Contacts of the helix formed by residues 178 - 195 (chain J) in PDB entry 5XTD
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 SER 178 (chain J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175J LYS* 5.2 0.2 - - - +
176J SER 3.7 1.4 + - - -
177J SER* 1.3 80.1 + - - +
179J ARG* 1.3 56.0 - - - +
180J TYR 3.1 1.1 - - - -
181J LEU* 2.6 32.6 - - - +
182J ARG* 2.7 26.2 + - - +
299J ARG* 5.9 2.6 - - - +
316J ARG 5.4 1.2 + - - -
317J ASP* 3.4 34.8 - - - +
320J GLU* 3.8 8.7 - - - +
321J ARG* 4.3 7.6 - - - -
324J ILE* 3.2 16.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 179 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135J GLU* 3.6 29.1 + - - -
141J PHE* 4.6 6.9 - - + +
142J GLU* 5.4 4.2 + - - +
176J SER 5.0 2.0 - - - +
178J SER* 1.3 69.3 - - - +
180J TYR* 1.3 54.4 + - - +
182J ARG* 3.3 34.3 - - - +
183J ASN* 2.6 60.0 + - - +
299J ARG* 6.3 0.7 - - - +
317J ASP* 4.7 1.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 180 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132J ARG 4.5 3.8 - - - -
133J ASP* 3.4 22.5 + - - +
141J PHE* 2.8 48.7 - + + -
145J PHE* 3.5 14.1 - + - -
169J HIS* 5.5 3.8 - + + +
179J ARG* 1.3 78.1 - - - +
181J LEU* 1.3 67.9 + - + +
183J ASN* 3.3 2.9 + - - +
184J LYS* 3.1 40.6 + - + +
317J ASP* 2.9 35.5 + - - +
321J ARG* 3.6 25.6 + - - -
401J NDP 2.4 49.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 181 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169J HIS* 5.0 2.2 - - + +
171J ASN* 1.9 62.1 - - + +
172J ALA* 3.1 15.4 - - - +
173J ASN 4.5 5.6 - - - +
175J LYS* 5.1 4.5 - - + -
177J SER 4.5 0.4 - - - +
178J SER* 2.6 23.9 + - - +
180J TYR* 1.3 91.4 - - + +
182J ARG* 1.3 58.7 + - - +
184J LYS* 3.4 18.9 + - + +
321J ARG* 4.7 11.9 - - + -
324J ILE* 3.3 28.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 182 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172J ALA 4.9 2.5 - - - -
174J ILE* 3.5 33.8 - - + +
175J LYS 2.8 21.9 + - - +
176J SER* 2.2 50.7 + - - +
177J SER 4.2 0.6 + - - -
178J SER 2.7 14.8 + - - +
179J ARG* 3.3 42.3 - - - +
181J LEU* 1.3 74.5 - - - +
183J ASN* 1.3 62.0 + - - +
185J ALA* 3.3 19.4 + - - +
186J VAL* 3.8 9.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 183 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141J PHE* 2.8 40.2 - - + -
142J GLU* 2.9 30.1 + - - +
145J PHE* 3.8 18.1 - - + +
146J VAL* 4.7 3.6 - - - +
179J ARG* 2.6 44.2 + - - +
180J TYR 3.6 0.7 - - - +
181J LEU 3.3 0.2 - - - -
182J ARG* 1.3 73.3 - - - +
184J LYS* 1.3 63.2 + - - +
186J VAL* 3.0 13.5 + - - +
187J GLY 3.0 17.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 184 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145J PHE* 3.1 40.6 - - + -
166J HIS* 5.3 0.9 - - - -
167J VAL 3.6 6.5 + - - -
168J SER* 3.0 53.6 + - - +
169J HIS* 3.6 15.7 - - + -
171J ASN 4.8 2.0 - - - +
172J ALA* 4.3 9.9 - - + -
180J TYR* 3.1 34.0 + - + +
181J LEU* 3.5 12.1 - - + +
182J ARG 3.2 0.2 - - - -
183J ASN* 1.3 75.9 - - - +
185J ALA* 1.3 52.6 + - - +
187J GLY* 3.1 1.9 + - - +
188J GLU* 2.6 38.0 + - - +
401J NDP 3.4 13.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 185 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172J ALA* 3.0 25.9 + - - +
173J ASN* 5.0 0.7 - - - -
174J ILE* 4.6 13.7 - - + +
181J LEU 3.9 1.4 + - - -
182J ARG 3.3 11.1 + - - +
184J LYS* 1.3 80.7 - - - +
186J VAL* 1.3 61.9 + - + +
188J GLU* 3.4 15.0 + - - +
189J LYS* 3.1 24.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 186 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142J GLU* 5.2 2.5 - - - +
146J VAL* 4.2 22.9 - - + -
174J ILE* 6.3 2.2 - - + -
