Contacts of the helix formed by residues 173 - 184 (chain A) in PDB entry 1R2Y
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 173 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3A GLN* 2.9 22.4 + - - +
60A LYS* 3.5 1.6 - - - -
164A LEU* 3.4 10.3 - - - -
172A PHE* 1.3 74.7 - - - +
174A ASN* 1.3 67.6 + - - -
175A ILE 3.3 0.2 + - - -
176A TYR* 4.5 0.4 - - - +
177A VAL* 2.9 24.4 + - - +
19C G 3.3 20.6 - - - -
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Residues in contact with ASN 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A GLN* 3.6 1.2 + - - -
160A LYS* 2.9 28.4 + - - -
164A LEU* 3.7 6.8 - - - +
173A GLY* 1.3 70.6 - - - -
175A ILE* 1.3 64.2 - - - +
177A VAL* 4.8 0.7 - - - -
178A ASP* 3.4 29.0 + - - +
242A TYR* 3.9 9.0 - - - -
264A ARG* 3.8 20.1 + - - +
265A GLY* 3.0 28.2 + - - +
267A HIS* 5.0 0.4 - - - -
18C 8OG 3.0 37.5 + - - +
19C G 3.0 19.4 + - - +
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Residues in contact with ILE 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A GLN* 3.3 16.6 + - - +
173A GLY 3.3 0.6 - - - -
174A ASN* 1.3 78.3 - - - +
176A TYR* 1.3 73.9 + - + +
178A ASP* 3.3 2.4 + - - +
179A GLU* 3.0 30.1 + - - +
220A SER* 4.4 5.8 - - - +
222A VAL* 3.9 26.5 - - + -
239A LEU* 3.8 28.7 - - + -
242A TYR* 3.6 36.9 - - + +
18C 8OG 3.5 34.1 - - + +
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Residues in contact with TYR 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A GLN* 3.0 37.1 + - + +
5A PRO* 3.5 9.9 - - + -
6A GLU* 2.6 40.2 + - - -
172A PHE* 3.9 11.4 - - + -
173A GLY 4.4 1.8 - - - +
175A ILE* 1.3 82.9 - - + +
177A VAL* 1.3 60.6 + - - +
179A GLU* 3.9 4.4 - - + +
180A SER* 2.8 34.0 + - - -
210A THR* 3.8 18.6 - - + -
211A ILE* 3.6 28.3 - - + -
214A ALA* 3.5 26.5 - - + +
220A SER* 2.9 20.3 + - - -
235A PHE* 3.8 17.9 - + - -
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Residues in contact with VAL 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A LYS* 3.7 32.5 - - + +
163A LEU* 3.5 34.5 - - + -
164A LEU* 3.7 17.5 - - + -
172A PHE* 3.8 18.6 - - + -
173A GLY 2.9 21.0 + - - +
174A ASN 4.3 2.0 - - - +
176A TYR* 1.3 76.5 - - - +
178A ASP* 1.3 65.3 + - - +
180A SER* 3.5 4.1 + - - -
181A LEU* 3.1 37.7 + - + +
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Residues in contact with ASP 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A LYS* 2.6 40.3 + - - +
174A ASN 3.4 13.7 + - - +
175A ILE* 3.3 5.0 + - - +
177A VAL* 1.3 78.8 - - - +
179A GLU* 1.3 61.3 + - - +
181A LEU* 4.1 5.2 - - - +
182A PHE* 3.1 16.8 + - - +
188A PRO* 5.0 1.7 - - - +
241A VAL* 3.5 19.5 - - + +
242A TYR* 4.5 4.0 - - + -
265A GLY 3.9 1.0 - - - +
266A THR* 3.4 2.9 - - - +
267A HIS* 2.7 53.9 + - + +
273A GLN* 4.5 1.1 + - - +
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Residues in contact with GLU 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A ILE* 3.0 23.9 + - + +
176A TYR* 4.1 5.8 - - + +
177A VAL 3.3 0.4 - - - -
178A ASP* 1.3 75.9 - - - +
180A SER* 1.3 60.3 + - - +
182A PHE* 3.3 2.5 + - - +
183A ARG* 2.9 38.4 + - - +
210A THR* 4.2 15.7 - - + -
235A PHE* 5.0 3.2 - - + -
238A HIS 4.1 1.6 - - - +
239A LEU* 3.5 28.6 - - + +
240A TYR* 2.7 38.5 + - - +
241A VAL* 2.8 26.2 + - - +
242A TYR* 2.9 15.8 + - + +
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Residues in contact with SER 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163A LEU* 5.2 1.1 - - - -
172A PHE* 3.8 4.8 - - - -
176A TYR 2.8 22.1 + - - -
177A VAL* 3.9 4.7 - - - -
179A GLU* 1.3 75.1 - - - +
181A LEU* 1.3 60.6 + - - +
183A ARG* 3.3 1.9 + - - +
184A ALA* 2.9 31.0 + - - +
203A LEU* 4.0 4.9 - - - +
206A GLU* 3.8 5.4 - - - +
207A MET* 3.5 42.8 - - - +
210A THR* 3.8 17.0 - - - -
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Residues in contact with LEU 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A VAL* 3.8 25.8 - - + -
160A LYS* 4.2 7.2 - - + -
163A LEU* 3.9 11.9 - - + -
177A VAL* 3.1 40.1 + - + +
178A ASP* 4.1 4.5 - - - +
180A SER* 1.3 75.8 - - - +
182A PHE* 1.3 61.5 + - - +
184A ALA* 3.3 1.6 + - - -
185A GLY 2.9 3.6 + - - -
186A ILE* 2.9 50.8 + - + +
188A PRO* 3.8 29.2 - - + -
203A LEU* 3.7 21.3 - - + -
273A GLN* 3.4 7.4 - - - +
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Residues in contact with PHE 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178A ASP 3.1 19.0 + - - +
179A GLU* 3.5 4.0 - - - +
180A SER 3.2 0.2 - - - -
181A LEU* 1.3 78.4 - - - +
183A ARG* 1.3 64.6 + - + +
185A GLY* 2.9 20.3 + - - -
240A TYR* 3.3 47.6 - + + -
241A VAL* 3.4 25.8 - - + -
249A CYS* 3.7 21.3 - - - -
251A ARG* 4.2 11.9 - - + -
269A CYS* 3.6 22.4 - - + -
272A CYS* 3.7 20.7 - - + +
273A GLN* 3.4 27.3 - - + +
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Residues in contact with ARG 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179A GLU* 2.9 25.3 + - - +
180A SER 3.3 2.0 + - - +
182A PHE* 1.3 80.2 - - + +
184A ALA* 1.3 56.4 + - - +
185A GLY 3.3 0.4 - - - -
202A ARG* 3.0 23.0 + - - -
206A GLU* 2.9 41.3 + - + +
209A ALA* 3.8 11.5 - - - +
210A THR* 3.2 28.7 + - - +
213A GLU* 3.0 42.8 + - - -
235A PHE* 4.3 10.9 - - - -
238A HIS 5.3 1.0 + - - -
240A TYR* 3.8 40.2 - - + -
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Residues in contact with ALA 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A SER 2.9 18.0 + - - +
181A LEU 3.9 2.0 - - - +
183A ARG* 1.3 75.7 - - - +
185A GLY* 1.3 63.0 + - - +
186A ILE* 3.5 20.2 - - + +
199A GLU* 5.5 2.1 - - - +
202A ARG* 3.9 24.1 + - + +
203A LEU* 3.7 34.5 - - + +
206A GLU* 3.6 8.3 - - + +
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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