Contacts of the helix formed by residues 176 - 189 (chain A) in PDB entry 1Y9A
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 176 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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174A GLY* 3.6 3.4 + - - -
175A ILE* 1.3 83.3 - - - +
177A PRO* 1.3 71.4 - - - +
178A VAL 3.3 2.9 - - - -
179A GLY 3.1 3.1 + - - +
180A LEU* 2.9 23.4 + - - +
203A CYS* 4.9 5.4 - - - -
242A ALA 5.3 2.0 + - - -
340A LYS* 5.6 4.0 - - - -
345A ILE* 5.0 0.4 - - - -
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Residues in contact with PRO 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A THR* 5.9 3.8 - - + -
151A MET* 3.6 19.7 - - + -
176A GLY* 1.3 83.5 - - - +
178A VAL* 1.3 64.4 + - + +
180A LEU* 3.5 2.1 + - + +
181A MET* 3.1 27.2 + - - +
319A LEU* 4.2 11.1 - - + +
337A MET* 5.2 4.5 - - + -
340A LYS* 5.0 9.9 - - - +
345A ILE* 3.7 31.4 - - + +
346A LYS* 3.6 36.1 - - + -
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Residues in contact with VAL 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A CYS* 6.0 0.4 - - - -
151A MET* 3.7 37.0 - - + -
154A THR* 3.8 24.9 - - + -
155A GLY* 3.4 18.4 - - - -
176A GLY 3.3 0.6 - - - -
177A PRO* 1.3 77.9 - - + +
179A GLY* 1.3 51.5 + - - +
181A MET* 3.1 4.9 + - - -
182A SER* 2.8 31.4 + - - -
242A ALA* 4.1 14.4 - - + +
265A VAL* 3.9 16.4 - - + +
1001A CAC 5.4 1.3 - - - +
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Residues in contact with GLY 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A VAL* 3.7 1.9 - - - +
174A GLY 3.0 27.8 + - - -
175A ILE* 4.3 5.2 - - - -
176A GLY 3.1 8.4 + - - +
178A VAL* 1.3 75.5 - - - +
180A LEU* 1.3 58.9 + - - +
182A SER* 3.0 5.0 + - - -
183A VAL* 2.9 31.5 + - - +
242A ALA* 3.6 13.7 + - - +
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Residues in contact with LEU 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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175A ILE* 3.2 29.6 - - + +
176A GLY 2.9 19.1 + - - +
177A PRO 3.8 4.3 - - - +
178A VAL 3.3 0.2 - - - -
179A GLY* 1.3 75.1 - - - +
181A MET* 1.3 59.6 + - - +
183A VAL* 3.3 7.5 + - - +
184A ALA* 3.0 26.0 + - - +
203A CYS* 3.6 7.4 - - - +
206A ILE* 3.9 15.9 - - + -
207A ALA* 3.6 33.9 - - + +
210A TYR* 3.8 14.7 - - + -
319A LEU* 3.8 23.6 - - + -
345A ILE* 4.2 23.3 - - + -
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Residues in contact with MET 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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151A MET 3.3 28.9 - - - +
152A VAL* 3.7 30.1 - - - +
155A GLY* 3.8 6.1 - - - -
156A PHE* 3.2 23.6 - - - -
177A PRO 3.1 11.1 + - - +
178A VAL 3.1 7.0 + - - +
180A LEU* 1.3 79.0 - - - +
182A SER* 1.3 53.1 + - - +
184A ALA* 4.1 4.9 - - + -
185A GLY 2.8 28.4 + - - -
210A TYR* 3.3 50.3 - - + +
314A LEU* 4.3 9.0 - - + -
315A ASP 5.1 0.4 - - - +
316A THR* 5.0 2.5 - - - -
319A LEU* 4.0 18.6 - - + -
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Residues in contact with SER 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A GLY* 2.9 30.0 + - - -
159A ALA* 4.0 3.7 - - - +
172A VAL* 3.8 14.4 - - - +
178A VAL 2.8 14.7 + - - -
179A GLY* 3.0 9.2 + - - -
181A MET* 1.3 69.6 - - - +
183A VAL* 1.3 60.9 + - - +
