Contacts of the strand formed by residues 185 - 191 (chain A) in PDB entry 3N2Q
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 ILE 185 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144A VAL* 3.4 12.6 - - + +
146A ILE* 3.6 19.3 - - + -
171A ILE* 4.7 13.5 - - + -
174A ILE* 4.0 24.5 - - + -
175A ASN* 4.7 8.7 - - - +
180A TYR* 3.4 35.2 - - + +
183A SER 3.5 2.9 - - - +
184A PRO* 1.3 73.6 - - - +
186A THR* 1.3 64.8 + - - +
187A PHE* 3.5 30.6 + - + -
207A ALA 4.0 0.5 - - - +
208A THR* 3.2 2.6 - - - -
209A VAL* 2.7 46.3 + - + +
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Residues in contact with THR 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A LEU* 5.1 1.1 - - + +
87A ILE* 4.4 9.6 - - + -
91A GLN* 2.5 34.9 + - - +
144A VAL 2.9 7.1 + - - -
145A MSE 3.5 19.5 - - - +
146A ILE* 2.9 25.8 + - - +
185A ILE* 1.3 72.9 - - - +
187A PHE* 1.3 71.3 + - - +
188A ALA* 3.9 1.1 + - + -
206A SER* 4.1 14.6 - - - +
207A ALA 3.4 4.7 - - - +
208A THR* 3.0 27.0 - - + +
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Residues in contact with PHE 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A ILE* 3.4 37.2 - - + +
148A LEU* 4.5 9.2 - - + -
167A ALA* 3.7 34.8 - - + -
170A LEU* 3.8 20.9 - - + -
171A ILE* 3.8 24.2 - - + -
174A ILE* 5.3 0.2 - - + -
185A ILE* 3.5 24.7 - - + -
186A THR* 1.3 73.9 - - - +
188A ALA* 1.3 59.8 + - - +
206A SER* 3.1 5.4 - - - -
207A ALA 2.8 35.2 + - - +
209A VAL* 4.1 3.6 - - + -
216A LEU* 3.6 21.1 - - + -
219A TRP* 3.6 19.7 - - + -
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Residues in contact with ALA 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A LEU* 4.0 11.9 - - + -
87A ILE* 3.7 22.0 - - + -
146A ILE 2.9 7.2 + - - +
147A GLY* 3.7 1.2 - - - -
148A LEU* 2.9 27.9 + - - +
186A THR* 3.9 1.1 + - + +
187A PHE* 1.3 76.6 - - - +
189A ILE* 1.3 64.0 + - - +
203A TYR* 3.6 24.0 - - + -
205A ALA 3.2 7.9 - - - +
206A SER* 4.4 3.8 - - - -
219A TRP* 4.7 0.2 - - - -
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Residues in contact with ILE 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A LEU* 3.6 5.8 - - + +
150A MSE 3.7 31.2 - - + -
159A ALA* 3.8 10.3 - - + +
160A MSE 3.7 38.8 - - + -
163A GLY* 4.4 1.1 - - - -
188A ALA* 1.3 75.0 - - - +
190A PHE* 1.3 65.7 + - - +
191A LYS 4.2 0.2 - - - +
203A TYR* 3.2 6.7 - - - -
204A ILE* 3.0 54.2 + - + -
205A ALA* 2.8 15.0 + - + +
219A TRP* 3.6 33.7 - - + -
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Residues in contact with PHE 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A LEU 3.9 13.9 - - - -
76A ASP* 4.0 7.6 - - + -
79A GLU* 3.7 14.6 - - + -
80A TYR* 3.6 61.0 - + + -
148A LEU 2.8 13.9 + - - +
149A ALA* 3.6 4.2 - - + -
150A MSE 2.8 28.4 + - - -
189A ILE* 1.3 73.4 - - - +
191A LYS* 1.3 59.4 + - - +
192A GLN* 3.5 17.1 + - + -
201A GLY* 3.4 28.5 - - - -
202A THR* 3.5 21.1 - - - -
203A TYR* 3.4 31.4 - + + -
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Residues in contact with LYS 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A MSE 3.9 4.5 - - - +
151A SER 2.8 23.8 + - - -
152A SER* 3.7 11.1 + - - +
154A VAL* 2.7 31.5 + - - +
155A SER* 3.9 12.1 - - - +
156A ASN* 3.4 26.0 - - - +
159A ALA* 4.0 17.7 - - + -
189A ILE* 3.6 2.7 + - - -
190A PHE* 1.3 69.0 - - - +
192A GLN* 1.3 63.0 + - - +
193A GLU* 4.6 8.2 - - - +
201A GLY* 3.2 4.3 - - - -
202A THR* 2.7 38.0 + - + +
204A ILE* 3.8 23.6 - - + -
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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