Contacts of the helix formed by residues 154 - 163 (chain O) in PDB entry 1UW9
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 154 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151O HYP 4.6 3.9 - - - -
153O HIS* 1.3 74.6 - - - +
155O ILE* 1.3 59.5 + - - -
156O GLN 3.4 2.5 - - - -
157O VAL 3.3 1.4 + - - -
158O GLU* 2.9 32.3 + - - +
324O ASP* 2.9 21.0 + - - -
372O PRO* 3.8 12.3 - - - +
373O GLY 3.2 15.3 - - - -
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Residues in contact with ILE 155 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154O GLY* 1.3 70.8 - - - -
156O GLN* 1.3 64.8 + - - +
158O GLU* 3.3 7.2 + - - +
159O ARG* 3.0 29.6 + - - +
350O ARG* 3.8 29.2 - - + +
373O GLY* 3.1 23.3 + - - +
374O VAL 3.6 21.3 - - - +
375O MET* 3.6 34.5 - - + +
376O PRO* 4.7 0.2 - - + -
397O ASP* 3.8 31.9 - - + +
114T LYS* 6.1 0.9 - - - -
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Residues in contact with GLN 156 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A SER* 3.7 22.2 - - - -
182A ALA 5.1 1.6 - - - +
211A PHE 4.2 10.7 + - - +
154O GLY 3.4 0.6 - - - -
155O ILE* 1.3 80.8 - - - +
157O VAL* 1.3 81.4 + - + +
159O ARG* 3.4 2.3 + - - +
160O ASP* 3.0 38.6 + - - +
114T LYS* 3.2 17.8 - - + +
115T GLN* 2.8 33.0 - - - +
116T VAL* 4.2 15.2 - - + +
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Residues in contact with VAL 157 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A ALA* 5.7 5.2 - - + +
216A ASP* 3.4 39.5 - - + +
220A PHE* 5.2 3.6 - - + -
153O HIS* 3.7 37.9 - - + +
154O GLY 3.3 1.9 + - - +
156O GLN* 1.3 94.7 - - + +
158O GLU* 1.3 57.9 + - - +
160O ASP* 3.2 7.5 + - - +
161O LYS* 2.9 40.8 + - + +
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Residues in contact with GLU 158 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153O HIS* 5.4 0.2 - - + -
154O GLY 2.9 18.4 + - - +
155O ILE* 3.6 4.9 - - - +
156O GLN 3.2 0.2 - - - -
157O VAL* 1.3 77.3 - - - +
159O ARG* 1.3 64.0 + - - +
161O LYS 3.3 0.2 + - - -
162O LEU* 3.0 37.6 + - + +
169O LEU* 3.7 12.8 - - + +
199O PHE* 3.8 3.5 - - - -
290O PHE* 3.4 35.1 - - + -
324O ASP* 3.9 9.8 - - + +
325O HIS* 2.5 46.0 + - - -
375O MET* 3.7 19.2 - - + +
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Residues in contact with ARG 159 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155O ILE* 3.0 26.1 + - + +
156O GLN 3.8 4.0 - - - +
158O GLU* 1.3 75.6 - - - +
160O ASP* 1.3 52.6 + - - +
162O LEU* 3.4 4.7 + - - -
163O ASN* 2.8 30.3 + - - -
164O LYS* 2.8 50.3 + - + +
165O TYR* 3.6 27.6 + - + +
166O GLY 4.7 2.9 - - - -
167O ARG* 2.9 21.2 + - - +
168O GLY* 4.5 1.0 - - - -
169O LEU* 4.1 19.5 - - + +
375O MET* 4.7 9.0 - - + +
396O ASP* 2.8 33.1 + - - +
397O ASP* 3.0 25.5 + - - +
398O ALA 4.8 0.6 - - - +
116T VAL* 4.4 13.0 - - + -
117T GLN 4.9 2.5 - - - -
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Residues in contact with ASP 160 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181A SER* 4.4 5.5 + - - -
183A LYS* 3.5 36.4 + - + +
220A PHE* 3.5 29.1 - - + -
156O GLN* 3.0 39.2 + - - +
157O VAL* 3.5 7.6 - - - +
159O ARG* 1.3 76.0 - - - +
161O LYS* 1.3 61.5 + - - +
163O ASN* 3.5 7.6 + - - +
165O TYR* 2.8 27.2 + - - -
71T ARG* 4.5 2.9 + - - +
115T GLN 4.7 1.2 - - - +
116T VAL* 3.9 7.4 - - - +
117T GLN 5.0 1.4 + - - -
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Residues in contact with LYS 161 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215A ARG* 5.0 2.4 + - - +
216A ASP* 3.0 38.0 + - - +
219A LEU* 4.6 18.3 - - - +
220A PHE* 3.7 17.0 - - + -
153O HIS* 3.2 20.0 - - - -
157O VAL* 2.9 27.1 + - + +
160O ASP* 1.3 74.0 - - - +
162O LEU* 1.3 61.9 + - - +
288O GLY* 4.1 14.5 + - - -
290O PHE* 3.7 19.5 - - + -
66T LEU* 3.8 34.1 - - + +
68T TYR* 4.3 9.0 - - - -
71T ARG* 2.8 30.2 + - - +
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Residues in contact with LEU 162 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158O GLU* 3.0 38.4 + - + +
159O ARG* 4.0 2.9 - - - +
161O LYS* 1.3 75.0 - - - +
163O ASN* 1.3 71.3 + - - +
164O LYS* 3.6 28.6 - - + +
169O LEU* 4.2 11.9 - - + -
199O PHE* 3.6 36.6 - - + -
235O VAL* 3.7 41.4 - - + +
236O LYS 5.7 0.9 - - - +
263O PRO* 5.0 4.0 - - + -
290O PHE* 3.7 19.3 - - + -
13T GLU* 4.9 1.0 - - - +
66T LEU* 4.1 7.2 - - + -
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Residues in contact with ASN 163 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183A LYS* 2.9 27.0 - - - +
159O ARG 2.8 12.0 + - - -
160O ASP 3.5 3.5 + - - +
161O LYS 3.3 2.2 - - - -
162O LEU* 1.3 83.2 - - - +
164O LYS* 1.3 57.8 + - - +
165O TYR* 3.5 17.9 + - - -
235O VAL* 5.4 1.6 - - + -
13T GLU* 4.0 15.6 - - - +
52T VAL* 5.9 0.8 - - + +
70T ASN 5.0 0.3 - - - +
71T ARG* 3.7 46.1 + - + +
106T ARG* 4.0 19.5 + - - +
117T GLN* 5.4 0.4 + - - -
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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