Contacts of the helix formed by residues 126 - 134 (chain C) in PDB entry 2AAZ
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 VAL 126 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82C TRP* 4.7 7.2 - - + -
87C CYS 5.4 0.7 - - - +
88C THR* 3.9 14.3 - - + +
101C TRP* 6.2 4.5 - - + -
123C LEU* 3.8 45.8 - - + +
124C GLY 2.8 16.1 + - - +
125C PRO* 1.3 75.1 - - - +
127C TYR* 1.3 83.3 + - + +
128C GLY 5.0 0.9 - - - +
129C PHE 2.8 16.5 + - - -
130C GLN* 3.3 6.4 + - - -
182C MET* 3.9 25.8 - - + -
183C ALA 4.5 1.6 - - - +
184C LEU* 4.0 12.6 - - + +
186C PRO* 6.0 0.9 - - + -
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Residues in contact with TYR 127 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82C TRP* 5.4 0.2 - + - -
83C PHE* 3.5 34.1 - + + -
101C TRP* 3.7 30.1 - + - -
126C VAL* 1.3 85.6 - - + +
128C GLY* 1.3 65.7 + - - +
130C GLN* 3.0 2.9 + - - +
131C TRP* 2.9 33.0 + - - +
173C ALA* 3.9 23.3 - - + +
184C LEU 5.9 2.0 - - - -
185C PRO 4.3 1.3 + - - -
186C PRO* 3.5 23.8 - - + +
187C CYS* 2.7 29.1 + - - +
188C HIS* 3.2 49.7 - + + -
450C UMP 3.8 7.9 + - - -
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Residues in contact with GLY 128 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83C PHE* 3.1 34.6 - - - +
86C GLY* 3.3 21.3 - - - -
87C CYS 4.5 4.7 + - - -
126C VAL* 3.0 3.2 + - - +
127C TYR* 1.3 78.0 - - - +
129C PHE* 1.3 60.8 + - - +
131C TRP* 3.4 6.0 + - - +
132C ARG* 3.2 18.9 + - - +
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Residues in contact with PHE 129 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86C GLY 3.6 11.5 + - - -
88C THR* 3.5 18.2 - - + +
125C PRO* 3.5 28.7 - - + -
126C VAL 2.8 16.0 + - - +
128C GLY* 1.3 71.9 - - - -
130C GLN* 1.3 63.8 + - - +
133C HIS* 2.7 63.5 + + + +
135C GLY 5.3 0.7 - - - -
136C ALA* 3.7 36.3 - - + -
138C TYR* 3.6 28.5 - + + -
145C TYR* 3.6 37.7 - + - -
178C ASP* 4.2 2.2 - - - -
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Residues in contact with GLN 130 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125C PRO* 2.8 32.3 + - - +
126C VAL 3.3 6.0 + - - +
127C TYR 3.0 4.3 + - - +
129C PHE* 1.3 80.8 - - - +
131C TRP* 1.3 62.8 + - - +
134C PHE* 3.1 36.1 + - + +
135C GLY 4.4 0.2 + - - -
152C GLN* 2.8 19.6 + - - -
172C SER 4.1 1.8 - - - +
173C ALA* 3.2 38.4 - - - +
175C ASN* 3.0 25.9 + - + +
178C ASP* 3.0 31.7 + - - +
182C MET* 4.1 1.3 - - + +
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Residues in contact with TRP 131 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80C LEU* 4.4 9.6 - - + -
83C PHE* 3.5 45.1 - + + -
84C VAL* 4.4 10.5 - - + -
127C TYR* 2.9 22.7 + - + +
128C GLY* 3.6 8.7 - - - +
130C GLN* 1.3 77.9 - - - +
132C ARG* 1.3 66.0 + - + +
152C GLN* 2.9 35.7 + - - +
153C LEU* 3.4 11.3 + - + -
171C LEU* 3.8 40.0 + - + +
172C SER* 4.0 6.2 - - - +
173C ALA* 3.8 25.3 - - + +
188C HIS* 4.4 10.2 + + - -
190C PHE* 6.3 0.2 - - - +
230C SER* 6.0 0.2 - - - -
231C TYR* 3.3 28.1 + + - -
234C LEU* 4.0 24.5 - - + -
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Residues in contact with ARG 132 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84C VAL* 2.6 50.2 + - - +
85C SER* 4.6 1.9 - - - +
86C GLY* 4.0 6.5 - - - -
128C GLY 3.2 16.5 + - - +
131C TRP* 1.3 79.4 - - + +
133C HIS* 1.3 85.2 + - + +
148C LYS 3.9 1.9 - - - +
149C GLY 4.6 0.2 - - - -
150C VAL 3.3 12.7 - - - +
151C ASP* 2.8 53.8 + - - +
153C LEU* 3.6 26.4 - - - +
154C GLN* 4.4 7.5 - - - +
292C ILE* 4.2 6.7 - - - +
293C ASP* 2.7 37.4 + - - -
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Residues in contact with HIS 133 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85C SER 5.1 2.6 + - - -
86C GLY* 4.7 11.3 + - - -
129C PHE* 2.7 51.0 + + + +
132C ARG* 1.3 96.1 + - + +
134C PHE* 1.3 65.9 + - - +
135C GLY 3.2 0.3 + - - -
136C ALA* 2.9 21.5 + - + +
145C TYR* 3.0 41.1 + + + +
146C LYS* 4.2 6.1 - - - -
147C GLY 4.6 2.5 - - - -
148C LYS 2.9 26.1 + - - +
149C GLY* 3.8 0.4 - - - -
150C VAL 3.7 3.6 - - - -
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Residues in contact with PHE 134 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130C GLN* 3.1 42.0 + - - +
133C HIS* 1.3 74.5 - - - +
135C GLY* 1.3 64.4 + - - +
149C GLY* 3.3 3.1 - - - -
150C VAL* 2.8 43.6 + - + +
152C GLN* 3.6 20.4 - - - +
172C SER* 4.3 5.6 - - - -
174C TRP 3.3 23.8 - - - -
175C ASN* 3.5 20.9 - - - -
134D PHE* 3.9 16.4 - + - -
175D ASN* 3.6 15.0 - - - -
176D PRO* 3.4 36.8 - - + -
177D LYS* 4.0 8.9 - - + +
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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