Contacts of the helix formed by residues 198 - 211 (chain A) in PDB entry 4QYJ
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 PRO 198 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A LEU* 5.7 2.5 - - + -
34A VAL* 3.3 34.5 - - + -
46A VAL* 4.2 25.1 - - + -
103A ASN* 3.9 4.0 - - - +
193A PRO* 4.0 17.3 - - + +
194A ALA 4.0 10.5 - - - +
195A GLU* 4.1 4.9 - - - +
197A THR* 1.3 86.9 - - - +
199A LEU* 1.3 66.6 + - + +
200A THR 3.5 1.8 - - - -
201A ALA* 3.5 9.1 + - - +
202A LEU* 3.4 21.4 + - + +
222A THR* 4.4 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 199 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A VAL* 4.7 1.8 - - + -
43A LEU* 3.6 32.3 - - + -
44A THR* 3.9 26.2 - - + -
46A VAL* 4.1 17.9 - - + -
99A LEU* 3.8 32.1 - - + +
103A ASN* 3.7 15.9 - - + +
197A THR 3.8 0.2 - - - -
198A PRO* 1.3 75.6 - - + +
200A THR* 1.3 64.5 + - - +
202A LEU* 3.1 23.9 + - + +
203A ARG* 3.2 13.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 200 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A LEU* 4.2 16.0 - - + +
99A LEU* 4.2 29.8 - - + -
100A GLU* 3.4 35.6 + - - +
103A ASN* 5.1 2.8 + - + +
171A PRO* 3.5 17.2 - - - +
172A LEU* 3.9 22.1 + - + +
197A THR 5.0 1.0 + - - -
198A PRO 4.8 0.9 - - - -
199A LEU* 1.3 76.9 + - - +
201A ALA* 1.3 58.4 + - - +
203A ARG* 3.7 3.1 + - - +
204A LEU* 3.2 24.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 201 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A ILE* 5.1 3.4 - - + -
171A PRO 5.3 1.7 + - - +
175A ALA* 4.7 10.1 - - + -
191A LEU* 3.9 21.9 - - + +
193A PRO* 3.9 31.4 - - + -
198A PRO 3.5 3.1 + - - +
199A LEU 3.3 0.6 - - - -
200A THR* 1.3 78.5 + - - +
202A LEU* 1.3 61.6 + - - +
203A ARG 3.3 0.2 - - - -
204A LEU* 3.4 11.4 - - - +
205A ALA* 3.0 26.7 + - - +
220A VAL* 4.1 6.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 202 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A GLN 3.9 27.8 - - - +
17A MET* 4.2 9.9 - - - -
23A TRP* 3.6 21.6 - - + -
46A VAL* 4.1 24.7 - - + -
198A PRO 3.4 13.9 + - - +
199A LEU* 3.1 24.2 + - + +
201A ALA* 1.3 76.0 - - - +
203A ARG* 1.3 62.9 - - - +
205A ALA* 3.5 5.3 + - - +
206A GLU* 3.4 16.5 + - - +
220A VAL* 3.9 28.3 - - + -
222A THR* 4.4 8.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 203 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A HIS* 4.0 25.3 + - - +
95A GLU* 5.8 6.3 - - - +
96A LEU* 3.5 30.5 - - + +
99A LEU* 4.3 12.3 - - + -
199A LEU 3.2 14.3 + - - +
200A THR 4.0 1.1 - - - +
202A LEU* 1.3 72.7 - - - +
204A LEU* 1.3 64.6 + - - +
206A GLU* 2.8 46.1 + - - +
207A LEU* 3.1 51.3 + - + +
210A GLU* 5.0 3.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 204 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A LEU* 4.3 19.7 - - + -
89A LEU* 4.4 13.7 - - + -
96A LEU* 5.0 1.3 - - - +
123A LEU* 5.5 0.2 - - + -
172A LEU* 4.1 23.3 - - + -
175A ALA* 3.8 31.0 - - + -
176A VAL* 4.3 18.8 - - + +
179A ILE* 4.6 12.6 - - + -
