Contacts of the helix formed by residues 184 - 199 (chain U) in PDB entry 5IYB
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 ASP 184 (chain U).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180U ILE* 4.7 5.6 - - + -
182U ASN* 3.1 30.6 + - + +
183U THR* 1.3 81.1 - - - +
185U MET* 1.3 69.4 + - - +
186U LYS* 3.2 29.3 + - + +
187U TYR* 3.1 8.3 + - - +
188U LYS* 2.9 26.0 + - - +
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Residues in contact with MET 185 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1199A MET* 4.7 15.7 - - + +
1200A PRO* 4.0 31.9 - - + -
183U THR 5.3 0.4 - - - +
184U ASP* 1.3 79.5 - - - +
186U LYS* 1.3 53.6 + - - +
188U LYS* 3.1 28.4 + - - +
189U ASN* 2.6 52.0 + - - +
192U ARG* 6.1 0.2 - - - -
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Residues in contact with LYS 186 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1229A GLU* 6.0 2.9 - - - +
1233A GLU* 4.1 26.6 + - - -
2E ASP 5.8 1.8 + - - -
180U ILE* 5.0 15.3 - - + -
184U ASP* 3.2 17.6 + - + +
185U MET* 1.3 76.3 - - - +
187U TYR* 1.3 63.7 + - - +
189U ASN* 4.0 8.0 - - - +
190U ARG* 3.1 38.4 + - - +
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Residues in contact with TYR 187 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140U VAL* 6.2 2.2 - - + -
141U ARG* 4.5 7.8 + - + +
144U CYS* 4.7 16.6 - - - +
173U GLU* 2.7 36.2 + - - +
176U ILE* 3.5 30.9 - - + +
177U TYR* 4.1 21.5 - + + -
180U ILE* 3.5 29.9 - - + +
182U ASN 3.3 26.9 - - - +
183U THR* 4.4 9.9 - - + -
184U ASP 3.1 7.6 + - - +
186U LYS* 1.3 78.6 - - - +
188U LYS* 1.3 73.9 + - + +
190U ARG* 3.2 4.7 + - - +
191U VAL* 2.9 43.8 + - + +
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Residues in contact with LYS 188 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1198A GLU* 5.0 17.7 + - + +
1199A MET* 6.3 0.2 - - - -
1200A PRO* 5.4 4.5 - - + +
140U VAL* 4.7 19.3 - - + +
144U CYS* 5.5 8.1 - - - -
183U THR* 3.2 24.8 + - - +
184U ASP 2.9 14.1 + - - +
185U MET* 3.1 31.9 + - - +
187U TYR* 1.3 89.2 - - + +
189U ASN* 1.3 54.0 + - - +
191U VAL* 3.4 5.4 + - - +
192U ARG* 2.8 55.6 + - - +
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Residues in contact with ASN 189 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1196A TYR* 5.3 0.2 - - - -
1199A MET* 4.8 7.8 - - - +
1229A GLU* 5.7 8.0 - - + +
1247A PHE* 4.3 31.4 - - + -
185U MET* 2.6 37.7 + - - +
186U LYS* 4.0 7.5 - - - +
188U LYS* 1.3 71.6 - - - +
190U ARG* 1.3 52.4 + - - +
192U ARG* 2.6 36.0 + - - +
193U SER* 2.7 37.9 + - - -
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Residues in contact with ARG 190 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1229A GLU* 5.0 15.6 + - - -
176U ILE* 4.9 14.6 - - + -
179U GLU* 5.1 13.8 - - - +
180U ILE* 4.8 16.9 - - - +
186U LYS* 3.1 34.2 + - - +
187U TYR* 3.2 6.3 + - - +
189U ASN* 1.3 73.4 - - - +
191U VAL* 1.3 63.7 + - - +
193U SER* 2.8 20.3 + - - +
194U ARG* 3.0 40.9 + - + +
221U ALA 4.4 17.0 + - - +
222U ARG* 5.6 3.8 - - - +
223U MET* 6.1 4.2 - - + +
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Residues in contact with VAL 191 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144U CYS* 4.9 15.5 - - + -
147U MET* 5.9 0.9 - - + -
148U LEU* 4.2 22.2 - - + -
173U GLU* 5.6 1.3 - - + -
176U ILE* 3.6 25.4 - - + -
187U TYR* 2.9 48.0 + - + +
188U LYS* 3.7 5.8 - - - +
190U ARG* 1.3 76.0 - - - +
192U ARG* 1.3 52.9 + - - +
194U ARG* 3.1 9.2 + - - +
195U ILE* 2.8 49.8 + - + +
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Residues in contact with ARG 192 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1195A VAL* 3.4 39.9 + - + +
