 + - - +
204C GLU* 3.3 8.7 + - - +
205C LYS* 3.0 26.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 202 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C LEU* 4.2 17.5 - - + -
49C PHE* 4.7 4.5 - - + -
51C PHE* 3.8 29.3 - - + -
165C TYR* 3.7 36.1 - - + +
198C ALA 2.8 22.0 + - - +
199C ILE* 3.4 13.7 - - + +
201C ALA* 1.3 77.7 - - - +
203C LYS* 1.3 62.4 + - - +
205C LYS* 3.1 9.3 + - - +
206C ILE* 3.1 30.7 + - + +
218C LEU* 3.6 33.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 203 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C LEU* 3.8 35.9 + - + -
37C ASP* 5.6 4.6 - - - +
196C GLU* 4.8 8.0 + - - +
199C ILE* 2.8 43.7 + - + +
200C LYS* 3.7 8.5 - - - +
202C ILE* 1.3 74.0 - - - +
204C GLU* 1.3 63.0 + - - +
206C ILE* 3.2 9.8 + - - +
207C LYS* 3.0 44.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 204 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200C LYS* 2.9 37.1 + - + +
201C ALA* 3.5 9.0 - - - +
203C LYS* 1.3 75.1 - - - +
205C LYS* 1.3 66.1 + - - +
207C LYS* 3.0 46.5 + - - +
208C ASN* 3.5 14.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 205 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C PHE* 3.9 17.5 - - + -
53C PHE* 3.8 33.4 - - + -
59C GLU* 2.8 42.9 + - - +
62C LYS* 6.2 1.8 - - - +
163C VAL* 4.9 0.2 - - - -
165C TYR* 3.7 21.3 - - - -
174C GLU* 3.9 19.0 + - - +
176C ASP* 5.1 1.2 + - - -
179C ARG* 4.8 1.2 - - - +
201C ALA 3.0 14.2 + - - +
202C ILE 3.1 10.5 + - - +
204C GLU* 1.3 75.8 - - - +
206C ILE* 1.3 63.7 + - - +
208C ASN* 3.1 27.9 + - - +
209C TYR* 3.3 14.8 - - + +
216C PHE* 5.8 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 206 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C LEU* 3.9 27.4 - - + -
51C PHE* 4.3 8.7 - - + -
202C ILE* 3.1 23.6 + - + +
203C LYS* 3.2 8.9 + - - +
205C LYS* 1.3 76.4 - - - +
207C LYS* 1.3 64.8 + - + +
209C TYR* 3.2 25.5 + - - +
210C GLY 3.9 6.8 + - - +
213C GLU 5.4 1.3 - - - +
216C PHE* 3.9 27.6 - - + -
8D LEU* 5.2 3.1 - - + -
9D THR* 4.0 37.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 207 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203C LYS* 3.0 33.7 + - - +
204C GLU* 3.0 36.7 + - - +
205C LYS 3.2 0.4 - - - -
206C ILE* 1.3 78.2 - - + +
208C ASN* 1.3 61.8 + - - +
209C TYR 3.2 1.1 + - - -
210C GLY* 4.1 7.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 208 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C LEU* 4.5 5.4 - - + +
58C LYS* 3.0 54.9 + - + +
59C GLU* 5.4 6.7 + - - -
62C LYS* 6.4 0.4 - - - +
204C GLU 3.5 9.9 + - - +
205C LYS* 3.1 21.5 + - - +
207C LYS* 1.3 77.3 - - - +
209C TYR* 1.3 63.2 + - + +
----------------------------------------------------------
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