Contacts of the helix formed by residues 72 - 84 (chain B) in PDB entry 2OG9
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 72 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79A HIS* 3.7 15.1 - - - -
82A GLU* 2.8 9.9 + - - -
109A ALA* 5.2 0.2 - - - -
68B SER* 3.1 17.4 + - - -
71B ALA* 1.3 74.5 - - - +
73B GLY* 1.3 67.2 + - - +
74B PRO* 3.5 2.5 - - - -
75B GLY* 3.3 3.4 + - - -
76B GLN* 3.0 23.7 + - - +
114B LEU* 3.8 11.8 - - - +
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Residues in contact with GLY 73 (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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82A GLU* 4.6 0.4 + - - -
22B SER* 4.3 5.6 + - - -
24B TYR* 4.1 3.6 - - - -
48B ALA* 3.6 27.4 - - - +
50B LEU* 6.0 0.7 - - - +
68B SER* 3.3 9.3 + - - -
70B ARG 4.4 1.4 + - - -
72B GLY* 1.3 77.4 - - - +
74B PRO* 1.3 69.2 - - - +
76B GLN* 3.3 5.7 + - - +
77B PHE* 3.1 23.4 + - - +
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Residues in contact with PRO 74 (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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78A ALA* 3.5 25.4 - - + +
81A ARG* 5.0 8.1 - - - +
82A GLU* 3.2 34.3 - - + +
24B TYR* 3.3 19.1 - - + +
72B GLY 3.8 0.2 - - - -
73B GLY* 1.3 88.4 - - - +
75B GLY* 1.3 55.4 + - - +
77B PHE* 3.4 1.6 + - - +
78B ALA* 3.0 30.8 + - - +
377B GLU* 4.2 17.5 - - - +
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Residues in contact with GLY 75 (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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75A GLY* 3.7 27.2 - - - -
78A ALA* 3.8 4.8 - - - +
79A HIS* 4.3 5.0 - - - +
114A LEU* 4.9 0.3 - - - +
72B GLY* 3.3 7.1 + - - -
73B GLY 3.3 0.6 - - - -
74B PRO* 1.3 76.7 - - - +
76B GLN* 1.3 65.3 + - - +
78B ALA 3.4 0.2 + - - -
79B HIS* 3.1 25.5 + - - +
114B LEU* 4.2 16.6 - - - -
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Residues in contact with GLN 76 (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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48B ALA 5.1 0.5 - - - +
50B LEU* 4.0 20.2 + - + +
66B SER* 3.7 17.7 + - - -
67B TYR* 3.0 22.9 + - - -
68B SER* 2.9 24.5 + - - -
72B GLY 3.0 15.8 + - - +
73B GLY* 3.7 5.5 - - - +
75B GLY* 1.3 74.9 - - - +
77B PHE* 1.3 59.4 + - - +
79B HIS* 3.5 0.6 + - - -
80B ALA* 2.9 29.8 + - - +
114B LEU* 3.8 30.4 - - + +
117B GLN* 2.7 33.5 + - + +
118B ALA* 3.5 6.5 - - + +
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Residues in contact with PHE 77 (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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20B ILE* 3.6 36.6 - - + -
22B SER* 3.8 26.7 - - - -
50B LEU* 4.1 16.3 - - + +
73B GLY 3.1 16.7 + - - +
74B PRO 3.8 3.1 - - - +
76B GLN* 1.3 78.5 - - - +
78B ALA* 1.3 61.9 + - - +
80B ALA* 3.2 2.3 + - - +
81B ARG* 2.9 55.5 + - - +
377B GLU* 3.6 32.1 - - + +
378B GLU* 3.5 34.8 - - - -
379B ALA* 3.9 9.2 - - + -
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Residues in contact with ALA 78 (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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74A PRO* 3.5 40.6 - - + +
75A GLY* 3.8 1.6 - - - +
78A ALA* 4.0 4.9 - - + -
74B PRO 3.0 17.9 + - - +
75B GLY 3.8 2.0 - - - +
