Contacts of the helix formed by residues 177 - 194 (chain B) in PDB entry 1J38
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 VAL 177 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B ALA* 4.6 3.1 - - + +
123B MET* 3.7 31.9 - - + +
126B ASN* 4.7 12.1 - - + +
173B ALA 4.1 4.9 - - - +
174B GLY 2.9 16.4 + - - +
175B THR 2.7 5.3 + - - -
176B ALA* 1.3 77.2 - - - +
178B ARG* 1.3 61.3 + - - -
179B SER 3.3 2.7 - - - +
180B GLN* 3.1 37.7 - - + +
181B PHE* 3.2 15.1 + - - +
490B PHE* 4.8 0.4 - - - -
493B PRO* 3.6 23.6 - - + -
499B SER* 5.0 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 178 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B GLY 4.1 0.6 + - - -
175B THR 3.3 10.3 + - - +
176B ALA 3.8 0.4 - - - -
177B VAL* 1.3 76.3 - - - +
179B SER* 1.3 57.2 + - - +
181B PHE* 3.5 1.2 + - - +
182B GLU* 2.9 55.6 + - - +
462B LYS* 2.7 35.2 + - - +
465B TRP* 3.3 29.5 - - + +
487B GLU* 4.9 13.2 + - - -
488B LYS 5.5 3.8 - - - -
489B ASP 5.1 2.2 + - - -
490B PHE* 3.5 49.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 179 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B VAL 3.3 0.4 - - - -
178B ARG* 1.3 76.3 - - - +
180B GLN* 1.3 83.3 + - - +
182B GLU* 3.1 9.8 + - - +
183B ARG* 3.0 20.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 180 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B THR* 3.6 19.1 + - - +
122B ALA* 3.4 30.4 - - + +
123B MET* 3.5 13.5 - - + -
176B ALA 4.2 3.0 + - - +
177B VAL* 3.1 41.5 - - + +
179B SER* 1.3 81.6 - - - +
181B PHE* 1.3 66.4 + - - +
183B ARG* 3.0 6.5 + - - +
184B TYR* 2.8 23.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 181 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B MET* 3.6 24.3 - - + -
177B VAL 3.2 15.9 + - - +
178B ARG 3.7 3.4 - - - +
180B GLN* 1.3 80.6 - - - +
182B GLU* 1.3 60.7 + - - +
184B TYR* 3.2 24.7 - + - +
185B VAL* 3.0 32.4 + - + +
451B TYR* 4.9 4.5 - + - -
452B ARG* 4.7 13.9 - - + -
455B LEU* 3.5 28.5 - - + -
465B TRP* 3.9 6.7 - + - -
490B PHE* 3.2 38.8 - + + -
493B PRO* 4.5 4.9 - - + -
498B ILE* 3.6 33.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 182 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B ARG* 2.9 36.7 + - - +
179B SER* 3.1 8.1 + - - +
180B GLN 3.1 0.2 + - - -
181B PHE* 1.3 71.4 - - - +
183B ARG* 1.3 66.6 + - - +
185B VAL* 3.3 3.8 + - - +
186B GLU* 3.1 34.2 + - - +
462B LYS* 2.5 38.6 + - - +
465B TRP* 3.6 30.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 183 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B ASP* 4.5 7.3 + - - -
115B GLU* 2.6 40.0 + - - +
119B THR* 4.1 22.4 - - + -
179B SER 3.0 10.7 + - - +
180B GLN* 3.0 9.2 + - - +
182B GLU* 1.3 75.8 - - - +
184B TYR* 1.3 57.3 + - - +
186B GLU* 3.3 26.4 + - - +
187B LEU* 2.8 74.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 184 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B TYR* 3.7 20.0 - + - -
116B LEU* 4.1 13.5 - - + -
119B THR* 4.0 12.3 + - - +
120B LEU* 3.7 15.7 - - + -
123B MET* 4.1 11.9 - - + -
180B GLN 2.8 12.5 + - - +
181B PHE* 3.2 42.2 - + - +
182B GLU 3.1 0.2 - - - -
183B ARG* 1.3 75.0 - - - +
185B VAL* 1.3 64.9 + - + +
187B LEU 2.9 1.7 + - - -
188B ASN* 2.5 47.7 + - + +
204B TRP* 4.2 4.5 - - - -
452B ARG* 4.8 5.1 + - - -
456B PHE* 3.8 26.1 - + - -
498B ILE 4.9 3.3 + - - -
501B ASP* 2.5 38.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 185 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B PHE* 3.0 35.3 + - + +
182B GLU 3.7 7.2 - - - +
184B TYR* 1.3 84.7 - - + +
186B GLU* 1.3 57.7 + - + +
188B ASN* 3.7 6.8 - - - +
