Contacts of the helix formed by residues 114 - 123 (chain A) in PDB entry 2AVD
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 114 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72A LEU* 3.6 4.0 - - - -
111A THR* 2.8 20.3 + - - -
112A PHE 3.2 1.6 + - - -
113A THR* 1.3 78.5 - - - +
115A TYR* 1.3 59.6 + - - +
116A SER 3.6 1.8 - - - -
117A ALA* 3.6 5.5 - - - +
118A LEU* 2.8 33.8 + - - +
147A TRP* 3.5 23.6 + - - -
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Residues in contact with TYR 115 (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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65A GLU* 2.6 29.2 + - - +
69A LEU* 3.3 47.9 - - + +
72A LEU* 3.6 11.6 - - + +
73A ARG* 3.6 16.2 - - + -
85A MET* 3.7 39.7 - - + -
86A MET* 3.8 14.1 - - + -
88A CYS* 3.3 22.3 + - - +
91A ALA* 3.3 27.9 - - + +
111A THR 4.1 2.4 + - - -
113A THR* 3.5 4.9 + - - +
114A GLY* 1.3 78.4 - - - +
116A SER* 1.3 60.5 + - - +
119A ALA* 2.9 27.2 + - - +
501A SAM 3.8 7.5 + - - +
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Residues in contact with SER 116 (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 MET* 4.1 17.7 - - - -
91A ALA* 4.9 2.0 - - - +
94A LEU* 6.0 0.7 - - - -
108A ASP* 2.6 28.5 + - - -
111A THR 4.9 0.7 + - - -
115A TYR* 1.3 77.6 - - - +
117A ALA* 1.3 59.2 + - - +
119A ALA* 3.6 7.0 - - - +
120A LEU* 2.9 39.1 + - - +
183A VAL* 4.9 6.7 - - - -
501A SAM 3.0 34.8 + - - -
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Residues in contact with ALA 117 (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 ASP* 3.5 20.6 + - - +
111A THR* 4.8 0.2 - - + -
114A GLY* 3.4 16.7 + - - +
115A TYR 3.3 0.6 - - - -
116A SER* 1.3 82.2 + - - +
118A LEU* 1.3 56.6 + - - +
120A LEU* 3.4 2.4 + - - +
121A ALA* 2.9 28.8 + - - +
130A VAL* 3.9 12.5 - - + +
132A THR* 3.8 24.7 - - + +
147A TRP* 4.9 0.4 - - + -
156A ILE* 4.1 14.7 - - + +
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Residues in contact with LEU 118 (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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68A ALA 4.3 2.0 - - - +
69A LEU* 3.8 35.4 - - + +
72A LEU* 4.1 14.8 - - + -
114A GLY 2.8 20.9 + - - +
115A TYR 3.8 2.7 - - - +
117A ALA* 1.3 72.8 - - - +
119A ALA* 1.3 65.6 + - - +
122A LEU* 3.0 32.2 + - + +
146A LEU 4.1 19.3 - - - +
147A TRP* 4.2 13.5 - - + -
150A ALA* 3.6 25.1 - - + -
152A ALA* 3.7 20.9 - - + -
156A ILE* 4.0 6.7 - - + +
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Residues in contact with ALA 119 (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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69A LEU* 3.7 23.4 - - + +
91A ALA* 3.8 35.9 - - + +
95A ALA* 3.4 18.6 - - + +
115A TYR 2.9 16.9 + - - +
116A SER* 3.6 5.2 - - - +
118A LEU* 1.3 78.2 - - - +
120A LEU* 1.3 64.2 + - + +
122A LEU* 3.5 9.8 + - - +
123A ALA 3.6 4.0 + - - -
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Residues in contact with LEU 120 (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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94A LEU* 4.4 25.4 - - + +
95A ALA* 4.6 1.3 - - - +
98A ALA* 4.5 8.1 - - + -
106A ALA* 4.3 18.2 - - + -
107A LEU 4.5 0.7 - - - +
108A ASP* 4.0 24.2 - - + +
116A SER* 2.9 23.0 + - - +
117A ALA 3.7 2.9 - - - +
119A ALA* 1.3 73.7 - - + +
121A ALA* 1.3 57.4 + - - +
123A ALA* 2.8 29.4 + - - +
124A LEU* 3.4 13.9 - - + +
130A VAL* 3.9 11.9 - - + -
181A VAL* 4.2 22.2 - - + -
183A VAL* 3.9 24.9 - - + -
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Residues in contact with ALA 121 (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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117A ALA 2.9 21.0 + - - +
118A LEU 3.7 4.5 - - - +
120A LEU* 1.3 72.3 - - - +
122A LEU* 1.3 57.3 + - - +
124A LEU* 3.1 16.2 + - - +
130A VAL* 3.5 12.9 - - + +
152A ALA* 4.0 13.7 - - + -
155A LYS* 2.9 35.5 + - + +
156A ILE* 3.7 26.7 - - + -
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Residues in contact with LEU 122 (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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66A HIS* 3.6 39.7 - - + -
69A LEU* 4.3 15.0 - - + -
118A LEU* 3.0 41.6 + - + +
119A ALA 3.8 5.6 - - - +
120A LEU 3.2 0.4 + - - -
121A ALA* 1.3 75.2 - - - +
123A ALA* 1.3 58.1 + - - +
124A LEU 3.3 3.9 - - - +
150A ALA* 4.0 29.6 - - + +
152A ALA* 5.0 2.9 - - + -
155A LYS* 4.5 6.5 + - - +
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Residues in contact with ALA 123 (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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95A ALA* 3.1 42.0 - - + +
98A ALA* 4.1 5.4 - - + -
99A ARG* 3.9 33.4 - - + +
103A ALA 4.7 1.9 + - - +
119A ALA 3.6 1.2 + - - -
120A LEU 2.8 11.9 + - - +
122A LEU* 1.3 76.9 - - - +
124A LEU* 1.3 62.7 + - - +
125A PRO* 4.4 1.4 - - - +
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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