Contacts of the helix formed by residues 198 - 214 (chain B) in PDB entry 4HI7
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 TYR 198 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B LEU* 4.4 10.8 - - + -
165B ILE* 3.4 32.0 - - + +
169B SER* 4.1 6.2 - - - -
189B ILE* 4.9 1.6 - - - +
192B LEU* 3.1 32.1 - - + +
193B GLU* 3.6 42.3 + - + +
195B LEU* 3.1 21.9 + - + +
196B PRO 3.5 1.0 + - - -
197B TYR* 1.3 78.4 - - - +
199B ALA* 1.3 57.5 + - - +
200B GLU 3.0 0.2 - - - -
201B ASN* 2.8 50.9 + - + -
202B SER* 2.8 35.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 199 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B PRO 5.2 0.4 + - - -
197B TYR* 3.1 2.3 + - - -
198B TYR* 1.3 77.6 - - - +
200B GLU* 1.3 64.6 + - - +
201B ASN 3.0 0.2 - - - -
202B SER* 3.3 15.5 - - - +
203B THR* 3.1 36.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 200 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B ASP* 5.9 0.7 - - - +
16B ARG* 3.5 19.4 - - - +
19B LYS* 3.2 57.3 + - + +
20B LEU* 4.2 6.5 - - + -
23B ALA* 4.2 18.5 - - + +
29B TYR* 3.7 13.0 + - - -
197B TYR* 3.1 20.6 + - + +
198B TYR 3.0 1.2 - - - -
199B ALA* 1.3 78.4 - - - +
201B ASN* 1.3 58.8 + - - +
203B THR* 5.6 0.2 - - - -
204B GLY 5.1 1.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 201 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B ARG* 2.8 39.7 + - + +
20B LEU* 3.9 27.2 - - + +
165B ILE* 4.1 4.0 + - - +
166B SER* 3.7 9.5 - - - -
169B SER* 3.0 23.4 + - - -
198B TYR* 2.8 37.7 + - + +
200B GLU* 1.3 79.8 - - - +
202B SER* 1.3 64.8 + - - +
203B THR 3.3 2.2 - - - -
205B ALA* 2.9 22.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 202 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B TYR* 2.8 36.0 + - - -
199B ALA* 3.3 19.6 + - - +
201B ASN* 1.3 75.2 - - - +
203B THR* 1.3 65.4 + - - +
205B ALA* 3.8 6.4 - - - +
206B GLN* 3.0 43.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 203 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B ASP* 4.9 9.9 - - - +
199B ALA* 3.1 26.6 + - - +
202B SER* 1.3 78.5 + - - +
204B GLY* 1.3 63.0 + - - +
206B GLN* 3.3 10.5 + - - +
207B GLN* 3.1 40.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 204 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B ASP* 3.3 25.4 - - - +
11B ALA* 3.6 8.0 - - - -
16B ARG* 3.5 11.3 - - - +
199B ALA 4.8 0.2 + - - -
200B GLU 5.1 1.2 + - - -
201B ASN 3.5 3.0 + - - -
202B SER 3.4 0.2 - - - -
203B THR* 1.3 77.0 - - - +
205B ALA* 1.3 60.5 + - - +
207B GLN* 3.2 16.7 + - - +
208B PHE* 2.9 24.9 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
16B ARG* 3.4 23.6 - - - +
169B SER* 3.7 28.4 - - - +
201B ASN* 2.9 23.1 + - - +
202B SER* 3.8 6.3 - - - +
204B GLY* 1.3 73.8 - - - +
206B GLN* 1.3 57.9 + - + +
208B PHE* 3.2 3.7 + - - +
209B VAL* 2.9 34.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 206 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B SER* 3.0 36.5 + - - +
203B THR* 3.6 8.3 - - - +
205B ALA* 1.3 74.4 - - + +
207B GLN* 1.3 58.7 + - + +
209B VAL* 3.4 7.8 + - - +
210B ALA* 2.9 30.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 207 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B ILE* 6.0 0.3 - - - +
10B ASP* 3.6 17.8 + - - +
11B ALA* 3.8 14.3 + - + +
203B THR* 3.1 32.7 + - - +
204B GLY* 3.2 16.9 + - - +
206B GLN* 1.3 73.9 - - + +
208B PHE* 1.3 63.5 + - - +
210B ALA* 3.3 7.4 + - - +
211B ALA* 3.0 24.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 208 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B ALA* 3.6 29.5 - - + +
13B PRO* 4.5 8.7 - - + -
16B ARG* 4.0 5.2 - - - +
112B LEU* 4.1 27.1 - - + -
116B ALA* 4.2 8.5 - - + -
120B LEU* 4.2 15.7 - - + -
170B SER* 3.4 40.6 - - - +
173B ALA* 4.2 1.6 - - + -
174B PHE* 4.0 12.8 - + - -
204B GLY 2.9 13.1 + - - +
205B ALA 3.4 7.6 - - - +
207B GLN* 1.3 75.6 - - - +
209B VAL* 1.3 66.1 + - - +
211B ALA* 3.2 7.1 + - + +
212B VAL* 2.9 43.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 209 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B SER 4.2 15.3 - - - +
170B SER 4.8 1.1 - - - +
172B VAL* 4.7 5.4 - - + -
173B ALA* 3.8 27.8 - - + +
205B ALA 2.9 21.6 + - - +
206B GLN* 3.7 8.3 - - - +
207B GLN 3.3 0.2 - - - -
208B PHE* 1.3 78.0 - - + +
210B ALA* 1.3 58.1 + - - +
212B VAL* 3.2 2.9 + - - +
213B LYS* 2.8 57.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 210 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B GLN 2.9 18.0 + - - +
207B GLN* 3.6 7.6 - - - +
209B VAL* 1.3 78.4 - - - +
211B ALA* 1.3 62.1 + - - +
213B LYS* 3.4 6.7 + - - +
214B SER* 3.1 26.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 211 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B MET* 6.6 0.2 - - + -
120B LEU* 3.5 26.7 - - + +
207B GLN 3.0 14.0 + - - +
208B PHE* 3.6 9.4 - - + +
210B ALA* 1.3 75.6 - - - +
212B VAL* 1.3 63.5 + - - +
214B SER* 3.3 19.1 - - - -
215B LYS* 3.6 5.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 212 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B ILE* 5.0 2.7 - - + -
120B LEU* 4.0 19.7 - - + -
173B ALA* 3.8 21.8 - - + +
174B PHE* 3.5 38.8 - - + -
208B PHE* 2.9 44.4 + - + +
209B VAL 3.7 6.1 - - - +
211B ALA* 1.3 72.9 - - - +
213B LYS* 1.3 67.8 + - + +
215B LYS* 3.0 22.4 + - - +
216B PRO* 4.9 0.3 - - - +
217B PHE* 4.9 7.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 213 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B VAL 5.2 1.9 + - - -
173B ALA* 3.5 28.3 + - - +
176B PRO* 5.8 6.7 - - - +
209B VAL* 2.8 41.9 + - + +
210B ALA* 3.4 6.5 + - - +
212B VAL* 1.3 74.5 - - + +
214B SER* 1.3 60.8 + - - +
215B LYS 3.3 1.0 + - - -
216B PRO* 4.2 10.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 214 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B ALA 3.1 13.6 + - - -
211B ALA* 3.3 15.6 - - - -
212B VAL 3.1 0.2 - - - -
213B LYS* 1.3 76.4 - - - +
215B LYS* 1.3 68.6 + - - +
216B PRO* 3.3 10.4 - - - +
----------------------------------------------------------
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