Contacts of the helix formed by residues 184 - 200 (chain J) in PDB entry 1MVW
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 GLY 184 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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127J ASN* 4.8 6.3 - - - -
180J GLU 4.4 0.4 + - - -
181J SER 4.6 2.8 + - - -
182J GLY 3.1 6.2 + - - -
183J ALA* 1.3 78.6 - - - +
185J LYS* 1.3 64.5 + - - +
186J THR* 5.8 0.2 - - - -
187J VAL* 3.3 28.1 - - - +
188J ASN* 3.1 19.6 + - - -
240J ASN* 4.9 11.2 - - - +
674J CYS* 4.8 0.2 - - - -
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Residues in contact with LYS 185 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177J ILE* 3.6 20.2 - - + +
178J THR* 4.3 2.7 - - - -
179J GLY* 2.9 45.8 - - - +
180J GLU 3.9 11.6 + - - +
181J SER* 4.9 8.0 + - - +
184J GLY* 1.3 75.3 - - - +
186J THR* 1.3 55.4 + - - +
187J VAL 3.0 2.2 - - - -
188J ASN* 2.6 29.7 + - - +
189J THR* 2.5 24.0 + - - +
243J SER* 5.8 1.0 + - - -
244J SER* 4.6 18.8 + - - +
463J ASP* 4.4 16.7 + - - +
464J ILE 3.8 20.2 + - - +
465J ALA* 4.6 7.2 - - - +
674J CYS* 4.2 6.7 - - + -
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Residues in contact with THR 186 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184J GLY* 3.7 0.4 - - - -
185J LYS* 1.3 75.2 + - - +
187J VAL* 1.3 58.1 + - - +
189J THR* 3.1 7.1 + - - -
190J MLY 2.6 46.9 + - - +
230J GLU* 3.6 23.8 - - + +
234J ASN* 4.6 5.0 + - - +
240J ASN* 5.5 2.4 + - - -
242J ASN* 4.5 8.8 + - - -
244J SER* 3.7 28.8 + - - +
248J MLY 3.3 31.4 - - - -
463J ASP* 3.8 4.3 + - - -
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Residues in contact with VAL 187 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135J TYR* 5.5 6.1 - - + -
184J GLY* 3.3 32.5 - - - +
186J THR* 1.3 78.6 - - - +
188J ASN* 1.3 63.0 + - - +
190J MLY 3.7 15.7 - - - +
191J ARG* 3.0 46.3 + - - +
240J ASN* 5.5 5.4 - - - +
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Residues in contact with ASN 188 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116J TYR* 4.4 1.2 + - - -
125J THR* 4.1 14.5 - - - +
135J TYR* 3.9 17.3 + - - -
155J ILE* 3.3 30.4 - - + +
177J ILE* 4.8 7.4 - - + -
183J ALA 5.1 0.2 + - - -
184J GLY 3.1 14.8 + - - -
185J LYS* 2.6 12.0 + - - +
187J VAL* 1.3 75.7 - - - +
189J THR* 1.3 54.0 + - - +
191J ARG* 2.8 8.0 + - - +
192J VAL* 2.6 41.4 + - + +
674J CYS* 2.9 35.3 - - - +
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Residues in contact with THR 189 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177J ILE* 4.4 10.1 - - + +
185J LYS* 2.5 26.1 + - - +
186J THR* 3.3 6.1 - - - -
188J ASN* 1.3 71.9 - - - +
190J MLY 1.3 64.1 + - - +
192J VAL* 3.0 9.5 + - - +
193J ILE* 2.9 31.1 + - + +
248J MLY 4.8 15.7 - - + -
250J ILE* 5.0 2.5 - - + -
461J VAL* 3.7 26.5 - - + +
463J ASP* 3.1 35.9 + - + +
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Residues in contact with MLY 190 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186J THR* 2.6 39.2 + - + +
187J VAL* 3.7 15.5 - - - +
189J THR* 1.3 72.2 + - - +
191J ARG* 1.3 99.7 + - - +
193J ILE* 2.8 26.1 + - - +
194J GLN* 2.9 20.7 + - - +
226J ASN* 4.1 30.5 - - + +
227J PRO* 6.1 1.8 - - - -
230J GLU* 2.8 43.5 - - - +
242J ASN* 4.0 9.0 - - - -
248J MLY 4.8 5.2 - - - -
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Residues in contact with ARG 191 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135J TYR* 3.1 46.7 - - + -
155J ILE* 5.8 5.2 - - + -
156J PHE* 4.4 15.3 - - + -
187J VAL* 3.0 36.7 + - - +
188J ASN* 2.8 6.7 + - - +
190J MLY 1.3 114.5 + - - +
192J VAL* 1.3 61.2 + - - +
194J GLN* 3.6 29.0 + - + +
195J TYR* 3.3 18.5 + - - +
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Residues in contact with VAL 192 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155J ILE* 4.4 26.7 - - + +
158J ILE* 6.5 0.7 - - + -
159J SER* 4.0 13.5 - - - -
