Contacts of the helix formed by residues 126 - 134 (chain I) 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 I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82I TRP* 4.7 7.0 - - + -
87I CYS 5.3 0.7 - - - +
88I THR* 4.0 14.7 - - + +
101I TRP* 6.2 4.5 - - + -
123I LEU* 3.7 45.3 - - + +
124I GLY 2.8 16.5 + - - +
125I PRO* 1.3 74.8 - - - +
127I TYR* 1.3 84.0 + - + +
128I GLY 3.0 1.3 + - - +
129I PHE 2.8 16.3 + - - -
130I GLN* 3.3 6.2 + - - -
182I MET* 3.9 25.4 - - + -
183I ALA* 4.5 1.8 - - + +
184I LEU* 4.1 13.5 - - + +
186I PRO* 6.0 0.9 - - + -
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Residues in contact with TYR 127 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82I TRP* 5.4 0.2 - + - -
83I PHE* 3.4 33.9 - + + -
101I TRP* 3.7 30.2 - + - -
126I VAL* 1.3 84.1 - - + +
128I GLY* 1.3 66.7 + - - +
130I GLN* 3.0 3.3 + - - +
131I TRP* 2.9 32.4 + - - +
173I ALA* 3.9 23.2 - - + +
184I LEU 5.8 2.0 - - - -
185I PRO 4.3 1.1 + - - -
186I PRO* 3.5 26.8 - - + +
187I CYS* 2.7 24.0 + - - -
188I HIS* 3.2 41.0 - + + -
350I UMP 3.3 17.7 - + - -
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Residues in contact with GLY 128 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82I TRP* 6.2 0.2 - - - -
83I PHE* 3.1 34.2 - - - -
86I GLY* 3.3 21.6 - - - -
87I CYS 4.5 5.3 + - - -
126I VAL* 3.0 3.4 + - - +
127I TYR* 1.3 78.0 - - - +
129I PHE* 1.3 60.5 + - - +
131I TRP* 3.4 5.8 + - - +
132I ARG* 3.1 19.1 + - - +
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Residues in contact with PHE 129 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86I GLY 3.6 11.0 + - - -
88I THR* 3.6 18.8 - - + +
125I PRO* 3.5 28.3 - - + -
126I VAL 2.8 16.6 + - - +
128I GLY* 1.3 71.7 - - - -
130I GLN* 1.3 64.1 + - - +
133I HIS* 2.7 62.2 + + + +
135I GLY 5.3 0.7 - - - -
136I ALA* 3.7 36.6 - - + -
138I TYR* 3.6 29.2 - + + -
145I TYR* 3.6 36.3 - + - -
178I ASP* 4.3 2.5 - - - -
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Residues in contact with GLN 130 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125I PRO* 2.9 32.5 + - - +
126I VAL 3.3 5.4 + - - +
127I TYR 3.0 7.2 + - - +
129I PHE* 1.3 81.2 - - - +
131I TRP* 1.3 62.9 + - - +
134I PHE* 3.1 35.0 + - + +
135I GLY 4.4 0.2 + - - -
150I VAL 4.1 0.2 - - - +
152I GLN* 2.8 19.3 + - - -
172I SER 4.1 1.8 - - - +
173I ALA* 3.2 36.1 - - - +
175I ASN* 3.1 27.0 + - + +
178I ASP* 2.9 30.9 + - - +
182I MET* 4.2 1.3 - - + +
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Residues in contact with TRP 131 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80I LEU* 4.5 9.0 - - + -
83I PHE* 3.5 44.6 - + + -
84I VAL* 4.4 10.8 - - + -
127I TYR* 2.9 21.8 + - + +
128I GLY* 3.5 10.1 - - - +
130I GLN* 1.3 77.5 - - - +
132I ARG* 1.3 64.2 + - + +
152I GLN* 3.0 30.8 + - - +
153I LEU* 3.4 15.9 + - + -
171I LEU* 3.8 40.0 + - + +
172I SER* 4.0 6.4 - - - +
173I ALA* 3.7 25.5 - - + +
188I HIS* 4.4 10.2 + + - -
189I MET 6.3 0.2 - - - -
190I PHE* 6.2 0.2 - - - +
230I SER* 6.0 0.2 - - - -
231I TYR* 3.4 28.1 + + - -
234I LEU* 4.0 24.2 - - + -
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Residues in contact with ARG 132 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83I PHE 4.5 0.2 - - - +
84I VAL* 2.6 48.1 + - - +
85I SER* 4.7 2.2 - - - +
86I GLY* 4.1 6.1 - - - -
128I GLY 3.1 16.0 + - - +
131I TRP* 1.3 79.3 - - + +
133I HIS* 1.3 87.2 + - + +
148I LYS 3.9 1.6 - - - +
149I GLY 4.7 0.2 - - - +
150I VAL 3.4 12.2 - - - +
151I ASP* 2.7 53.4 + - - +
153I LEU* 3.6 27.4 - - - +
154I GLN* 4.4 7.1 - - - +
292I ILE* 4.3 6.1 - - - +
293I ASP* 2.8 36.7 + - - -
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Residues in contact with HIS 133 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85I SER 5.2 2.8 + - - -
86I GLY* 4.7 11.1 + - - -
129I PHE* 2.7 48.0 + + + +
132I ARG* 1.3 96.2 + - + +
134I PHE* 1.3 64.9 + - - +
135I GLY 3.2 0.5 + - - -
136I ALA* 3.0 25.5 + - + +
145I TYR* 3.0 41.3 + + + +
146I LYS* 4.2 6.5 - - - -
147I GLY 4.6 2.7 - - - -
148I LYS 2.9 27.0 + - - +
149I GLY* 3.8 2.0 - - - -
150I VAL 3.8 1.8 - - - -
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Residues in contact with PHE 134 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130I GLN* 3.1 35.9 + - - +
133I HIS* 1.3 74.7 - - - +
135I GLY* 1.3 65.7 + - - +
149I GLY* 3.3 2.8 - - - -
150I VAL* 2.8 39.2 + - + +
152I GLN* 3.6 21.3 - - - +
172I SER* 4.3 6.1 - - - -
174I TRP 3.4 22.9 - - - -
175I ASN* 3.4 26.7 - - - -
134J PHE* 3.9 17.5 - + - -
174J TRP 4.9 0.4 - - - -
175J ASN* 3.6 15.0 - - - -
176J PRO* 3.5 39.9 - - + -
177J LYS* 4.0 7.5 - - + +
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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