Contacts of the helix formed by residues 81 - 94 (chain B) in PDB entry 2A79
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 ASN 81 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39B ILE* 3.5 10.9 - - - +
80B ARG* 1.3 77.8 - - - +
82B ARG* 1.3 64.8 + - - +
83B PRO* 3.3 16.7 - - - +
84B SER* 2.5 45.3 + - - +
85B PHE* 4.0 6.2 + - - +
104B VAL* 4.4 2.5 - - - +
108B ILE* 4.1 23.8 - - + +
112B GLU* 3.8 19.8 + - + +
116B TYR* 5.0 2.3 + - - -
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Residues in contact with ARG 82 (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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39B ILE* 3.4 23.5 + - - +
40B SER* 3.3 28.5 + - - -
41B GLY* 4.0 4.0 + - - -
42B LEU* 3.7 57.6 - - + +
44B PHE* 4.6 0.7 - - - -
80B ARG 3.3 1.3 + - - +
81B ASN* 1.3 70.5 - - - +
83B PRO* 1.3 78.1 - - + +
84B SER 3.0 1.6 + - - -
85B PHE* 3.2 17.0 + - - +
86B ASP* 4.2 2.6 + - - +
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Residues in contact with PRO 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B ASN* 3.3 18.4 - - - +
82B ARG* 1.3 96.0 - - + +
84B SER* 1.3 61.3 + - - +
86B ASP* 3.8 15.9 - - + +
101B PRO* 3.9 11.3 - - - +
103B ASN* 4.0 15.2 + - - +
104B VAL* 3.6 21.7 - - + +
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Residues in contact with SER 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B ASN* 2.5 28.7 + - - -
82B ARG 3.0 0.4 + - - -
83B PRO* 1.3 72.4 - - - +
85B PHE* 1.3 59.5 + - - +
86B ASP 2.9 11.8 + - - -
87B ALA* 3.0 18.0 + - - +
88B ILE* 3.4 9.9 + - - +
101B PRO* 4.9 0.4 - - - -
104B VAL* 3.5 19.5 - - - +
108B ILE* 4.2 1.9 - - - +
109B PHE* 4.0 20.0 - - - -
112B GLU* 3.7 29.2 - - - +
116B TYR* 5.8 0.7 - - - -
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Residues in contact with PHE 85 (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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37B ILE* 3.7 23.1 - - + -
39B ILE* 3.6 20.0 - - + -
44B PHE* 3.3 47.6 - + + -
59B LEU* 3.5 33.4 - - + -
81B ASN 4.0 5.4 + - - +
82B ARG 3.2 8.1 + - - +
84B SER* 1.3 74.6 - - - +
86B ASP* 1.3 65.8 + - - +
87B ALA 3.2 0.2 - - - -
88B ILE* 3.6 16.8 - - + +
89B LEU* 2.9 35.9 + - + +
116B TYR* 3.4 37.2 - + - +
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Residues in contact with ASP 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B LEU* 5.9 1.6 - - - +
44B PHE* 4.2 21.9 - - + -
82B ARG 4.2 1.2 + - - +
83B PRO* 3.8 14.4 + - - +
84B SER 2.9 0.6 + - - -
85B PHE* 1.3 80.4 - - - +
87B ALA* 1.3 59.0 + - - +
89B LEU* 3.9 2.9 - - - +
90B TYR* 3.2 23.2 + - - +
93B GLN* 5.2 0.5 - - - +
101B PRO* 5.0 5.8 - - + -
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Residues in contact with ALA 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B SER 3.0 9.4 + - - +
86B ASP* 1.3 76.6 - - - +
88B ILE* 1.3 67.5 + - - +
89B LEU 3.1 1.8 - - - -
90B TYR* 3.0 8.8 + - + +
91B TYR* 2.8 25.3 + - - +
97B ARG 4.6 1.9 - - - +
98B LEU* 4.8 2.9 - - + +
99B ARG 3.2 30.1 - - - +
101B PRO* 3.8 10.9 - - + +
109B PHE* 3.7 14.6 - - + -
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Residues in contact with ILE 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B LEU* 4.8 0.9 - - + -