182J ARG* 4.1 13.9 - - + +
183J ASN* 3.0 14.4 + - - +
185J ALA* 1.3 75.2 - - + +
187J GLY* 1.3 61.5 + - - +
189J LYS* 3.3 5.7 + - - +
190J VAL* 2.9 45.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 187 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145J PHE* 3.0 26.5 + - - -
146J VAL* 5.1 0.2 - - - -
149J PRO* 5.3 2.2 - - - -
166J HIS* 4.9 7.9 - - - -
183J ASN 3.0 11.0 + - - -
184J LYS* 3.5 2.7 - - - -
186J VAL* 1.3 74.4 - - - +
188J GLU* 1.3 66.6 + - - +
190J VAL* 4.5 4.5 - - - -
191J VAL* 2.9 35.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 188 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166J HIS* 5.3 1.1 - - - -
168J SER* 4.0 11.4 + - - +
172J ALA* 4.0 8.3 - - - +
173J ASN* 5.5 1.9 - - - +
184J LYS 2.6 19.6 + - - +
185J ALA* 3.5 10.5 - - - +
187J GLY* 1.3 73.7 - - - +
189J LYS* 1.3 57.3 + - - +
191J VAL* 3.9 2.1 - - - +
192J ARG* 2.9 30.5 + - + +
200J ILE* 3.6 28.9 - - + +
202J LYS* 2.6 41.9 + - - -
262J SER* 4.8 6.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 189 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185J ALA 3.1 16.4 + - - +
186J VAL* 3.8 5.2 - - - +
188J GLU* 1.3 78.1 - - + +
190J VAL* 1.3 62.8 + - + +
192J ARG* 2.9 10.6 + - + +
193J ASP* 2.9 41.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 190 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146J VAL* 4.4 12.6 - - + +
149J PRO* 6.3 0.2 - - + -
150J GLN* 3.3 51.1 - - + +
186J VAL* 2.9 34.5 + - + +
187J GLY* 4.1 4.9 - - - +
189J LYS* 1.3 77.0 - - + +
191J VAL* 1.3 58.8 + - + +
193J ASP* 3.1 6.8 + - - +
194J ALA* 2.9 29.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 191 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149J PRO* 3.7 29.4 - - + +
150J GLN 4.8 0.2 - - - +
153J ALA* 4.6 6.1 - - - -
164J PHE* 3.4 27.8 - - + -
166J HIS* 3.6 27.4 - - + +
187J GLY* 2.9 21.8 + - - +
188J GLU 4.0 2.0 - - - +
190J VAL* 1.3 76.7 - - + +
192J ARG* 1.3 63.6 + - - +
193J ASP 3.2 0.7 + - - -
195J PHE* 3.1 24.1 + - - +
198J ALA* 3.9 4.9 - - + +
200J ILE* 3.8 22.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 192 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188J GLU* 2.9 24.9 + - + +
189J LYS* 2.9 15.1 + - + +
191J VAL* 1.3 78.2 - - - +
193J ASP* 1.3 62.8 + - - +
195J PHE 4.6 1.3 - - - -
196J PRO* 3.0 33.2 + - - +
198J ALA* 2.6 25.0 + - - -
200J ILE* 3.1 30.1 - - + +
260J GLY* 2.6 38.5 + - - -
261J LYS 4.0 0.4 + - - -
262J SER* 3.4 22.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 193 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189J LYS* 2.9 31.2 + - - +
190J VAL* 3.8 4.9 - - - +
192J ARG* 1.3 87.6 - - - +
194J ALA* 1.3 66.6 + - - +
195J PHE 3.1 2.3 + - - -
196J PRO* 3.4 15.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 194 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150J GLN* 4.2 15.3 - - + +
153J ALA* 3.7 23.5 - - + +
154J GLN* 3.7 28.0 - - + +
157J LYS* 4.3 11.6 - - - +
190J VAL 2.9 19.2 + - - +
193J ASP* 1.3 74.4 - - - +
195J PHE* 1.3 59.8 + - - +
196J PRO* 3.8 3.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 195 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153J ALA* 3.4 35.0 - - + +
156J SER* 3.8 8.3 - - - -
157J LYS* 3.4 37.2 - - + -
160J GLY 5.7 0.4 - - - -
161J VAL* 3.6 22.0 - - + -
162J GLU 5.4 0.7 - - - -
163J LYS* 5.2 1.6 - - - -
164J PHE* 3.4 37.9 - - + -
191J VAL 3.1 16.8 + - - +
194J ALA* 1.3 79.2 - - - +
196J PRO* 1.3 60.6 - - - +
197J GLU* 2.9 35.0 - - + -
198J ALA* 2.9 30.7 + - + +
----------------------------------------------------------
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