Contacts of the strand formed by residues 206 - 212 (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 206 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126M PRO* 6.3 0.7 - - + -
140M LEU* 3.3 32.8 - - + -
157M TRP* 4.5 8.5 - + + -
162M ASN* 3.6 13.9 - - - -
166M LEU* 3.4 28.7 - - + -
191M VAL* 5.7 0.2 - - + -
193M VAL* 3.6 27.5 - - + +
194M PRO* 4.8 1.9 - - - +
197M SER* 2.9 35.0 + - - -
198M LEU* 4.9 8.5 - - + -
203M GLN* 3.6 39.2 + - + -
205M THR* 1.3 80.1 - - - +
207M ILE* 1.3 64.6 + - - +
222M LYS* 3.8 0.5 - - - +
225M VAL* 2.9 39.3 + - - +
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Residues in contact with ILE 207 (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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157M TRP* 3.8 4.6 - - - -
162M ASN* 2.9 35.5 + - - +
205M THR* 5.1 9.0 - - + -
206M TYR* 1.3 82.2 - - - +
208M CYS* 1.3 61.0 + - - +
209M ASN* 3.4 6.1 - - - +
220M ASP* 3.2 34.3 - - + +
221M LYS 3.0 17.7 - - - +
222M LYS* 3.5 26.7 - - + -
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Residues in contact with CYS 208 (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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121M VAL* 4.3 0.9 - - - -
142M CYS* 2.0 55.0 - - - -
154M VAL* 4.2 6.1 - - + -
156M SER 3.2 7.0 - - - +
157M TRP* 3.5 33.1 - - + -
207M ILE* 1.3 72.2 - - - +
209M ASN* 1.3 61.8 + - - +
210M VAL* 3.5 15.0 + - - +
219M VAL 3.6 0.3 - - - +
220M ASP* 3.5 18.7 - - - -
221M LYS 3.3 10.3 + - - -
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Residues in contact with ASN 209 (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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153M THR 3.5 1.7 - - - +
154M VAL* 3.4 5.0 - - - -
156M SER* 2.6 47.9 + - - +
162M ASN* 4.1 0.3 - - - -
163M SER* 3.0 42.0 + - - +
207M ILE* 3.4 12.4 - - - +
208M CYS* 1.3 68.3 - - - +
210M VAL* 1.3 61.9 + - - +
211M ASN* 5.1 1.4 - - - +
219M VAL 3.5 6.5 - - - +
220M ASP* 2.8 23.4 + - - +
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Residues in contact with VAL 210 (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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119M PRO* 4.3 11.0 - - + -
121M VAL* 4.0 29.4 - - + -
144M VAL* 3.5 46.0 - - + -
152M VAL* 4.3 8.1 - - + -
153M THR 3.4 6.3 - - - +
154M VAL* 4.2 9.4 - - + -
208M CYS* 3.5 13.4 + - - +
209M ASN* 1.3 77.1 - - - +
211M ASN* 1.3 63.5 + - - +
212M HIS 4.2 0.4 - - - +
217M THR* 3.9 1.0 - - + +
218M LYS* 3.5 3.3 - - - +
219M VAL* 2.8 38.7 + - + +
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Residues in contact with ASN 211 (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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151M PRO 4.5 0.3 - - - +
152M VAL* 3.5 5.1 - - - -
153M THR* 2.9 54.4 + - - +
209M ASN 5.1 2.0 - - - +
210M VAL* 1.3 75.5 - - - +
212M HIS* 1.3 60.4 + - - +
213M LYS* 3.9 32.1 + - - +
216M ASN 5.7 0.2 - - - -
217M THR 3.1 13.2 + - - +
218M LYS* 3.5 30.6 - - + +
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Residues in contact with HIS 212 (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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117M LYS 3.4 21.8 - - - -
118M GLY* 3.7 4.6 - - - -
119M PRO* 3.6 22.7 - - + -
147M TYR* 3.8 4.9 - + + -
148M PHE 3.5 11.9 - - - -
149M PRO 2.8 23.4 + - - -
151M PRO 3.1 25.6 - - - -
152M VAL* 3.6 15.7 - - + -
210M VAL 4.2 0.4 - - - -
211M ASN* 1.3 72.1 + - - +
213M LYS* 1.3 62.6 + - - +
214M PRO* 3.8 11.7 - - + +
215M SER* 2.7 36.4 + - - +
216M ASN 3.2 2.6 + - - -
217M THR* 2.9 33.1 + - - +
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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