Contacts of the strand formed by residues 173 - 182 (chain N) 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 173 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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172M HIS* 5.8 0.7 - - - -
105N GLU* 2.9 33.3 + - - +
138N ASN* 3.0 8.3 + - - -
139N PHE* 2.8 57.5 + - + +
140N TYR* 3.7 27.4 - + - -
142N ARG* 3.7 47.8 - - + +
163N VAL* 4.4 5.2 - - + -
164N THR* 3.6 22.9 - - - +
165N GLU* 4.7 1.3 - - - -
166N GLN* 3.5 41.5 + - + -
172N THR* 1.3 74.1 - - - +
174N SER* 1.3 61.2 + - - +
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Residues in contact with SER 174 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172M HIS* 3.5 18.4 + - - -
174M PHE* 3.4 17.9 - - - -
136N LEU 3.3 8.3 - - - -
137N ASN* 2.9 24.3 + - - -
138N ASN* 3.1 12.0 + - - -
139N PHE* 3.7 2.2 - - - -
163N VAL* 3.3 6.1 - - - +
164N THR* 2.9 43.2 + - - -
173N TYR* 1.3 71.4 - - - +
175N LEU* 1.3 61.5 + - - +
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Residues in contact with LEU 175 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174M PHE* 3.4 4.6 - - - -
134N CYS 3.7 0.3 - - - +
135N LEU* 3.6 0.7 - - - -
136N LEU* 2.7 45.4 + - + -
139N PHE* 3.8 22.4 - - + -
142N ARG 5.2 3.1 - - - +
144N ALA* 4.4 17.9 - - + +
146N VAL* 4.0 22.4 - - + -
161N GLU* 3.6 30.3 - - + +
162N SER 3.2 12.1 - - - +
163N VAL* 3.9 15.9 - - + -
174N SER* 1.3 78.4 - - - +
176N SER* 1.3 74.0 + - - +
177N SER* 3.9 2.7 - - - +
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Residues in contact with SER 176 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174M PHE* 3.5 36.2 - - - +
188M SER* 3.5 16.5 + - - -
190M VAL* 5.7 1.8 - - - -
133N VAL* 4.6 10.1 - - - -
134N CYS 3.2 7.9 - - - -
135N LEU* 4.5 4.9 - - - +
160N GLN 3.9 0.3 - - - +
161N GLU* 3.0 4.2 - - - +
162N SER* 2.9 34.1 + - - -
175N LEU* 1.3 75.9 - - - +
177N SER* 1.3 60.6 + - - +
178N THR* 5.2 2.5 + - - -
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Residues in contact with SER 177 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133N VAL* 3.4 4.9 - - - +
134N CYS* 2.8 39.7 + - - -
146N VAL* 4.1 21.9 + - - +
148N TRP* 3.0 30.1 + - - -
159N SER* 4.3 4.0 + - - -
160N GLN 3.5 9.5 + - - -
161N GLU* 4.0 15.6 + - - +
175N LEU* 3.9 5.1 - - - +
176N SER* 1.3 73.5 - - - +
178N THR* 1.3 60.2 + - - +
179N LEU 4.1 0.2 - - - -
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Residues in contact with THR 178 (chain N).
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* 4.5 11.6 - - + +
145M LYS* 5.5 2.5 - - - -
188M SER* 5.3 3.5 + - - -
131N SER* 3.8 20.4 - - - +
132N VAL 3.3 9.9 - - - +
133N VAL* 3.7 17.8 - - + +
148N TRP* 4.3 0.2 - - - -
159N SER* 3.0 6.6 - - - -
160N GLN* 2.8 45.9 + - - +
176N SER* 4.2 3.3 + - - -
177N SER* 1.3 75.8 + - - +
179N LEU* 1.3 61.8 + - - +
180N THR* 3.7 19.5 + - - +
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Residues in contact with LEU 179 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130N ALA 3.6 1.4 - - - +
131N SER* 3.3 2.9 - - - -
132N VAL* 2.8 46.5 + - + +
148N TRP* 3.7 49.6 - - + +
150N VAL* 3.9 26.9 - - + -
155N GLN* 4.4 1.6 - - + -
158N ASN* 3.2 34.1 - - - +
159N SER* 3.8 4.7 - - - -
178N THR* 1.3 70.8 - - - +
180N THR* 1.3 59.4 + - - +
181N LEU* 3.3 25.7 + - + +
192N TYR* 4.4 11.9 - - + -
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Residues in contact with THR 180 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145M LYS* 4.0 14.5 + - - +
179M GLN* 5.1 2.7 + - - +
129N THR* 3.7 21.8 - - + -
130N ALA 3.4 2.0 - - - +
131N SER* 3.5 21.7 + - - +
158N ASN* 3.2 19.5 + - - +
159N SER* 5.6 0.2 - - - -
178N THR* 3.7 13.4 + - - +
179N LEU* 1.3 73.9 - - - +
181N LEU* 1.3 72.0 + - - +
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Residues in contact with LEU 181 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129N THR* 3.8 3.8 - - - -
130N ALA* 2.7 39.5 + - + +
132N VAL* 6.5 1.1 - - + -
150N VAL* 4.9 7.6 - - + -
155N GLN* 5.4 2.0 - - - +
158N ASN* 3.9 17.0 - - + +
179N LEU* 3.3 28.9 + - + -
180N THR* 1.3 85.0 - - - +
182N SER* 1.3 67.6 + - - +
185N ASP* 3.8 29.2 - - + +
186N TYR* 4.4 7.9 - - + +
189N HIS* 5.1 5.8 - - + -
192N TYR* 4.2 29.4 - - + +
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Residues in contact with SER 182 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128N GLY 3.3 12.3 - - - -
129N THR* 4.4 2.7 - - - +
181N LEU* 1.3 74.8 - - - +
183N LYS* 1.3 64.7 + - - +
184N ALA* 2.9 9.4 + - - +
185N ASP* 2.8 44.5 + - - +
186N TYR 3.0 8.8 + - - -
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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