Contacts of the helix formed by residues 198 - 210 (chain B) in PDB entry 3IML
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 ASP 198 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B GLU 4.0 2.1 + - - +
197B ILE* 1.3 78.3 - - - +
199B LEU* 1.3 66.9 + - - +
200B PRO* 3.6 17.1 - - + +
201B ALA* 3.3 31.6 + - - +
202B LEU* 3.0 21.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 199 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B HIS* 4.3 16.4 - - + +
197B ILE 5.1 1.1 - - - +
198B ASP* 1.3 69.5 - - - +
200B PRO* 1.4 79.9 - - + +
202B LEU* 2.7 12.1 + - + -
203B ARG* 2.7 54.7 + - + +
229B ASN* 5.2 5.6 - - + +
232B GLY* 3.7 29.8 - - - +
233B ARG* 4.0 24.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 200 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B ASP* 3.6 14.6 - - + +
199B LEU* 1.4 94.7 - - + +
201B ALA* 1.3 61.2 + - - +
203B ARG* 3.6 12.0 + - + +
204B GLU* 3.2 21.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 201 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B ILE* 4.4 10.5 - - + -
198B ASP* 3.3 24.0 + - - +
199B LEU 3.1 0.6 - - - -
200B PRO* 1.3 78.0 - - - +
202B LEU* 1.3 60.5 + - - +
204B GLU* 3.9 4.9 - - - +
205B ALA* 3.0 31.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 202 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B TRP* 3.6 18.8 - - + -
191B THR* 4.2 5.2 - - + -
193B HIS* 3.4 50.3 - - + +
197B ILE* 3.8 16.5 - - + +
198B ASP 3.0 13.5 + - - +
199B LEU* 2.7 20.7 + - + +
201B ALA* 1.3 71.4 - - - +
203B ARG* 1.3 61.4 + - + +
205B ALA* 3.2 3.1 + - - +
206B VAL* 2.9 33.3 + - + +
228B VAL* 3.7 22.7 - - + -
229B ASN* 4.0 16.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 203 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B LEU* 2.7 57.2 + - + +
200B PRO* 4.0 9.3 - - + +
202B LEU* 1.3 78.2 - - + +
204B GLU* 1.3 61.3 + - - +
206B VAL* 4.0 0.2 - - - -
207B ILE* 3.1 34.9 + - + +
228B VAL* 2.5 45.1 + - + +
229B ASN* 2.7 24.5 + - + +
230B PRO* 4.3 8.5 + - - +
232B GLY* 4.3 3.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 204 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200B PRO 3.2 16.6 + - - +
201B ALA* 3.9 6.1 - - - +
203B ARG* 1.3 75.0 - - - +
205B ALA* 1.3 66.9 + - - +
207B ILE* 3.5 5.4 + - - +
208B GLU* 3.0 34.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 205 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B LEU* 4.5 10.5 - - + -
163B TRP* 3.6 26.5 - - + -
201B ALA 3.0 19.3 + - - +
202B LEU 3.6 3.8 - - - +
204B GLU* 1.3 78.7 - - - +
206B VAL* 1.3 57.0 + - - +
208B GLU* 4.9 0.7 - - - -
209B GLU* 2.8 44.7 + - - +
210B VAL* 4.6 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 206 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B GLN* 6.5 0.2 - - + -
161B LEU* 5.5 0.4 - - + -
163B TRP* 4.5 10.1 - - + -
164B LEU* 4.9 2.9 - - + -
189B LEU* 4.0 15.7 - - + -
191B THR* 4.1 21.3 - - + -
202B LEU* 2.9 22.2 + - + +
203B ARG 4.1 0.2 - - - +
205B ALA* 1.3 73.2 - - - +
207B ILE* 1.3 61.6 - - - +
210B VAL* 2.8 46.6 + - + -
211B ILE* 2.9 19.4 + - + -
228B VAL* 3.6 35.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 207 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B ARG* 3.1 23.5 + - + +
204B GLU* 3.9 5.4 - - - +
206B VAL* 1.3 75.1 - - - +
208B GLU* 1.3 64.4 + - - +
211B ILE* 3.7 7.6 - - + +
212B LYS* 2.9 58.5 + - + +
226B PHE* 3.5 50.0 - - + +
228B VAL* 3.7 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 208 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B GLU* 3.0 22.5 + - + +
205B ALA* 4.2 2.0 - - - +
207B ILE* 1.3 83.1 - - + +
209B GLU* 1.3 64.5 + - + +
212B LYS* 2.8 43.2 + - - +
213B PRO* 3.4 18.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 209 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B ARG* 2.9 34.8 + - - +
155B LEU* 3.5 18.8 - - + +
160B ARG* 5.6 6.1 - - - +
161B LEU* 3.7 28.2 - - + +
205B ALA* 2.8 28.9 + - - +
208B GLU* 1.3 83.1 - - + +
210B VAL* 1.3 61.1 + - - +
213B PRO* 3.5 5.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 210 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B LEU* 3.6 19.0 - - + +
151B ARG* 3.6 13.2 - - + +
152B GLN* 3.9 17.9 - - + -
155B LEU* 4.1 13.2 - - + -
161B LEU* 4.4 9.0 - - + -
164B LEU* 5.4 1.1 - - + -
189B LEU* 3.5 25.8 - - + -
206B VAL* 2.8 38.3 + - + +
209B GLU* 1.3 79.4 - - - +
211B ILE* 1.3 62.7 - - - +
213B PRO* 3.9 2.9 - - - +
214B THR* 3.2 22.7 + - - -
----------------------------------------------------------
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