Contacts of the helix formed by residues 154 - 163 (chain R) 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 R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151R HYP 4.6 4.1 - - - -
153R HIS* 1.3 75.5 - - - +
155R ILE* 1.3 60.2 + - - -
156R GLN 3.4 2.0 - - - -
157R VAL 3.3 1.7 + - - -
158R GLU* 2.9 31.9 + - - +
324R ASP* 3.0 20.1 + - - -
372R PRO* 3.8 13.0 - - - +
373R GLY 3.2 14.4 - - - -
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Residues in contact with ILE 155 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114M LYS* 6.1 0.4 - - - -
154R GLY* 1.3 70.9 - - - -
156R GLN* 1.3 66.0 + - - +
158R GLU* 3.2 7.8 + - - +
159R ARG* 3.0 29.7 + - - +
350R ARG* 3.8 29.6 - - + +
373R GLY* 3.1 22.5 + - - +
374R VAL 3.6 21.5 - - - +
375R MET* 3.6 35.2 - - + +
376R PRO* 4.7 0.2 - - + -
397R ASP* 3.8 31.0 - - + +
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Residues in contact with GLN 156 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114M LYS 3.1 18.1 - - - +
115M GLN* 3.0 31.0 - - - +
116M VAL* 4.3 15.4 - - + +
181O SER* 3.7 20.9 - - - -
182O ALA 5.2 1.6 - - - +
211O PHE 4.2 11.2 + - - +
154R GLY 3.4 0.8 - - - -
155R ILE* 1.3 80.9 - - - +
157R VAL* 1.3 74.2 + - + +
159R ARG* 3.4 2.5 + - - +
160R ASP* 2.9 45.2 + - - +
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Residues in contact with VAL 157 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182O ALA* 5.8 4.3 - - + -
216O ASP* 3.4 39.5 - - + +
220O PHE* 5.2 3.1 - - + -
153R HIS* 3.7 35.9 - - + +
154R GLY 3.3 2.7 + - - +
156R GLN* 1.3 94.3 - - + +
158R GLU* 1.3 57.6 + - - +
160R ASP* 3.1 6.7 + - - +
161R LYS* 2.9 41.9 + - + +
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Residues in contact with GLU 158 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153R HIS* 5.4 0.2 - - + -
154R GLY 2.9 17.5 + - - +
155R ILE* 3.5 6.3 - - - +
156R GLN 3.2 0.2 - - - -
157R VAL* 1.3 77.9 - - - +
159R ARG* 1.3 63.4 + - - +
162R LEU* 3.0 51.1 + - + +
169R LEU* 3.8 6.4 - - + +
199R PHE* 3.8 3.3 - - - -
290R PHE* 3.4 33.1 - - + -
324R ASP* 3.9 10.7 - - + +
325R HIS* 2.5 45.4 + - - -
375R MET* 3.8 19.1 - - + +
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Residues in contact with ARG 159 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116M VAL* 4.5 11.7 - - + -
117M GLN 4.9 2.2 - - - -
155R ILE* 3.0 26.1 + - + +
156R GLN* 3.7 4.0 - - - +
158R GLU* 1.3 75.6 - - + +
160R ASP* 1.3 57.4 + - - +
162R LEU* 4.7 4.5 - - - -
163R ASN* 2.8 26.3 + - - -
164R LYS* 2.8 51.5 + - + +
165R TYR* 3.6 27.2 + - + +
166R GLY 4.7 3.1 - - - -
167R ARG* 2.8 22.0 + - - +
168R GLY* 4.5 0.6 - - - -
169R LEU* 4.1 19.7 - - + +
375R MET* 4.7 9.6 - - + +
396R ASP* 2.8 33.3 + - - +
397R ASP* 3.0 25.9 + - - +
398R ALA 4.8 0.4 - - - +
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Residues in contact with ASP 160 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71M ARG* 4.5 2.8 + - - -
115M GLN 4.8 1.4 - - - +
116M VAL* 3.8 7.4 - - - +
117M GLN 5.0 1.2 + - - -
181O SER* 4.4 5.7 + - - -
183O LYS* 3.6 33.9 + - + +
220O PHE* 3.5 29.5 - - + -
156R GLN* 2.9 39.3 + - - +
157R VAL* 3.1 7.7 + - - +
159R ARG* 1.3 77.5 - - - +
161R LYS* 1.3 60.0 - - - +
163R ASN* 3.5 7.6 + - - +
165R TYR* 2.7 32.3 + - - -
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Residues in contact with LYS 161 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66M LEU* 3.8 37.0 - - + +
68M TYR* 4.4 9.0 - - - -
71M ARG* 2.9 29.2 + - - +
215O ARG* 5.0 2.0 - - - +
216O ASP* 2.9 38.1 + - - +
219O LEU* 4.7 16.3 - - - +
220O PHE* 3.8 17.3 - - + -
153R HIS* 3.3 20.0 - - - -
157R VAL* 2.9 25.7 + - + +
160R ASP* 1.3 76.5 - - - +
162R LEU* 1.3 61.7 + - - +
163R ASN 3.5 0.5 + - - -
235R VAL* 5.1 0.2 - - - +
288R GLY* 4.0 14.6 + - - -
290R PHE* 3.8 17.9 - - + -
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Residues in contact with LEU 162 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13M GLU* 4.9 1.2 - - - +
66M LEU* 4.2 7.4 - - + -
158R GLU* 3.0 38.6 + - + +
159R ARG* 4.0 2.9 - - - +
161R LYS* 1.3 75.0 - - - +
163R ASN* 1.3 70.3 + - - +
164R LYS* 3.5 28.9 + - + +
169R LEU* 4.2 11.4 - - + -
199R PHE* 3.6 36.3 - - + -
235R VAL* 3.7 40.8 - - + +
236R LYS 5.8 0.7 - - - +
263R PRO* 5.0 4.3 - - + -
290R PHE* 3.7 19.3 - - + -
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Residues in contact with ASN 163 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13M GLU* 4.0 15.8 - - - +
52M VAL* 5.9 0.6 - - + +
70M ASN 5.1 0.3 - - - +
71M ARG* 3.7 45.6 + - + +
106M ARG* 4.0 18.3 + - - +
117M GLN* 5.3 0.8 + - - -
183O LYS* 2.9 26.5 - - - +
159R ARG 2.8 9.2 + - - -
160R ASP 3.5 3.9 + - - +
161R LYS 3.3 3.0 - - - -
162R LEU* 1.3 80.7 - - - +
164R LYS* 1.3 58.7 + - - +
165R TYR* 3.6 18.3 + - - -
235R VAL* 5.4 1.6 - - + -
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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