Contacts of the helix formed by residues 171 - 182 (chain A) in PDB entry 2AYN
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 PRO 171 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106A LEU* 3.7 27.6 - - + -
107A THR 3.9 15.0 - - - +
109A LEU* 3.9 10.3 - - + -
115A MET* 5.2 6.1 - - - -
116A ASN* 4.7 7.2 - - - +
158A LEU* 3.8 25.6 - - + -
169A ILE* 3.1 16.8 - - + +
170A PRO* 1.3 79.2 - - + +
172A ILE* 1.3 65.3 + - - +
173A ILE* 3.2 4.7 - - + -
174A LEU* 3.2 11.7 + - + +
175A LEU* 2.9 21.6 + - - +
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Residues in contact with ILE 172 (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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109A LEU* 3.7 20.6 - - + +
170A PRO* 3.0 19.8 + - + +
171A PRO* 1.3 71.5 - - - +
173A ILE* 1.3 68.1 + - + +
175A LEU* 3.0 6.3 + - + +
176A GLN* 2.7 38.8 + - + +
163B ASP 3.8 9.2 - - - +
164B LYS* 2.8 57.2 - - + +
165B THR 4.6 0.2 - - - -
166B SER* 3.6 21.5 - - - -
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Residues in contact with ILE 173 (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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154A ALA* 4.7 11.0 - - + +
157A ASP* 6.2 4.9 - - + -
170A PRO 5.5 1.3 - - - +
171A PRO* 4.9 2.0 - - + -
172A ILE* 1.3 80.6 - - + +
174A LEU* 1.3 64.7 + - - +
176A GLN* 3.2 9.7 + - - +
177A PHE* 3.0 45.9 + - + -
100B MET* 6.4 2.2 - - - -
101B GLU* 3.2 39.0 - - + +
166B SER* 5.7 2.7 + - - +
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Residues in contact with LEU 174 (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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115A MET* 3.6 28.0 - - + -
119A VAL* 4.1 8.5 - - + -
151A ILE* 4.2 20.9 - - + +
154A ALA* 4.0 29.5 + - + +
155A LEU* 4.1 25.8 - - + +
158A LEU* 3.5 29.4 - - + -
171A PRO* 3.2 13.8 + - + +
173A ILE* 1.3 78.8 - - - +
175A LEU* 1.3 65.6 + - - +
177A PHE* 2.8 5.0 + - - +
178A LEU* 2.8 22.8 + - + +
206A MET* 4.8 6.3 - - + -
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Residues in contact with LEU 175 (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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109A LEU* 3.5 33.7 - - + +
112A THR* 3.8 24.2 - - + -
114A TYR* 4.4 7.9 - - - +
115A MET* 3.6 27.7 - - + +
171A PRO* 2.9 16.1 + - + +
172A ILE* 3.3 11.9 - - + +
174A LEU* 1.3 72.7 - - - +
176A GLN* 1.3 67.2 + - + +
178A LEU* 3.0 3.7 + - + +
179A HIS* 2.8 56.1 + - + +
194A TYR* 5.2 9.9 - - + -
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Residues in contact with GLN 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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172A ILE* 2.7 35.7 + - + +
173A ILE* 3.5 12.9 - - - +
175A LEU* 1.3 76.0 - - + +
177A PHE* 1.3 60.6 + - + +
179A HIS* 2.9 16.7 + - + +
180A MET* 2.7 40.6 + - + +
194A TYR* 5.9 1.6 - - - +
165B THR* 2.9 27.0 - - - +
166B SER* 3.8 12.5 + - - +
167B SER* 4.7 2.6 + - - -
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Residues in contact with PHE 177 (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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150A TYR* 3.2 58.3 - + + -
151A ILE* 3.4 23.9 - - + +
154A ALA* 4.5 5.6 - - + -
173A ILE* 3.0 32.5 - - + +
174A LEU* 2.8 10.1 + - - +
176A GLN* 1.3 81.3 - - + +
178A LEU* 1.3 68.2 + - - +
180A MET* 3.4 14.5 - - + +
181A ALA* 2.9 19.4 + - - +
100B MET* 4.7 24.0 - - + -
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Residues in contact with LEU 178 (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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114A TYR* 3.8 21.1 - - + +
115A MET* 3.3 32.5 - - + -
151A ILE* 3.8 14.3 - - + +
174A LEU* 2.8 7.8 + - + +
175A LEU* 3.3 9.2 - - + +
177A PHE* 1.3 76.4 - - - +
179A HIS* 1.3 53.7 + - - +
181A ALA 3.2 0.2 + - - -
182A PHE* 2.7 55.3 + - + +
185A PHE* 3.4 32.5 - - + -
202A CYS* 4.3 4.0 - - - -
206A MET* 4.0 33.4 - - + -
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Residues in contact with HIS 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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112A THR* 6.0 1.1 - - + -
114A TYR* 4.4 3.4 - - - -
175A LEU* 2.8 56.7 + - + +
176A GLN* 3.2 13.7 - - + +
178A LEU* 1.3 76.1 - - + +
180A MET* 1.3 67.8 + - + +
182A PHE 3.0 23.9 + - - -
183A PRO* 3.3 6.8 - - - +
185A PHE* 3.7 17.2 - - + +
186A ALA* 3.3 42.0 + - + +
194A TYR* 3.6 32.3 - + + -
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Residues in contact with MET 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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147A SER* 4.8 6.2 + - - +
176A GLN* 2.7 22.3 + - + +
177A PHE* 3.4 20.0 - - + +
179A HIS* 1.3 75.8 - - + +
181A ALA* 1.3 60.9 + - + +
183A PRO* 4.2 9.4 - - - +
453C LYS* 5.6 7.6 - - - +
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Residues in contact with ALA 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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147A SER* 3.7 27.1 - - - -
148A ALA* 5.3 0.7 - - - +
151A ILE* 3.4 32.3 - - + -
177A PHE 2.9 5.5 + - - +
178A LEU 3.8 0.9 - - - +
180A MET* 1.3 78.5 - - - +
182A PHE* 1.3 79.8 + - + +
183A PRO* 3.5 7.2 - - - +
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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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151A ILE* 4.0 18.2 - - + -
178A LEU* 2.7 36.0 + - + +
179A HIS 3.0 5.6 + - - +
181A ALA* 1.3 91.3 - - + +
183A PRO* 1.3 66.3 - - - +
184A GLN* 2.9 27.6 - - - +
185A PHE* 2.8 44.2 + + + +
186A ALA 3.9 0.7 + - - -
205A GLN* 3.3 53.4 - - + -
206A MET* 5.5 0.4 - - + -
209A VAL* 4.1 12.3 - - + -
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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