189B THR* 2.7 45.2 + - - +
455B LEU* 4.1 30.3 - - + +
456B PHE* 4.1 20.2 - - + -
462B LYS* 6.1 0.4 - - - -
465B TRP* 4.1 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 186 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B GLU* 3.1 19.2 + - + +
183B ARG* 3.3 40.2 + - - +
184B TYR 3.1 0.8 - - - -
185B VAL* 1.3 79.8 - - + +
187B LEU* 1.3 60.5 + - - +
189B THR* 3.8 5.6 - - - -
190B LYS* 3.2 23.7 + - - +
462B LYS* 4.2 21.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 187 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B LEU* 4.0 8.5 - - + +
112B ASP* 4.0 33.2 - - + +
115B GLU* 4.3 7.4 - - - +
116B LEU* 3.9 39.3 - - + +
119B THR* 5.0 0.7 - - + -
183B ARG* 2.8 63.5 + - + +
184B TYR 3.6 1.8 - - - +
186B GLU* 1.3 74.4 - - - +
188B ASN* 1.3 68.6 + - - +
189B THR 3.0 1.1 - - - -
190B LYS* 2.9 14.6 + - + +
191B ALA* 2.9 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 188 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B TYR* 2.6 42.1 + - - +
116B LEU* 5.0 1.2 - - - +
184B TYR* 2.5 36.5 + - + +
185B VAL* 3.7 6.3 - - - +
187B LEU* 1.3 72.8 - - - +
189B THR* 1.3 62.3 + - - +
191B ALA* 3.6 3.1 + - - +
192B ALA* 3.2 19.2 + - - +
200B GLY* 3.4 23.8 + - - -
204B TRP* 5.0 4.9 - - - +
456B PHE* 3.6 32.0 - - + -
501B ASP* 4.8 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 189 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B VAL* 2.7 26.2 + - - +
186B GLU* 3.8 6.5 - - - -
188B ASN* 1.3 79.2 + - - +
190B LYS* 1.3 66.0 + - - +
192B ALA* 3.1 14.8 + - - +
193B LYS* 3.2 37.4 + - - +
199B SER* 4.5 8.1 - - - -
200B GLY 4.5 1.6 - - - +
456B PHE* 3.7 30.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 190 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B LEU* 4.0 9.2 - - + -
109B PRO* 4.3 13.4 - - - +
112B ASP* 2.8 32.8 + - - +
186B GLU 3.2 13.3 + - - +
187B LEU* 2.9 19.1 + - + +
189B THR* 1.3 79.8 - - - +
191B ALA* 1.3 62.9 + - - +
192B ALA 3.2 0.2 + - - -
193B LYS* 3.3 7.2 + - - +
194B LEU* 3.1 41.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 191 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B GLY 4.1 3.1 - - - +
105B TYR* 3.7 38.4 - - + -
108B LEU* 3.3 25.3 - - + +
187B LEU 2.9 12.3 + - - +
188B ASN 3.9 2.0 - - - +
190B LYS* 1.3 76.3 - - - +
192B ALA* 1.3 58.3 + - - +
194B LEU* 3.5 9.7 + - - +
195B ASN* 2.6 30.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 192 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B ASN 3.2 9.1 + - - +
189B THR 3.1 9.8 + - - +
190B LYS 3.1 0.6 - - - -
191B ALA* 1.3 78.6 - - - +
193B LYS* 1.3 58.1 + - - +
195B ASN* 3.1 15.7 + - - +
196B ASN 3.4 0.2 + - - -
197B PHE* 2.9 33.6 + - + +
199B SER* 3.3 12.1 - - - +
200B GLY* 3.2 35.2 - - - +
203B ALA* 4.7 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 193 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B THR* 3.2 31.9 + - + +
190B LYS* 3.3 7.8 + - - +
192B ALA* 1.3 75.2 - - - +
194B LEU* 1.3 66.4 + - + +
195B ASN 3.1 0.2 - - - -
196B ASN* 3.3 14.4 + - - +
197B PHE 3.4 16.2 - - - +
198B THR* 3.3 22.4 + - - +
199B SER* 5.5 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 194 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B ALA* 3.1 44.9 - - + +
108B LEU* 3.8 15.3 - - + -
109B PRO* 4.1 11.4 - - + -
190B LYS* 3.1 39.3 + - + +
191B ALA 3.7 3.4 - - - +
192B ALA 3.1 1.0 - - - -
193B LYS* 1.3 82.5 - - + +
195B ASN* 1.3 61.6 + - - +
196B ASN* 3.4 4.2 + - - -
----------------------------------------------------------
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