Contacts of the strand formed by residues 143 - 150 (chain X) in PDB entry 1UNF
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 143 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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139X GLN* 4.2 2.2 - - - -
141X GLY 4.1 1.0 + - - -
142X SER* 1.3 78.0 - - - +
144X TRP* 1.3 65.3 + - - -
176X SER 3.2 11.4 - - - -
178X ASN 3.3 16.4 - - - -
196X VAL* 2.9 31.6 + - - +
197X TRP* 3.3 14.0 - - - +
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Residues in contact with TRP 144 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91X GLN* 3.2 17.6 + - - -
94X ASN* 3.3 47.0 - - + +
95X HIS* 3.7 18.8 - + - -
98X PHE* 3.9 10.5 - - + -
139X GLN* 4.3 1.6 - - - +
143X GLY* 1.3 73.7 - - - -
145X ALA* 1.3 61.2 + - - +
146X TRP* 3.3 30.1 - + + +
175X LYS* 3.4 5.2 - - - +
176X SER* 2.9 31.6 + - - +
178X ASN 2.9 29.4 + - - -
180X VAL 4.1 13.9 - - - -
193X THR* 3.3 24.7 - - + +
194X ILE 3.4 6.1 - - - -
195X ASP* 3.4 50.0 - - + -
196X VAL* 3.9 6.4 - - - +
197X TRP* 3.6 3.6 - + - +
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Residues in contact with ALA 145 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132X PHE* 3.9 10.0 - - + +
135X ALA* 4.1 9.6 - - + +
136X ALA* 3.6 41.3 - - + +
144X TRP* 1.3 73.1 - - - +
146X TRP* 1.3 63.7 + - - +
174X ILE 3.5 7.2 - - - +
175X LYS* 4.6 0.4 - - + -
193X THR* 3.0 18.7 + - - -
194X ILE* 3.0 26.6 + - + +
196X VAL* 4.8 0.8 - - - +
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Residues in contact with TRP 146 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93X TRP* 4.0 9.4 - + - -
94X ASN* 3.6 13.7 - - + -
97X PHE* 3.9 15.9 - + - -
132X PHE* 3.7 6.1 - - - -
144X TRP* 3.3 27.5 - + + +
145X ALA* 1.3 77.5 - - - +
147X LEU* 1.3 62.9 + - - +
148X ALA* 4.1 2.0 - - + +
173X VAL* 3.2 11.3 - - - +
174X ILE* 2.7 54.4 + - + +
176X SER* 2.9 28.1 + - - -
180X VAL 3.8 3.1 + - - -
181X ASN* 3.5 29.2 - - + -
182X PRO* 3.5 34.9 - - + +
185X TRP* 5.0 0.2 - + - -
190X PRO* 4.1 9.4 - - + -
192X LEU 3.3 10.3 - - - +
193X THR* 3.4 31.6 - - + -
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Residues in contact with LEU 147 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114X LEU* 4.5 11.9 - - + -
118X ILE* 4.7 6.3 - - + -
122X PHE* 4.1 9.0 - - + -
128X PHE* 3.8 37.9 - - + -
132X PHE* 3.8 4.0 - - + -
146X TRP* 1.3 73.5 - - - +
148X ALA* 1.3 61.8 + - - +
171X LEU* 3.9 25.8 - - + -
172X VAL 3.4 14.6 - - - +
173X VAL* 4.6 0.4 - - + -
190X PRO* 4.0 1.2 - - - +
191X LEU* 2.8 42.8 + - + -
192X LEU* 3.0 27.0 + - + +
223X TRP* 4.9 2.5 - - + -
226X VAL* 4.3 17.5 - - + -
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Residues in contact with ALA 148 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146X TRP* 4.1 1.1 - - + -
147X LEU* 1.3 75.6 - - - +
149X TYR* 1.3 60.3 + - - +
171X LEU* 3.4 4.2 - - - +
172X VAL* 2.9 44.9 + - + +
174X ILE* 4.3 14.8 - - + -
182X PRO* 4.5 7.2 - - + -
188X TYR* 4.3 11.9 - - + -
189X TYR 3.2 18.4 - - - +
190X PRO* 4.2 4.0 - - + -
191X LEU* 4.1 6.5 - - - +
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Residues in contact with TYR 149 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117X LEU* 3.8 20.6 - - + +
120X ARG* 5.1 1.1 + - - -
148X ALA* 1.3 73.0 - - - +
150X LYS* 1.3 58.6 + - - +
151X ALA* 3.7 20.2 + - + -
154X LEU* 3.9 4.8 - - + +
169X ASN* 3.5 27.6 + - - +
170X LYS* 3.7 22.7 - - - -
171X LEU* 4.1 12.3 - - + -
188X TYR* 3.4 3.3 - - - -
189X TYR 2.8 40.7 + - - +
191X LEU* 3.9 9.0 - - + +
230X LEU* 4.1 5.8 - - + -
233X ALA* 4.0 29.6 - - + -
234X LYS* 3.5 27.4 - - + +
237X SER* 3.4 23.1 + - - -
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Residues in contact with LYS 150 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148X ALA 3.7 1.2 + - - -
149X TYR* 1.3 70.7 - - - +
151X ALA* 1.3 56.5 + - - +
167X GLU 4.0 7.7 + - - -
168X ASP* 3.9 25.9 + - - +
169X ASN* 2.7 30.7 + - - -
170X LYS* 2.7 29.0 + - + +
172X VAL* 4.1 18.4 - - + -
187X GLY 3.5 8.7 - - - +
188X TYR* 3.5 42.3 + - + +
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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