1196A TYR* 3.7 33.9 + - - -
1198A GLU* 2.9 28.9 + - - +
1199A MET* 3.9 20.7 - - - +
1247A PHE* 5.6 1.6 - - - -
147U MET* 6.1 0.2 - - + -
188U LYS* 2.8 45.3 + - - +
189U ASN* 2.6 38.8 + - - +
191U VAL* 1.3 72.7 - - - +
193U SER* 1.3 56.7 + - - +
195U ILE* 3.3 19.3 + - + +
196U SER* 2.9 28.9 + - - -
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Residues in contact with SER 193 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1247A PHE* 5.7 9.2 - - - -
1249A ASP* 4.2 2.8 - - - +
189U ASN 2.7 19.2 + - - -
190U ARG* 2.8 26.7 + - - +
192U ARG* 1.3 70.2 - - - +
194U ARG* 1.3 72.2 + - - +
196U SER* 3.0 19.5 + - - -
197U ASN* 3.2 15.9 + - - +
223U MET* 5.8 1.9 - - - +
227U GLU* 5.4 8.7 - - - +
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Residues in contact with ARG 194 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148U LEU* 4.8 5.6 - - + -
176U ILE* 4.5 13.0 - - + -
190U ARG* 3.0 42.3 + - - +
191U VAL* 3.2 12.1 - - - +
193U SER* 1.3 84.5 + - - +
195U ILE* 1.3 56.0 + - - +
197U ASN* 3.4 7.2 + - - +
198U LEU* 3.0 35.3 + - - +
220U PHE* 3.5 45.1 + - + +
221U ALA 3.0 24.6 + - - -
222U ARG* 3.4 1.4 - - - +
223U MET* 3.1 58.3 - - - +
228U MET* 5.2 5.9 - - - +
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Residues in contact with ILE 195 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1195A VAL* 5.9 4.3 - - + -
147U MET* 4.1 35.7 - - + +
148U LEU* 3.6 24.2 - - + -
151U ALA* 4.1 11.4 - - + +
191U VAL* 2.8 37.7 + - + +
192U ARG* 3.3 19.7 - - + +
194U ARG* 1.3 73.7 - - - +
196U SER* 1.3 58.0 + - - +
198U LEU* 3.3 9.3 + - - +
199U LYS* 3.0 47.1 + - + +
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Residues in contact with SER 196 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1195A VAL* 5.3 15.7 - - - -
1249A ASP* 2.9 44.0 + - - +
192U ARG 2.9 15.5 + - - -
193U SER* 3.0 16.8 + - - -
195U ILE* 1.3 74.2 - - - +
197U ASN* 1.3 56.5 + - - +
199U LYS* 3.1 24.9 + - - +
200U ASP* 3.4 10.6 + - - -
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Residues in contact with ASN 197 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1249A ASP* 3.7 6.7 - - - +
1251A ASN* 2.4 36.9 + - - +
193U SER 3.2 15.7 + - - +
194U ARG* 3.7 7.0 - - - +
196U SER* 1.3 81.0 + - - +
198U LEU* 1.3 61.7 + - - +
199U LYS 3.5 0.2 + - - -
200U ASP* 3.5 20.3 + - - +
203U ASN 5.2 1.6 - - - +
206U LEU* 3.1 31.6 - - - +
220U PHE* 5.2 6.5 - - + -
227U GLU* 4.3 2.6 - - - +
228U MET* 3.0 33.1 + - - +
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Residues in contact with LEU 198 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148U LEU* 4.7 12.8 - - + -
151U ALA* 4.4 15.9 - - + +
152U LEU* 3.9 34.3 - - + -
154U THR* 5.1 0.2 - - - -
172U ILE* 5.2 1.3 - - + -
194U ARG 3.0 20.8 + - - +
195U ILE* 3.5 7.9 - - - +
197U ASN* 1.3 76.6 - - - +
199U LYS* 1.3 58.6 + - - +
200U ASP 3.2 2.9 + - - -
206U LEU* 5.5 4.7 - - + -
207U ARG* 3.0 52.4 + - + +
210U VAL* 4.6 9.2 - - + -
220U PHE* 3.5 38.8 - - + -
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Residues in contact with LYS 199 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1191A GLU* 4.1 25.5 + - - +
1194A ASN* 4.5 17.7 + - - +
1195A VAL* 3.6 27.6 - - + +
151U ALA* 4.3 14.1 - - + -
154U THR* 4.5 22.1 - - + +
195U ILE* 3.0 39.7 + - + +
196U SER* 3.1 12.7 + - - +
198U LEU* 1.3 76.8 - - - +
200U ASP* 1.3 64.2 + - - +
201U ALA* 3.3 4.9 + - - +
207U ARG* 4.9 1.8 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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