77B PHE* 1.3 83.8 - - + +
79B HIS* 1.3 62.7 + - - +
81B ARG* 3.4 18.4 + - - +
82B GLU* 3.1 22.0 + - - +
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Residues in contact with HIS 79 (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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71A ALA* 3.7 36.1 - - + +
72A GLY* 3.7 12.4 + - - -
75A GLY* 4.3 3.9 + - - +
114A LEU* 3.6 21.1 - - + +
75B GLY 3.1 17.4 + - - +
76B GLN* 3.9 3.6 - - - +
78B ALA* 1.3 73.8 - - - +
80B ALA* 1.3 66.6 + - - +
82B GLU* 3.1 7.6 + - - +
83B ILE* 3.0 46.4 + - + +
102B LEU 5.2 1.6 + - - -
106B GLY* 4.5 7.9 - - - -
109B ALA* 4.6 1.8 - - + -
115B SER* 3.4 42.3 + - - -
118B ALA* 4.3 5.4 - - + -
119B ILE* 5.5 1.0 - - - +
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Residues in contact with ALA 80 (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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20B ILE* 3.7 14.1 - - + -
50B LEU* 3.9 20.2 - - + -
76B GLN 2.9 19.0 + - - +
77B PHE* 3.5 5.2 - - - +
79B HIS* 1.3 75.9 - - - +
81B ARG* 1.3 58.0 + - - +
83B ILE* 3.4 2.9 + - - -
84B ALA* 2.9 33.3 + - - +
118B ALA* 3.9 7.9 - - + +
122B PHE* 3.6 23.3 - - + -
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Residues in contact with ARG 81 (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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74A PRO* 4.9 7.5 - - - +
377A GLU* 5.3 7.3 + - - -
20B ILE* 3.2 18.3 - - + +
77B PHE* 2.9 37.2 + - + +
78B ALA* 3.6 22.6 + - - +
79B HIS 3.2 0.2 - - - -
80B ALA* 1.3 76.5 - - - +
82B GLU* 1.3 62.1 + - - +
84B ALA* 3.7 3.6 + - - +
85B PRO* 3.5 16.8 - - - +
377B GLU* 4.4 7.9 + - - -
378B GLU 5.7 0.6 + - - -
379B ALA* 3.8 26.2 - - + -
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Residues in contact with GLU 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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24A TYR* 5.0 3.8 + - - -
70A ARG 4.3 3.3 - - - +
71A ALA* 3.4 25.4 + - + +
72A GLY* 2.8 22.9 + - - -
73A GLY 4.6 0.3 + - - -
74A PRO* 3.1 33.0 - - + +
78B ALA 3.1 12.3 + - - +
79B HIS* 3.1 13.0 + - - +
81B ARG* 1.3 79.3 - - - +
83B ILE* 1.3 58.1 + - + +
85B PRO* 3.5 12.8 - - - +
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Residues in contact with ILE 83 (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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71A ALA* 3.5 30.7 - - + -
79B HIS* 3.0 39.3 + - + +
80B ALA* 3.7 6.1 - - - +
82B GLU* 1.3 74.1 - - - +
84B ALA* 1.3 69.8 + - - +
85B PRO* 3.2 4.0 - - - -
86B ALA* 2.9 23.3 + - - +
102B LEU* 3.7 28.7 - - + +
105B ALA* 4.5 13.5 - - + -
119B ILE* 3.7 31.4 - - + +
122B PHE* 4.1 12.3 - - + -
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Residues in contact with ALA 84 (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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18B VAL* 4.3 11.3 - - + +
20B ILE* 5.2 4.7 - - + -
80B ALA 2.9 19.3 + - - +
81B ARG* 3.9 6.7 - - - +
83B ILE* 1.3 76.4 - - - +
85B PRO* 1.3 70.1 - - + +
87B LEU* 2.9 24.4 + - - +
88B ILE* 4.1 1.7 + - - +
122B PHE* 4.0 20.2 - - + -
381B VAL* 4.2 18.6 - - + +
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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