Contacts of the helix formed by residues 198 - 211 (chain A) in PDB entry 1LDJ
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 198 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A ILE* 3.7 4.5 - - + -
197A ASN* 1.3 72.6 - - - +
199A ARG* 1.3 56.6 + - - +
201A ILE* 2.6 27.0 + - - -
202A SER* 2.9 9.6 + - - -
274A ARG* 3.9 17.0 - - - +
277A VAL* 4.8 9.5 + - + +
278A TYR* 1.5 79.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 199 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A THR* 4.3 6.1 - - - +
197A ASN* 3.0 32.7 + - - +
198A THR* 1.3 83.6 + - - +
200A LEU* 1.3 63.4 + - + +
201A ILE 3.3 0.7 + - - -
202A SER* 4.1 9.2 - - - -
203A GLY* 3.5 17.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 200 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A LEU* 3.4 54.1 - - + +
117A LYS* 5.2 10.5 - - + +
120A THR* 3.2 14.4 - - + +
186A LEU* 4.5 5.4 - - + -
195A THR 5.5 0.4 - - - +
196A ILE 3.2 22.0 - - - +
197A ASN* 2.9 35.2 + - + +
198A THR 2.8 0.2 + - - -
199A ARG* 1.3 82.8 - - + +
201A ILE* 1.3 53.0 + - + +
204A VAL* 2.8 29.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 201 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A LEU* 5.8 0.4 - - + -
183A VAL* 3.4 30.5 - - + -
186A LEU* 3.8 25.6 - - + -
187A ILE* 3.7 29.2 - - + +
196A ILE* 5.2 6.3 - - + -
197A ASN 5.2 0.7 - - - +
198A THR 2.6 9.4 + - - +
200A LEU* 1.3 79.5 - - + +
202A SER* 1.3 52.2 + - - -
203A GLY 3.3 1.8 - - - -
204A VAL* 3.1 5.3 + - - +
205A VAL* 2.7 45.5 + - + +
232A PHE* 5.1 1.8 - - + -
278A TYR* 2.9 39.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 202 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A THR* 2.9 22.2 + - - -
199A ARG* 4.0 9.9 - - - -
201A ILE* 1.3 77.8 - - - +
203A GLY* 1.3 52.6 + - - +
205A VAL* 3.2 5.8 + - - +
206A GLN* 2.7 38.7 + - - +
277A VAL 3.3 21.9 + - - -
278A TYR* 3.6 6.1 - - - +
280A HIS* 5.0 1.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 203 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A TYR* 5.5 0.2 - - - -
120A THR* 4.8 12.6 - - - -
123A TRP* 4.3 7.4 - - - -
199A ARG 3.5 10.5 + - - -
201A ILE 3.3 0.4 - - - -
202A SER* 1.3 77.0 - - - +
204A VAL* 1.3 66.9 + - - +
206A GLN* 3.0 15.7 - - - +
207A SER* 2.9 21.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 204 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A LEU* 5.4 4.9 - - - -
119A TYR* 4.2 16.6 - - + -
120A THR* 3.7 13.2 - - + +
179A VAL* 4.0 11.4 - - + -
183A VAL* 3.5 29.6 - - + -
200A LEU 2.8 30.3 - - - +
201A ILE* 3.1 9.8 + - + +
203A GLY* 1.3 73.3 - - - +
205A VAL* 1.3 55.2 + - + +
207A SER* 2.8 17.5 - - - -
208A TYR* 2.7 56.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 205 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A VAL* 5.4 0.4 - - + -
201A ILE* 2.7 40.1 + - + +
202A SER* 3.4 7.9 - - - +
204A VAL* 1.3 68.9 - - + +
206A GLN* 1.3 62.1 - - - +
207A SER 2.8 4.9 - - - -
208A TYR* 2.8 21.7 + - - +
209A VAL* 2.8 15.1 + - - +
228A TYR* 3.4 11.8 - - + -
232A PHE* 4.2 18.6 - - + -
278A TYR 4.5 7.9 - - - +
279A LEU 2.7 5.2 - - - +
280A HIS* 2.4 51.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 206 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A TRP* 2.9 39.0 + - - +
127A ARG* 4.6 13.6 + - - +
202A SER 2.7 19.7 + - - +
203A GLY* 3.0 23.8 - - - +
205A VAL* 1.3 74.8 - - - +
207A SER* 1.3 58.2 + - - +
209A VAL* 3.4 10.5 - - - +
210A GLU* 2.9 33.4 + - - +
280A HIS* 4.4 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 207 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A TYR* 2.6 34.0 + - - -
123A TRP* 3.4 19.5 - - - -
203A GLY 2.9 11.6 + - - -
204A VAL 2.8 16.6 - - - -
205A VAL 2.8 0.6 - - - -
206A GLN* 1.3 84.6 - - - +
208A TYR* 1.3 50.8 + - - -
210A GLU* 2.9 2.9 + - - -
211A LEU* 2.4 51.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 208 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A TYR* 4.3 7.9 - + - -
171A LEU* 4.2 15.7 - - + -
175A LEU 4.7 3.9 + - - -
176A ASN* 4.4 5.2 - - - -
179A VAL* 3.6 8.7 - - + +
180A THR* 2.7 46.7 + - - -
183A VAL* 5.5 0.2 - - + -
204A VAL* 2.7 56.0 - - + +
205A VAL* 2.8 12.3 + - - +
207A SER* 1.3 77.6 - - - +
209A VAL* 1.3 68.6 + - - +
211A LEU* 3.2 12.6 + - - -
212A GLY 3.3 5.9 + - - -
227A VAL* 3.4 28.8 - - + +
228A TYR* 4.0 15.2 + - + -
231A SER* 3.6 30.3 - - - -
232A PHE* 4.6 10.1 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 209 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A VAL* 2.8 33.6 + - + +
206A GLN* 3.4 11.0 - - - +
208A TYR* 1.3 76.5 - - - +
210A GLU* 1.3 54.1 + - - +
212A GLY* 2.8 24.6 + - - -
224A THR* 2.8 21.2 + - - +
225A LEU* 3.9 23.5 - - + +
228A TYR* 3.8 28.5 - - + -
280A HIS* 3.9 17.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 210 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A TRP* 3.6 7.3 - - + -
127A ARG* 2.9 22.0 + - - +
160A TYR* 2.6 31.2 + - - -
164A LEU* 3.5 22.0 - - - +
206A GLN* 2.9 27.7 + - - +
207A SER 3.4 2.7 - - - +
209A VAL* 1.3 72.8 - - + +
211A LEU* 1.3 57.4 + - - +
212A GLY* 2.8 13.1 + - - +
214A ASN* 3.3 12.8 + - - +
224A THR* 4.6 5.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 211 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A TYR* 4.3 3.8 - - - +
123A TRP* 3.6 27.6 - - + -
164A LEU* 3.5 34.3 - - + +
167A TRP* 3.8 14.8 - - + -
168A ARG* 4.2 15.2 - - + +
171A LEU* 4.9 6.1 - - + -
207A SER* 2.4 66.3 + - - +
208A TYR* 3.2 11.2 + - - +
210A GLU* 1.3 69.5 - - - +
212A GLY* 1.4 56.4 + - - +
213A LEU* 3.1 18.5 - - + +
214A ASN* 3.6 4.5 - - - +
227A VAL* 3.2 18.9 - - + +
----------------------------------------------------------
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