Contacts of the strand formed by residues 163 - 170 (chain G) in PDB entry 1U8R
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 VAL 163 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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157G LEU* 4.5 20.2 - - + -
158G PRO* 5.1 13.2 - - + +
161G SER 3.6 8.3 - - - +
162G PRO* 1.3 83.0 - - - +
164G ALA* 1.3 75.3 + - - +
165G VAL* 3.6 13.2 + - + -
196G THR* 3.1 7.2 - - - -
197G VAL* 3.0 36.5 + - - +
229G LYS* 4.9 12.6 - - + -
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Residues in contact with ALA 164 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163G VAL* 1.3 79.0 - - - +
165G VAL* 1.3 67.2 + - - +
194G ARG* 6.1 4.9 - - + -
195G VAL 3.6 6.3 - - - +
196G THR* 3.7 14.3 - - + +
230G VAL* 3.1 30.9 + - - +
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Residues in contact with VAL 165 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157G LEU* 4.7 3.4 - - + -
163G VAL* 3.8 18.2 - - + +
164G ALA* 1.3 82.3 - - - +
166G VAL* 1.3 62.1 + - - +
193G ALA 3.7 0.3 - - - +
194G ARG* 3.5 3.6 - - - +
195G VAL* 2.8 47.1 + - + +
197G VAL* 3.8 24.9 - - + -
227G VAL* 3.9 33.0 - - + -
228G GLU 3.4 9.4 - - - +
229G LYS* 3.9 18.4 - - + -
230G VAL* 3.5 6.3 + - - -
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Residues in contact with VAL 166 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165G VAL* 1.3 76.0 - - - +
167G VAL* 1.3 64.8 + - - +
168G ARG* 3.1 38.7 + - - +
192G ASN* 3.6 3.8 - - - -
193G ALA 3.3 31.6 - - - +
194G ARG* 4.3 13.7 - - + +
227G VAL* 3.6 2.2 - - - -
228G GLU* 3.1 39.1 + - + +
230G VAL* 4.4 13.9 - - + -
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Residues in contact with VAL 167 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165G VAL 4.1 0.6 - - - -
166G VAL* 1.3 68.8 - - - +
168G ARG* 1.3 61.4 + - - +
169G GLN 4.4 7.0 - - - +
170G LEU* 4.3 23.8 - - + -
189G VAL* 3.6 25.6 - - + -
190G VAL* 3.3 31.9 - - - +
191G PRO* 3.2 4.1 - - + +
192G ASN 2.8 31.2 + - - -
193G ALA* 3.1 14.1 + - + +
195G VAL* 4.0 15.5 - - + -
207G ILE* 6.1 0.7 - - + -
225G VAL* 4.7 5.8 - - + -
226G LYS 4.7 0.7 - - - +
227G VAL* 3.9 14.5 - - + +
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Residues in contact with ARG 168 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128G PHE 3.8 1.3 - - - +
129G GLY* 3.6 16.5 - - - +
151G LEU* 3.9 27.1 - - + -
166G VAL* 3.1 46.3 + - - +
167G VAL* 1.3 77.8 + - - +
169G GLN* 1.3 71.1 + - + +
191G PRO* 4.3 8.5 - - - +
192G ASN* 3.3 23.0 + - - +
226G LYS 3.0 13.3 + - - +
228G GLU* 2.9 31.1 + - + +
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Residues in contact with GLN 169 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20G GLU* 5.6 2.1 - - - +
128G PHE 3.5 4.7 - - - -
129G GLY 3.4 20.1 + - - +
130G ASN* 3.0 27.9 + - - +
131G PRO* 3.7 11.9 - - - +
151G LEU* 3.8 18.2 - - - +
167G VAL* 4.0 1.0 - - - +
168G ARG* 1.3 85.1 - - + +
170G LEU* 1.3 75.6 + - - +
171G THR* 3.9 3.5 - - + +
191G PRO* 5.8 0.2 - - - -
225G VAL* 3.5 4.2 - - - +
226G LYS* 3.0 68.4 + - + +
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Residues in contact with LEU 170 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94G TRP* 3.9 28.7 - - + -
128G PHE* 3.2 20.3 + - + +
130G ASN* 3.3 6.5 - - - +
167G VAL* 4.3 13.2 - - + -
169G GLN* 1.3 83.8 - - - +
171G THR* 1.3 66.6 + - - +
174G VAL* 3.6 13.5 - - + -
175G GLN* 3.2 19.9 + - - +
181G ILE* 3.9 16.6 - - + -
184G LEU* 4.4 12.1 - - + -
189G VAL* 4.2 17.9 - - + +
190G VAL* 4.8 2.7 - - - -
191G PRO* 4.9 2.2 - - + -
224G ALA 3.9 1.3 - - - -
225G VAL* 3.9 27.6 - - + -
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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