Contacts of the helix formed by residues 197 - 213 (chain C) in PDB entry 3E2A
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 197 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168C TRP* 3.4 32.9 - - - -
195C ALA* 3.8 0.2 - - - +
196C THR* 1.3 79.4 + - - +
198C ARG* 1.3 63.5 + - - +
199C GLU* 3.2 18.0 + - - +
200C THR* 3.0 34.0 + - - +
201C LEU* 3.1 7.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 198 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156C TYR* 3.9 2.2 + - - -
159C GLY 3.8 19.6 + - - -
160C ARG* 3.8 4.8 - - - +
165C LYS* 3.8 25.3 - - + +
168C TRP* 3.5 11.8 - - + +
197C SER* 1.3 73.5 - - - +
199C GLU* 1.3 76.6 + - - +
201C LEU* 3.3 25.3 + - - +
202C GLU* 3.0 57.9 + - + +
231C SO4 2.9 39.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 199 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197C SER* 3.2 22.2 + - - +
198C ARG* 1.3 87.2 + - - +
200C THR* 1.3 64.2 + - + +
202C GLU* 3.2 8.0 + - - +
203C ILE* 3.1 33.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 200 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194C MET* 3.8 9.6 - - - +
196C THR* 3.0 37.7 + - - +
197C SER* 3.0 18.7 + - - +
199C GLU* 1.3 74.9 - - + +
201C LEU* 1.3 52.2 + - - +
203C ILE* 4.5 9.4 - - + -
204C SER* 2.7 41.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 201 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155C VAL* 3.7 24.0 - - + +
156C TYR* 3.9 24.7 - - + +
159C GLY* 3.5 35.9 - - - +
160C ARG 4.1 0.2 - - - +
168C TRP* 4.4 0.9 - - + -
176C LEU* 4.4 1.1 - - + -
193C VAL* 4.3 9.2 - - + -
195C ALA* 3.5 24.2 - - + +
197C SER 3.1 15.6 + - - +
198C ARG* 3.3 34.3 - - - +
200C THR* 1.3 74.7 + - - +
202C GLU* 1.3 59.3 + - - +
204C SER* 3.3 2.4 + - - -
205C TYR* 2.9 33.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 202 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156C TYR* 2.3 33.9 + - - -
198C ARG* 3.0 41.1 + - + +
199C GLU* 3.6 9.2 - - - +
201C LEU* 1.3 75.6 - - - +
203C ILE* 1.3 61.5 + - + +
205C TYR* 3.7 5.4 - - - +
206C ARG* 2.9 33.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 203 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199C GLU* 3.1 24.0 + - + +
200C THR* 4.1 8.3 - - + +
202C GLU* 1.3 81.6 - - + +
204C SER* 1.3 58.7 + - - +
206C ARG* 3.4 9.7 + - + +
207C ASN* 3.0 45.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 204 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192C GLY 3.6 20.3 - - - +
193C VAL* 3.5 5.9 - - - +
194C MET* 3.3 26.5 + - - -
200C THR 2.7 23.8 + - - -
201C LEU* 3.3 4.3 + - - -
203C ILE* 1.3 75.5 - - - +
205C TYR* 1.3 63.1 + - - +
207C ASN* 3.7 7.5 - - - +
208C ALA* 2.8 32.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 205 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129C LYS* 2.8 21.2 + - - -
130C HIS* 4.3 1.0 + - - -
152C ALA 4.0 10.8 - - - -
153C GLU* 2.7 38.3 + - - -
156C TYR* 3.7 53.6 - + + -
193C VAL* 3.7 15.9 - - + -
201C LEU 2.9 21.9 + - - +
202C GLU* 3.7 6.5 - - - +
204C SER* 1.3 79.2 + - - +
206C ARG* 1.3 69.1 + - + +
208C ALA* 3.3 1.7 + - - +
209C ILE* 3.0 48.6 + - + +
128D PHE* 6.1 4.3 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 206 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202C GLU* 2.9 17.5 + - - +
203C ILE* 3.5 15.5 - - - +
205C TYR* 1.3 82.8 - - + +
207C ASN* 1.3 74.0 + - - +
209C ILE* 3.7 4.4 + - - +
210C ALA* 3.0 29.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 207 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192C GLY 6.0 0.2 - - - +
203C ILE* 3.0 36.8 + - - +
204C SER* 3.7 7.1 - - - +
206C ARG* 1.3 91.3 + - - +
208C ALA* 1.3 62.1 + - - +
210C ALA* 3.2 7.7 + - - +
211C ARG* 2.9 52.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 208 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152C ALA* 4.8 6.1 - - + -
191C GLN 3.4 24.8 - - - +
192C GLY* 4.1 6.3 + - - -
193C VAL* 3.4 22.0 - - + -
204C SER 2.8 18.1 + - - +
205C TYR 3.3 1.3 + - - +
207C ASN* 1.3 78.7 - - - +
209C ILE* 1.3 57.9 + - - +
211C ARG* 3.2 9.2 + - - +
212C LEU* 2.9 34.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 209 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130C HIS* 3.6 36.8 - - + +
133C LEU* 5.7 1.1 - - + -
149C ILE* 4.7 5.8 - - + -
152C ALA* 4.1 19.1 - - + -
153C GLU* 4.3 1.1 - - - +
205C TYR* 3.0 47.4 + - + +
206C ARG* 3.9 5.2 - - - +
208C ALA* 1.3 76.1 - - - +
210C ALA* 1.3 58.2 + - - +
212C LEU* 3.2 14.2 + - + +
213C SER* 2.6 40.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 210 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206C ARG* 3.0 21.4 + - + +
207C ASN* 3.4 9.4 - - - +
209C ILE* 1.3 77.2 - - - +
211C ARG* 1.3 62.2 + - + +
213C SER* 3.2 17.2 + - - -
214C ILE* 3.4 17.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 211 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192C GLY* 5.8 6.4 + - - -
207C ASN* 2.9 39.8 + - - +
208C ALA* 3.5 7.8 - - - +
210C ALA* 1.3 72.3 - - + +
212C LEU* 1.3 65.5 + - + +
214C ILE* 3.2 32.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 212 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133C LEU* 3.9 8.9 - - + +
145C MET* 3.8 28.8 - - + +
148C LYS* 4.3 13.9 - - + +
149C ILE* 3.9 34.8 - - + +
152C ALA* 4.8 5.4 - - + -
191C GLN* 4.2 25.1 - - + +
208C ALA 2.9 21.0 + - - +
209C ILE* 3.2 16.6 + - + +
211C ARG* 1.3 79.0 - - + +
213C SER* 1.3 61.2 + - - +
214C ILE 3.3 2.4 + - - +
215C LEU* 3.5 17.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 213 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133C LEU* 3.6 24.8 - - - +
136C LYS* 4.7 9.5 + - - -
209C ILE* 2.6 31.0 + - - +
210C ALA* 3.5 10.1 - - - -
211C ARG 3.1 0.2 - - - -
212C LEU* 1.3 75.2 - - - +
214C ILE* 1.3 58.7 + - - +
215C LEU* 3.2 15.7 + - - +
----------------------------------------------------------
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