84B SER 3.8 14.8 - - - +
85B PHE* 3.2 24.4 + - + +
87B ALA* 1.3 77.8 - - - +
89B LEU* 1.3 59.8 + - - +
91B TYR* 3.4 10.9 - - - +
92B TYR* 3.1 30.6 - - + -
98B LEU* 4.8 1.6 - - + -
109B PHE* 4.6 11.9 - - + -
112B GLU* 4.6 4.7 - - + -
113B ILE* 4.4 13.2 - - + +
116B TYR* 3.6 50.3 - - + -
118B LEU* 4.0 22.7 - - + -
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Residues in contact with LEU 89 (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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37B ILE* 5.0 3.4 - - + -
44B PHE* 4.0 28.9 - - + -
45B GLU 4.4 11.7 - - - +
46B THR* 3.8 31.0 - - + +
51B LEU* 4.7 12.3 - - + -
59B LEU* 5.9 0.4 - - + -
85B PHE* 2.9 33.5 + - + +
86B ASP 3.9 4.0 - - - +
88B ILE* 1.3 75.9 - - - +
90B TYR* 1.3 64.9 + - - +
91B TYR 3.1 1.8 - - - -
92B TYR* 3.1 17.0 + - + +
93B GLN* 3.2 34.9 + - + +
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Residues in contact with TYR 90 (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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86B ASP 3.2 12.0 + - - +
87B ALA* 3.0 12.0 + - + +
89B LEU* 1.3 76.5 - - - +
91B TYR* 1.3 58.1 + - - +
93B GLN* 3.3 20.6 + - + +
94B SER* 2.6 63.6 + - - -
97B ARG* 3.6 40.5 + - + -
99B ARG* 5.5 9.4 - - + -
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Residues in contact with TYR 91 (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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54B PHE* 3.1 47.3 - + + -
87B ALA 2.8 11.6 + - - +
88B ILE* 3.4 13.2 - - - +
90B TYR* 1.3 75.3 - - - +
92B TYR* 1.3 68.6 + + - +
94B SER* 2.9 4.3 + - - -
96B GLY* 2.8 63.3 + - - -
97B ARG 3.1 18.8 + - - +
98B LEU* 3.8 19.7 - - + -
118B LEU* 3.6 36.5 + - + -
122B ALA* 3.5 32.3 - - + +
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Residues in contact with TYR 92 (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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50B THR* 3.5 32.0 - - + +
51B LEU* 3.8 31.6 - - + -
53B GLN* 2.6 28.3 + - - -
54B PHE* 3.7 29.6 - + + -
57B THR* 2.7 38.4 + - - +
59B LEU* 3.7 23.4 + - + +
60B GLY 4.6 0.9 - - - -
88B ILE* 3.1 34.5 - - + -
89B LEU* 3.1 11.9 + - + +
91B TYR* 1.3 85.1 - + - +
93B GLN* 1.3 64.9 + - - +
95B GLY 3.3 2.9 + - - -
116B TYR* 4.5 2.9 + - - +
118B LEU* 4.1 11.7 - - + +
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Residues in contact with GLN 93 (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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45B GLU 5.1 2.6 + - - -
46B THR* 4.6 8.2 + - - +
50B THR* 4.0 20.4 - - + -
53B GLN* 5.2 0.3 + - - -
86B ASP 5.2 0.3 - - - +
89B LEU* 3.4 31.9 - - + +
90B TYR* 3.1 37.1 + - + +
92B TYR* 1.3 77.5 - - - +
94B SER* 1.3 59.8 + - - +
95B GLY 3.5 0.5 + - - -
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Residues in contact with SER 94 (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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90B TYR* 2.6 46.6 + - - -
91B TYR 2.9 2.9 + - - -
93B GLN* 1.3 73.5 - - - +
95B GLY* 1.3 58.4 + - - +
96B GLY 3.5 0.3 + - - -
97B ARG* 2.8 58.6 + - - +
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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