186A ALA* 2.9 30.8 + - - +
240A VAL* 3.4 30.6 - - - +
242A ALA* 3.9 7.2 - - - +
265A VAL* 4.4 2.4 - - - +
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Residues in contact with VAL 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A VAL* 3.9 24.7 - - + -
175A ILE* 4.1 13.2 - - + -
179A GLY 2.9 17.4 + - - +
180A LEU* 3.4 10.5 - - - +
182A SER* 1.3 71.9 - - - +
184A ALA* 1.3 61.5 + - - +
186A ALA* 3.3 4.9 + - - +
187A ASN* 2.9 28.2 + - - +
194A ILE* 3.9 8.4 - - + +
196A ALA* 4.3 11.0 - - + -
207A ALA* 3.7 15.0 - - + +
210A TYR* 3.7 9.6 - - + +
211A GLY 4.0 2.0 - - - -
212A ALA* 3.4 30.7 - - - +
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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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156A PHE* 3.9 11.7 - - + -
180A LEU 3.0 15.8 + - - +
181A MET* 3.7 20.0 - - + +
182A SER 3.3 0.2 - - - -
183A VAL* 1.3 77.4 - - - +
185A GLY* 1.3 56.1 + - - +
187A ASN* 3.3 2.1 + - - +
188A HIS* 2.7 42.6 + - + +
210A TYR* 3.6 26.2 - - + +
314A LEU* 4.3 8.1 - - + -
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Residues in contact with GLY 185 (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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156A PHE* 3.4 26.2 - - - -
159A ALA* 3.7 11.9 - - - -
181A MET 2.8 20.4 + - - -
182A SER 3.9 0.9 - - - -
184A ALA* 1.3 73.0 - - - +
186A ALA* 1.3 57.2 + - - +
188A HIS* 3.1 4.1 + - - +
189A LEU* 2.9 34.5 + - - +
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Residues in contact with ALA 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A ALA* 3.5 1.8 - - - +
164A ILE* 3.6 30.6 - - + +
170A VAL* 4.3 11.0 - - + -
172A VAL* 4.9 1.8 - - + -
182A SER 2.9 19.9 + - - +
183A VAL* 3.6 6.3 - - - +
185A GLY* 1.3 75.9 - - - +
187A ASN* 1.3 60.6 + - - +
189A LEU* 3.1 10.7 + - - +
190A GLY 3.1 0.7 + - - -
191A ALA* 3.0 28.1 + - + +
194A ILE* 4.0 13.5 - - + -
240A VAL* 5.4 0.2 - - + -
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Residues in contact with ASN 187 (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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183A VAL 2.9 10.6 + - - +
184A ALA* 3.4 4.3 - - - +
186A ALA* 1.3 76.0 - - - +
188A HIS* 1.3 64.9 + - + +
190A GLY* 3.2 17.7 + - - -
191A ALA 3.8 16.2 + - - +
192A GLY 5.3 0.6 + - - -
194A ILE* 3.9 9.1 - - + +
210A TYR 3.4 27.1 - - - +
211A GLY* 3.9 15.4 + - - -
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Residues in contact with HIS 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A PHE* 4.3 17.0 - + + -
184A ALA* 2.7 36.3 + - + +
185A GLY* 3.1 8.3 + - - +
187A ASN* 1.3 83.0 + - + +
189A LEU* 1.3 64.6 + - + +
190A GLY 3.4 0.4 - - - -
210A TYR 5.7 0.2 - - - -
308A LEU* 4.5 18.2 - - + +
313A LYS* 3.0 39.4 + - + +
314A LEU* 4.4 11.4 - - + +
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Residues in contact with LEU 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A PHE 4.9 0.2 - - - +
159A ALA* 3.6 43.5 - - + +
160A GLU* 3.8 17.0 - - + +
164A ILE* 4.0 32.8 - - + +
165A LYS* 4.0 9.5 - - - -
166A LEU* 4.1 6.4 + - - +
185A GLY 2.9 13.0 + - - +
186A ALA 3.1 6.0 + - - +
188A HIS* 1.3 83.5 - - + +
190A GLY* 1.3 58.7 + - - +
191A ALA 3.7 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