175J ILE* 4.7 11.7 - - + -
177J ILE* 4.4 13.7 - - + -
188J ASN 2.6 26.1 + - - +
189J THR* 3.3 9.0 - - - +
191J ARG* 1.3 72.8 - - - +
193J ILE* 1.3 62.9 + - + +
195J TYR* 2.8 27.4 - - - +
196J PHE* 3.1 30.7 + - + -
461J VAL* 4.8 9.6 - - + -
672J VAL* 6.4 0.9 - - + -
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Residues in contact with ILE 193 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189J THR* 3.0 20.2 - - + +
190J MLY 2.8 13.5 + - - +
192J VAL* 1.3 76.6 - - + +
194J GLN* 1.3 64.7 + - - +
196J PHE* 3.0 17.5 + - - +
197J ALA* 3.0 12.0 + - + +
222J ILE* 4.0 28.7 - - + +
223J ILE* 5.3 6.3 - - + -
226J ASN* 5.6 8.1 - - - +
248J MLY 5.6 2.9 - - - -
250J ILE* 3.1 37.7 - - + -
252J ILE* 3.9 24.2 - - + -
461J VAL* 4.7 7.9 - - + -
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Residues in contact with GLN 194 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190J MLY 2.9 17.9 + - - +
191J ARG* 3.8 37.0 + - + +
193J ILE* 1.3 73.9 - - - +
195J TYR* 1.3 54.9 + - - +
197J ALA* 2.9 5.2 + - - +
198J THR* 2.5 42.4 + - + +
223J ILE* 3.2 39.1 - - + +
226J ASN* 6.0 0.5 + - - -
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Residues in contact with TYR 195 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140J VAL* 3.4 36.7 + - + -
143J TYR* 3.9 6.2 + - - +
144J ARG* 4.0 1.0 + - - +
156J PHE* 2.9 41.0 - + + -
159J SER* 2.8 33.4 - - - +
160J ASP* 2.4 31.8 + - + +
191J ARG 3.3 10.2 + - - +
192J VAL* 2.8 16.4 + - - +
194J GLN* 1.3 80.1 - - - +
196J PHE* 1.3 63.2 + + - +
198J THR* 3.0 14.2 + - - -
199J ILE* 2.9 55.2 + - + +
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Residues in contact with PHE 196 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159J SER* 3.1 34.3 - - - -
162J ALA* 4.3 4.7 - - + -
163J TYR* 4.0 15.3 - + + -
175J ILE* 4.2 5.4 - - + -
192J VAL* 3.1 37.5 + - + -
193J ILE* 3.0 7.8 + - - +
195J TYR* 1.3 82.0 - + + +
197J ALA* 1.3 67.3 + - - +
198J THR 3.2 0.2 + - - -
199J ILE* 3.9 11.3 - - + -
200J ALA* 3.3 23.6 + - - +
252J ILE* 4.6 18.6 - - + -
254J PHE* 3.6 29.3 - + + -
260J LEU* 5.0 2.2 - - + -
459J ILE* 3.7 42.6 - - + -
461J VAL* 4.9 1.6 - - + -
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Residues in contact with ALA 197 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193J ILE 3.0 10.0 + - - +
194J GLN* 2.9 11.3 + - - +
196J PHE* 1.3 79.9 - - - +
198J THR* 1.3 63.3 + - - +
201J ALA* 3.0 28.0 + - - +
219J GLU* 4.3 24.0 - - + +
222J ILE* 5.2 6.3 - - + -
223J ILE* 4.9 7.2 - - + -
260J LEU* 3.9 19.5 - - + -
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Residues in contact with THR 198 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140J VAL* 5.1 12.3 - - + +
194J GLN* 2.5 32.4 + - + +
195J TYR* 3.0 12.1 + - - -
197J ALA* 1.3 76.3 - - + +
199J ILE* 1.3 60.9 + - - +
200J ALA 2.8 7.1 + - - -
201J ALA* 3.7 8.3 + - - +
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Residues in contact with ILE 199 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140J VAL* 4.8 7.6 - - + +
144J ARG* 4.5 17.1 + - + +
160J ASP* 4.1 6.7 - - - +
163J TYR* 4.3 22.0 + - + -
195J TYR* 2.9 69.1 + - + +
196J PHE* 4.1 19.7 - - + +
198J THR* 1.3 74.4 - - - +
200J ALA* 1.3 64.2 + - + +
259J LYS* 4.5 5.4 + - - -
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Residues in contact with ALA 200 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163J TYR* 3.1 35.2 - - + +
196J PHE 3.3 11.5 + - - +
197J ALA 3.8 3.1 - - - -
198J THR 2.8 9.5 + - - -
199J ILE* 1.3 80.9 - - + +
201J ALA* 1.3 60.2 + - - +
254J PHE* 4.3 5.8 - - + -
258J GLY 3.6 7.0 - - - +
259J LYS* 3.7 13.0 - - - +
260J LEU* 3.1 28.4 + - - +
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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
------------------------------------------------------------
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