Contacts of the helix formed by residues 171 - 180 (chain A) in PDB entry 2AWP
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 ASP 171 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168A TYR* 2.9 30.2 + - + +
169A ARG 3.1 1.5 - - - -
170A ASN* 1.3 82.0 - - - +
172A ARG* 1.3 64.6 + - - +
173A PRO* 3.3 18.8 - - - +
174A SER* 2.7 33.8 + - - -
175A TYR 3.4 7.1 + - - -
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Residues in contact with ARG 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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115A LEU 2.9 30.7 + - - -
116A CYS* 3.6 14.0 + - - +
118A HIS* 2.7 38.6 + - - +
120A GLY 3.9 15.6 + - - +
159A ILE* 3.8 21.5 + - - +
161A GLU* 5.3 4.4 + - - +
164A TYR* 3.1 50.6 + - + +
170A ASN 3.0 10.4 + - - +
171A ASP* 1.3 71.6 - - - +
173A PRO* 1.4 70.3 - - + +
175A TYR* 3.0 7.6 + - + +
176A VAL* 2.9 27.9 + - + +
160B TRP* 6.0 2.0 - - - -
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Residues in contact with PRO 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A CYS* 3.7 32.0 - - + +
170A ASN 4.7 1.6 - - - +
171A ASP* 3.3 15.3 - - - +
172A ARG* 1.4 93.2 - - + +
174A SER* 1.3 55.5 + - - +
176A VAL* 3.3 3.3 + - + +
177A LYS* 2.9 30.5 + - - +
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Residues in contact with SER 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A TYR* 3.6 23.4 - - - -
171A ASP* 2.7 30.9 + - - -
173A PRO* 1.3 75.1 - - - +
175A TYR* 1.3 65.5 + - - +
177A LYS* 3.4 7.8 + - - +
178A ALA* 3.0 25.1 + - - +
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Residues in contact with TYR 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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18A HIS 5.1 0.2 - - - -
19A ILE* 3.9 19.0 - - + +
77A TYR* 2.7 30.0 + - - -
157A CYS* 3.5 21.2 - - - -
158A ASP 2.6 30.5 + - - -
159A ILE* 4.1 5.4 - - + -
163A ALA* 3.8 17.1 - - + +
164A TYR* 3.4 43.1 - + + -
168A TYR* 3.6 26.5 - + + -
171A ASP 3.4 3.0 + - - +
172A ARG* 3.0 13.3 + - + +
174A SER* 1.3 79.6 - - - +
176A VAL* 1.3 69.1 + - + +
178A ALA* 3.4 2.4 + - - +
179A TRP* 3.0 24.4 + + + +
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Residues in contact with VAL 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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112A SER* 3.8 41.1 - - - +
115A LEU* 3.9 31.2 - - + -
116A CYS* 4.2 10.8 - - - +
157A CYS* 5.3 0.7 - - - -
159A ILE* 4.6 1.3 - - + -
172A ARG* 2.9 27.1 + - + +
173A PRO 3.7 7.6 - - - +
175A TYR* 1.3 87.4 - - + +
177A LYS* 1.3 62.9 + - - +
179A TRP* 3.2 18.2 + - + +
180A TRP* 3.0 21.0 + - - +
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Residues in contact with LYS 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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108A LYS* 5.8 7.1 - - - +
173A PRO 2.9 17.9 + - - +
174A SER* 3.7 8.5 - - - +
175A TYR 3.3 0.2 - - - -
176A VAL* 1.3 77.2 - - - +
178A ALA* 1.3 61.9 + - - +
179A TRP 3.4 0.5 + - - -
180A TRP* 3.4 25.0 + - + +
181A ASN* 3.9 6.1 + - - -
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Residues in contact with ALA 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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18A HIS* 3.6 27.5 - - + +
19A ILE* 6.2 0.2 - - + -
168A TYR* 3.2 27.4 - - + +
174A SER 3.0 14.1 + - - +
175A TYR 3.7 4.5 - - - +
177A LYS* 1.3 76.3 - - - +
179A TRP* 1.3 57.1 + - - +
181A ASN* 3.0 37.1 + - - +
182A LEU 4.1 0.7 + - - -
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Residues in contact with TRP 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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19A ILE* 4.7 5.2 - - + -
77A TYR* 4.2 5.4 - + - -
80A SER* 4.7 11.4 - - - -
81A MET* 3.6 35.6 - - + +
107A PHE* 6.3 0.2 - + - -
111A PHE* 3.8 25.8 - + - -
115A LEU* 5.0 2.9 - - + -
155A LEU* 4.9 9.4 - - + -
156A THR 3.6 21.2 + - - -
157A CYS* 3.8 30.0 - - + +
175A TYR* 3.0 22.9 + - + +
176A VAL* 3.2 15.8 + - - +
178A ALA* 1.3 76.8 - - - +
180A TRP* 1.3 86.1 + + - +
182A LEU* 2.9 27.4 + - - +
183A VAL* 3.2 45.6 + - + -
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Residues in contact with TRP 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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86A GLY* 3.3 17.2 - - - -
87A GLY 3.7 7.3 + - - +
104A PHE* 3.9 26.2 - + + -
107A PHE* 3.7 27.4 - + - -
108A LYS* 3.6 48.6 - - + +
111A PHE* 3.6 34.1 - + + -
112A SER* 2.9 29.0 + - - -
115A LEU* 5.1 0.7 - - + -
155A LEU* 6.4 0.2 - - + -
176A VAL* 3.0 31.5 + - - +
177A LYS* 3.4 16.5 + - - +
178A ALA 3.2 0.6 - - - -
179A TRP* 1.3 90.1 - + - +
181A ASN* 1.3 60.5 + - - +
182A LEU 3.2 0.8 + - - -
183A VAL* 3.7 20.3 - - + +
185A TRP* 4.6 2.5 - + - -
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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