191A LEU* 5.0 4.5 - - + -
200A THR 3.2 16.3 + - - +
201A ALA* 3.4 10.8 - - + +
203A ARG* 1.3 76.0 - - - +
205A ALA* 1.3 58.7 + - - +
207A LEU* 3.2 9.0 + - - +
208A ALA* 2.8 29.8 + - - +
218A LEU* 5.0 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 205 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A LEU* 3.7 23.4 - - + +
23A TRP* 4.7 0.9 - - + -
201A ALA 3.0 6.2 + - - +
202A LEU* 3.6 9.4 - - - +
204A LEU* 1.3 77.5 - - - +
206A GLU* 1.3 59.9 + - - +
208A ALA* 3.4 15.1 + - - +
209A MET* 3.4 14.9 + - - +
218A LEU* 3.8 17.2 - - + +
220A VAL* 3.4 32.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 206 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A TRP* 3.2 37.1 + - + +
202A LEU 3.4 6.0 + - - +
203A ARG* 2.8 40.6 + - - +
204A LEU 3.3 0.8 - - - -
205A ALA* 1.3 76.7 - - - +
207A LEU* 1.3 62.3 + - - +
208A ALA 3.2 0.4 - - - -
209A MET* 3.6 8.5 + - - +
210A GLU* 3.3 22.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 207 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A LEU* 3.1 22.3 - - + +
88A LEU* 3.6 29.7 - - + +
89A LEU* 3.6 19.7 - - + -
92A HIS* 3.5 28.9 - - + -
96A LEU* 4.1 13.7 - - + -
203A ARG* 3.1 39.6 + - + +
204A LEU* 3.6 5.2 - - - +
206A GLU* 1.3 72.2 - - - +
208A ALA* 1.3 65.5 + - - +
209A MET 3.2 0.7 - - - -
210A GLU* 3.4 17.2 + - - +
211A ALA* 3.1 18.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 208 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A ILE* 4.6 0.9 - - - +
85A LEU* 3.4 21.0 - - + +
183A LEU* 5.8 0.9 - - + -
204A LEU* 2.8 13.4 + - + +
205A ALA 3.4 11.4 - - - +
206A GLU 3.2 0.2 - - - -
207A LEU* 1.3 78.9 - - - +
209A MET* 1.3 58.9 + - + +
211A ALA* 3.4 9.9 + - - +
212A GLY 3.4 0.5 + - - -
213A LEU* 3.2 47.1 + - + +
218A LEU* 3.8 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 209 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A LEU* 4.3 19.3 - - + -
21A GLY* 3.8 23.8 - - - +
205A ALA 3.4 13.6 + - - +
206A GLU* 3.6 9.2 + - - +
207A LEU 3.2 0.2 - - - -
208A ALA* 1.3 77.2 - - + +
210A GLU* 1.3 63.9 + - - +
212A GLY* 3.2 12.8 + - - -
213A LEU* 3.8 18.6 + - + +
214A PRO 5.4 0.9 - - - +
215A ALA* 3.5 42.0 - - + +
216A GLY 5.7 0.2 - - - -
218A LEU 6.0 0.4 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
88A LEU* 3.7 30.2 - - + +
92A HIS* 4.0 9.9 + - - -
203A ARG* 5.0 4.5 + - - -
206A GLU* 3.3 14.2 + - - +
207A LEU* 3.4 23.7 + - - +
209A MET* 1.3 76.3 - - - +
211A ALA* 1.3 59.2 + - - +
212A GLY* 3.4 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 211 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A ILE* 3.6 36.9 - - + +
84A ARG* 4.0 26.5 + - - +
85A LEU* 3.8 22.0 - - + +
88A LEU* 3.9 4.2 - - + +
207A LEU 3.1 12.3 + - - +
208A ALA* 3.5 11.4 - - - +
209A MET 3.2 0.2 - - - -
210A GLU* 1.3 76.5 - - - +
212A GLY* 1.3 57.1 + - - +
213A LEU 3.7 0.7 - - - -
----------------------------------------------------------
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