Contacts of the helix formed by residues 208 - 220 (chain B) in PDB entry 4P9U
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 LEU 208 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A ILE* 4.0 16.8 - - + -
80B LEU* 3.3 36.6 - - + +
83B LEU* 3.7 24.9 - - + -
101B LEU* 3.9 23.8 - - + -
104B ALA* 5.9 0.4 - - + -
204B ILE* 3.1 33.1 + - + +
205B PHE* 3.1 9.1 + - + +
207B GLY* 1.3 75.4 - - - +
209B LYS* 1.3 64.2 + - - +
210B LYS 3.3 3.3 + - - -
211B LEU* 3.3 15.3 + - + +
212B TYR* 2.9 25.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 209 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A GLU 5.1 9.2 - - - +
155B GLU* 4.8 17.4 - - - +
183B PHE* 5.9 3.6 - - - -
186B TYR* 3.4 49.9 - - + +
205B PHE 3.1 4.9 + - - -
206B ASN 3.5 15.9 + - - +
207B GLY 3.2 3.2 - - - -
208B LEU* 1.3 78.2 - - - +
210B LYS* 1.3 61.8 + - + +
212B TYR* 3.3 1.4 + - - +
213B ASP* 2.7 65.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 210 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B HIS* 6.5 1.6 - - + -
84B ASP* 3.3 26.4 - - + +
206B ASN 6.0 0.2 - - - +
207B GLY 5.2 4.9 - - - +
208B LEU 3.3 0.6 - - - -
209B LYS* 1.3 78.4 - - + +
211B LEU* 1.3 60.1 + - - +
213B ASP* 3.4 6.7 + - - +
214B ARG* 2.9 30.3 + - - +
277B ASP* 5.4 6.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 211 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B LEU* 3.8 33.7 - - + +
84B ASP* 3.3 19.0 + - + +
87B MET* 3.5 37.7 - - + -
97B ILE* 4.0 12.1 - - + -
98B VAL* 5.4 0.4 - - + -
101B LEU* 3.7 32.1 - - + -
208B LEU* 3.3 13.3 + - + +
210B LYS* 1.3 76.0 - - - +
212B TYR* 1.3 60.2 + - - +
214B ARG* 3.4 4.3 + - - +
215B VAL* 2.9 46.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 212 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B LEU* 4.0 31.8 - - + +
105B ARG* 2.5 39.6 + - - -
182B ASN* 3.1 14.6 - - - +
185B ASP* 2.4 31.1 + - - -
186B TYR* 3.8 35.4 - + + -
189B PHE* 3.2 14.7 - + - -
205B PHE* 4.1 20.6 - + - -
208B LEU* 2.9 18.9 + - + +
209B LYS* 3.5 9.2 - - - +
211B LEU* 1.3 77.8 - - - +
213B ASP* 1.3 56.3 + - - +
215B VAL* 3.6 1.2 + - - +
216B GLY* 2.9 24.9 + - - -
220B PHE* 5.9 1.1 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 213 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B ASN* 3.1 23.2 + - - +
183B PHE* 5.5 1.0 - - - -
186B TYR* 4.4 12.6 - - - +
209B LYS* 2.7 57.9 + - - +
210B LYS* 3.8 6.3 - - - +
212B TYR* 1.3 74.5 - - - +
214B ARG* 1.3 57.9 + - - +
217B SER* 2.6 39.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 214 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B ASP* 3.0 49.2 + - - +
87B MET* 3.7 26.9 - - + +
88B THR* 4.3 9.5 - - - +
210B LYS 2.9 16.8 + - - +
211B LEU* 3.7 6.5 - - - +
213B ASP* 1.3 78.5 - - - +
215B VAL* 1.3 62.6 + - + +
217B SER* 3.7 10.0 + - - -
218B TYR* 4.0 3.8 + - - +
274B PHE* 3.3 44.2 + - + +
275B THR* 4.7 0.2 - - - +
276B GLU 2.8 29.9 + - - +
277B ASP* 4.0 13.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 215 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B MET* 5.1 0.9 - - + -
98B VAL* 3.7 44.6 - - + -
101B LEU* 4.1 15.3 - - + -
102B LEU* 5.4 8.1 - - + -
211B LEU* 2.9 31.1 + - + +
212B TYR 4.1 2.2 - - - +
214B ARG* 1.3 76.4 - - + +
216B GLY* 1.3 60.7 + - - +
218B TYR* 3.3 6.9 + - - +
219B TYR* 2.9 29.3 + - + +
263B TRP* 4.6 13.5 - - + -
274B PHE* 4.3 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 216 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B ASN* 3.2 25.7 - - - +
212B TYR* 2.9 12.3 + - - -
215B VAL* 1.3 74.2 - - - +
217B SER* 1.3 55.9 + - - +
218B TYR 3.0 5.4 - - - -
219B TYR* 4.2 8.3 - - - -
220B PHE* 2.9 42.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 217 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B ILE* 4.8 9.4 - - - +
178B ALA* 3.2 30.4 - - - +
179B LYS* 4.0 26.5 - - - +
182B ASN* 4.0 7.6 + - - -
213B ASP* 2.6 24.4 + - - +
214B ARG* 4.1 6.7 - - - -
215B VAL 3.3 0.6 - - - -
216B GLY* 1.3 74.7 - - - +
218B TYR* 1.3 57.1 + - - +
221B SER* 4.3 2.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 218 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B ARG 4.0 1.1 + - - +
215B VAL 3.3 6.5 + - - +
216B GLY 3.0 0.2 - - - -
217B SER* 1.3 79.7 - - - +
219B TYR* 1.3 65.5 + - - +
220B PHE 3.2 2.0 - - - -
221B SER* 2.6 33.2 + - - -
263B TRP* 3.8 21.8 - + - -
266B MET* 2.4 59.2 + - + +
269B THR* 2.8 22.0 + - - -
270B LEU* 3.8 16.2 - - + -
271B PRO* 3.6 30.1 - - + -
274B PHE* 4.1 19.1 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 219 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B LEU* 6.5 2.2 - - + -
105B ARG* 6.3 0.4 - - - -
215B VAL* 2.9 25.3 + - + +
216B GLY* 3.3 6.7 + - - +
218B TYR* 1.3 79.7 - - - +
220B PHE* 1.3 94.3 + + - +
221B SER 3.3 2.3 + - - -
222B ASN 3.7 5.0 + - - -
225B ALA* 3.5 36.0 + - + +
228B LEU* 5.3 0.5 - - - +
255B TYR* 4.6 8.7 + - - -
259B SER* 3.2 41.5 - - - -
262B ILE* 3.7 24.7 - - + +
263B TRP* 4.3 20.4 - + + -
266B MET* 3.7 20.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 220 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B ARG* 6.1 0.4 - - - -
178B ALA* 3.2 25.7 - - - +
181B PHE* 3.4 35.0 - + + -
182B ASN* 3.5 26.0 - - + -
185B ASP* 3.4 42.8 - - + -
212B TYR* 5.9 0.7 - + - -
216B GLY* 2.9 23.6 + - - +
219B TYR* 1.3 108.6 - + - +
221B SER* 1.3 55.0 + - - +
222B ASN 3.1 6.1 - - - +
225B ALA 4.3 1.8 - - - -
226B ARG* 2.8 35.2 + - + -
229B ALA* 3.9 11.4 - - + -
255B TYR* 4.5 2.7 - - - -
----------------------------------------------------------
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