Contacts of the strand formed by residues 185 - 194 (chain M) in PDB entry 3INU
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 185 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109L THR* 3.3 24.3 - - + +
146M ASP 2.8 29.8 + - - -
147M TYR* 2.9 48.7 + - + +
148M PHE* 3.7 28.4 - + - -
150M GLU* 3.8 47.2 + - + +
176M ALA* 4.2 7.2 - - + -
177M VAL* 3.5 16.6 - - - -
178M LEU* 4.1 19.7 - - + +
179M GLN* 3.5 1.6 - - - -
184M LEU* 1.3 74.6 - - - +
186M SER* 1.3 55.7 + - - +
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Residues in contact with SER 186 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143M LEU* 5.1 6.9 - - - +
144M VAL 3.4 5.6 - - - -
145M LYS* 3.0 28.5 - - - +
147M TYR* 4.0 1.1 - - - -
175M PRO 4.4 0.3 - - - +
176M ALA* 3.3 1.8 - - - -
177M VAL* 2.7 47.3 + - - +
179M GLN* 3.0 32.7 + - - -
185M TYR* 1.3 70.6 - - - +
187M LEU* 1.3 61.2 + - - +
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Residues in contact with LEU 187 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143M LEU* 5.0 2.7 - - - -
144M VAL* 2.8 38.7 + - + +
147M TYR* 3.7 22.7 - - + +
152M VAL* 3.8 22.2 - - + +
154M VAL* 3.9 22.9 - - + -
173M THR* 4.0 10.5 - - + -
174M PHE 3.4 21.5 - - - +
175M PRO 4.6 2.7 - - - -
176M ALA* 4.0 12.8 - - + +
186M SER* 1.3 78.7 - - - +
188M SER* 1.3 73.0 + - - +
189M SER 4.1 0.9 - - - +
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Residues in contact with SER 188 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124M LEU* 4.3 13.0 - - - -
142M CYS 3.2 11.4 - - - -
143M LEU* 4.2 16.8 - - - -
174M PHE* 2.9 37.1 + - - +
187M LEU* 1.3 78.8 - - - +
189M SER* 1.3 61.7 + - - +
190M VAL* 5.1 2.6 - - - +
133N VAL* 5.2 5.3 - - - +
176N SER* 3.5 26.0 + - - -
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Residues in contact with SER 189 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141M GLY* 3.0 2.3 - - - -
142M CYS* 2.7 38.9 + - - +
144M VAL* 5.9 0.2 - - - -
154M VAL* 3.7 24.3 - - - +
157M TRP* 3.0 24.7 + - - -
171M VAL* 4.4 0.3 - - - +
172M HIS 3.6 5.7 + - - -
173M THR* 2.9 29.7 + - - +
187M LEU* 4.1 1.2 - - - +
188M SER* 1.3 73.5 - - - +
190M VAL* 1.3 64.5 + - - +
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Residues in contact with VAL 190 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124M LEU* 4.7 11.9 - - + -
139M ALA* 5.6 0.7 - - + -
140M LEU 3.3 13.2 - - - +
141M GLY* 4.0 4.0 - - - -
157M TRP* 4.5 0.9 - - - -
169M GLY 5.4 0.2 - - - +
171M VAL* 3.5 3.8 - - - +
172M HIS* 2.9 56.8 + - + +
174M PHE* 4.0 19.5 - - + -
188M SER* 5.1 2.9 - - - +
189M SER* 1.3 81.0 + - - +
191M VAL* 1.3 68.6 + - - +
192M THR* 5.5 1.1 - - + +
118N PHE* 5.4 4.5 - - + -
133N VAL* 6.3 2.0 - - + -
135N LEU* 4.0 34.1 - - + -
137N ASN* 4.7 2.5 - - - +
176N SER* 5.7 1.8 - - - -
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Residues in contact with VAL 191 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139M ALA* 3.5 2.1 - - - -
140M LEU* 2.8 64.9 + - + +
157M TRP* 4.1 25.6 - - + -
166M LEU* 4.2 12.3 - - + -
168M SER 3.9 9.2 - - - +
169M GLY 3.3 12.3 - - - +
171M VAL* 3.8 20.9 - - + -
190M VAL* 1.3 79.8 - - - +
192M THR* 1.3 76.8 + - - +
193M VAL* 4.0 9.4 - - + -
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Residues in contact with THR 192 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137M THR* 4.6 15.3 - - - +
138M ALA 3.0 10.5 - - - +
139M ALA* 4.5 10.5 - - + -
166M LEU* 5.7 0.2 - - - +
168M SER 4.6 4.7 - - - +
169M GLY* 3.2 19.6 + - - +
172M HIS* 6.2 0.2 - - + -
190M VAL* 5.9 2.0 - - + -
191M VAL* 1.3 82.1 - - - +
193M VAL* 1.3 66.2 + - - +
194M PRO* 4.7 0.7 - - - +
116N PHE* 5.1 5.4 - - + -
135N LEU* 5.6 0.9 - - + -
137N ASN* 3.0 33.2 - - - +
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Residues in contact with VAL 193 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137M THR* 3.1 5.7 - - - -
138M ALA* 2.4 45.7 + - - +
140M LEU* 3.2 30.5 - - + -
166M LEU* 4.3 5.2 - - + -
191M VAL* 4.0 11.9 - - + -
192M THR* 1.3 82.2 - - - +
194M PRO* 1.3 73.9 - - + +
197M SER* 4.2 0.4 - - - +
198M LEU* 4.1 19.7 - - + -
206M TYR* 3.6 37.7 - - + +
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Residues in contact with PRO 194 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134M GLY 3.2 13.9 - - - +
137M THR* 4.2 5.6 - - + -
192M THR 4.7 0.9 - - - +
193M VAL* 1.3 86.7 - - + +
195M SER* 1.3 67.6 + - - +
196M SER* 2.9 21.7 + - - +
197M SER* 2.9 28.2 + - - +
198M LEU* 3.5 5.6 + - - +
206M TYR* 4.8 1.3 - - - +
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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