Contacts of the helix formed by residues 114 - 124 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72B LEU* 3.8 4.0 - - - -
111B THR* 2.9 20.9 + - - -
112B PHE 3.3 1.0 + - - -
113B THR* 1.3 80.1 - - - +
115B TYR* 1.3 55.9 + - - +
116B SER 3.5 2.5 - - - -
117B ALA* 3.6 5.3 - - - +
118B LEU* 2.8 37.1 + - - +
147B TRP* 3.6 21.0 + - - -
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Residues in contact with TYR 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B MET* 5.1 0.2 - - - +
65B GLU* 2.5 23.7 + - - +
69B LEU* 3.3 51.3 - - + +
72B LEU* 3.8 11.6 - - + +
73B ARG* 3.6 17.3 - - + -
85B MET* 3.6 22.9 - - + -
86B MET* 3.4 28.9 - - + -
87B THR 4.0 3.6 - - - -
88B CYS* 3.3 18.9 + - - +
91B ALA* 3.5 27.2 - - + +
111B THR 4.2 0.4 + - - -
113B THR* 3.6 5.7 - - - +
114B GLY* 1.3 76.5 - - - +
116B SER* 1.3 59.4 + - - +
118B LEU 3.3 0.2 + - - -
119B ALA* 2.9 29.3 + - - +
601B SAM 3.5 12.0 + - - +
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Residues in contact with SER 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B MET* 3.5 35.7 - - - -
108B ASP* 2.7 28.7 + - - -
111B THR 4.8 1.2 + - - -
115B TYR* 1.3 70.9 - - - +
117B ALA* 1.3 65.1 + - - +
119B ALA* 3.4 5.0 + - - +
120B LEU* 3.0 32.8 + - - +
183B VAL* 4.9 0.7 - - - -
601B SAM 3.0 31.0 + - - -
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Residues in contact with ALA 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B ASP* 3.6 20.3 + - - +
111B THR* 4.8 0.4 - - + -
114B GLY* 3.4 16.4 + - - +
115B TYR 3.3 0.4 - - - -
116B SER* 1.3 82.9 + - - +
118B LEU* 1.3 57.4 + - - +
120B LEU* 3.4 2.3 + - - +
121B ALA* 2.9 28.2 + - - +
130B VAL* 3.9 12.5 - - + +
132B THR* 3.9 19.1 - - + +
156B ILE* 4.1 20.8 - - + +
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Residues in contact with LEU 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B ALA 4.4 1.6 - - - -
69B LEU* 3.8 34.1 - - + +
72B LEU* 3.9 16.4 - - + -
114B GLY 2.8 21.9 + - - +
115B TYR 3.8 3.4 - - - +
117B ALA* 1.3 69.9 - - - +
119B ALA* 1.3 68.5 + - - +
121B ALA* 3.1 0.9 + - - +
122B LEU* 3.0 36.5 + - + +
146B LEU 4.2 13.2 - - - +
147B TRP* 4.1 20.4 - - + -
150B ALA* 3.8 15.7 - - + -
152B ALA* 3.7 28.5 - - + -
156B ILE* 4.0 8.5 - - + -
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Residues in contact with ALA 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B LEU* 3.7 23.2 - - + +
86B MET* 5.7 0.2 - - - -
91B ALA* 3.7 37.5 - - + +
95B ALA* 3.6 16.8 - - + +
115B TYR 2.9 17.3 + - - +
116B SER* 3.7 4.9 - - - +
118B LEU* 1.3 77.3 - - - +
120B LEU* 1.3 61.8 + - + +
122B LEU* 3.6 5.1 + - - +
123B ALA 3.5 11.8 + - - -
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Residues in contact with LEU 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94B LEU* 4.5 28.7 - - + +
95B ALA* 4.7 1.3 - - - +
98B ALA* 4.5 8.7 - - + -
106B ALA* 4.2 20.0 - - + -
107B LEU 4.8 1.6 - - - +
108B ASP* 4.2 20.0 - - + +
116B SER* 3.0 23.0 + - - +
117B ALA 3.6 3.1 - - - +
119B ALA* 1.3 75.2 - - + +
121B ALA* 1.3 66.9 + - - +
123B ALA* 2.9 18.1 + - - +
124B LEU* 3.3 15.6 + - + +
130B VAL* 3.8 13.7 - - + -
181B VAL* 4.2 20.6 - - + -
183B VAL* 4.1 21.8 - - + -
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Residues in contact with ALA 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117B ALA 2.9 21.9 + - - +
118B LEU 3.1 4.9 + - - +
120B LEU* 1.3 72.5 - - - +
122B LEU* 1.3 57.5 + - - +
124B LEU* 3.1 16.5 + - - +
130B VAL* 3.7 11.8 - - + +
152B ALA* 4.0 14.6 - - + -
155B LYS* 3.0 35.1 + - + -
156B ILE* 3.8 26.2 - - + -
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Residues in contact with LEU 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66B HIS* 3.7 46.9 - - + +
69B LEU* 4.3 13.7 - - + -
118B LEU* 3.0 37.8 + - + +
119B ALA 3.8 4.9 - - - +
120B LEU 3.2 0.2 - - - -
121B ALA* 1.3 74.5 - - - +
123B ALA* 1.3 58.8 + - - +
124B LEU 3.3 4.9 + - - +
150B ALA* 4.1 24.7 - - + +
152B ALA* 4.5 6.1 - - + -
155B LYS* 4.8 4.3 + - - +
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Residues in contact with ALA 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B ALA* 3.3 44.9 - - + +
98B ALA* 4.0 10.7 - - + -
99B ARG* 4.1 25.9 + - + +
103B ALA 4.8 1.7 - - - +
119B ALA 3.5 2.0 + - - -
120B LEU 2.9 11.8 + - - +
122B LEU* 1.3 76.2 - - - +
124B LEU* 1.3 62.9 + - - +
125B PRO* 4.2 1.7 - - - +
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Residues in contact with LEU 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B ALA* 4.6 6.7 - - + -
103B ALA* 3.4 36.1 - - + +
104B LYS 3.7 7.4 - - - +
105B LYS 5.0 0.2 - - - +
106B ALA* 4.6 9.0 - - + -
120B LEU* 3.3 16.6 - - - +
121B ALA* 3.1 10.0 + - - +
122B LEU 4.2 3.8 - - - +
123B ALA* 1.3 84.4 - - - +
125B PRO* 1.3 74.0 - - + +
128B GLY* 3.9 3.4 - - - -
129B ARG 3.5 41.7 - - - +
130B VAL* 3.8 13.7 - - + -
155B LYS* 2.8 21.2 + - + +
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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