Contacts of the helix formed by residues 72 - 84 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68A SER* 3.1 13.7 - - - -
71A ALA* 1.3 74.3 - - - +
73A GLY* 1.3 66.3 + - - +
74A PRO* 3.4 2.2 - - - -
75A GLY* 3.2 3.7 + - - -
76A GLN* 3.0 26.3 + - - +
114A LEU* 3.8 11.6 - - - +
79B HIS* 3.7 13.8 - - - -
82B GLU* 2.8 12.6 + - - -
109B ALA* 5.2 0.2 - - - -
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Residues in contact with GLY 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A SER* 4.3 6.2 + - - -
24A TYR* 4.1 3.1 - - - -
48A ALA* 3.6 27.0 - - - +
50A LEU* 5.9 0.7 - - - +
68A SER* 3.3 10.5 + - - -
70A ARG 4.4 1.2 + - - -
72A GLY* 1.3 76.5 - - - +
74A PRO* 1.3 69.9 - - - +
76A GLN* 3.3 6.1 + - - +
77A PHE* 3.1 23.4 + - - +
82B GLU* 4.6 0.4 + - - -
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Residues in contact with PRO 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A SER* 5.5 0.2 - - - +
24A TYR* 3.3 19.3 - - - +
72A GLY 3.7 0.2 - - - -
73A GLY* 1.3 88.2 - - - +
75A GLY* 1.3 60.9 + - - +
77A PHE* 3.4 1.4 + - - +
78A ALA* 3.0 26.0 + - - +
377A GLU* 4.4 16.6 - - - +
78B ALA* 3.5 25.4 - - + +
81B ARG* 4.9 8.7 - - - +
82B GLU* 3.1 33.2 - - + +
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Residues in contact with GLY 75 (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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72A GLY 3.2 7.4 + - - -
74A PRO* 1.3 79.8 - - - +
76A GLN* 1.3 62.0 + - - +
78A ALA 3.5 0.2 + - - -
79A HIS* 3.1 25.5 + - - +
114A LEU* 4.2 16.6 - - - -
75B GLY* 3.7 26.6 - - - -
78B ALA* 3.8 4.8 - - - +
79B HIS* 4.3 5.0 - - - +
114B LEU* 4.8 0.5 - - - +
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Residues in contact with GLN 76 (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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48A ALA 5.1 0.7 - - - +
50A LEU* 3.9 18.1 + - + +
66A SER* 3.1 21.0 + - - -
67A TYR* 3.0 28.5 + - - +
68A SER* 3.0 16.0 + - - +
72A GLY 3.0 17.6 + - - +
73A GLY* 3.7 6.1 - - - +
75A GLY* 1.3 74.9 - - - +
77A PHE* 1.3 58.5 + - - +
79A HIS* 3.4 0.6 + - - -
80A ALA* 2.9 30.0 + - - +
114A LEU* 3.8 28.4 - - + +
117A GLN* 2.7 35.5 + - + +
118A ALA* 3.6 6.6 - - + +
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Residues in contact with PHE 77 (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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20A ILE* 3.5 32.5 - - + -
22A SER* 3.9 20.9 - - - -
50A LEU* 4.1 18.5 - - + +
73A GLY 3.1 14.3 + - - +
74A PRO 3.8 3.1 - - - +
76A GLN* 1.3 80.2 - - - +
78A ALA* 1.3 61.4 + - - +
80A ALA* 3.1 2.6 + - - +
81A ARG* 2.8 59.1 + - - +
377A GLU* 3.4 33.4 - - + +
378A GLU* 3.5 42.2 - - - -
379A ALA* 4.0 6.5 - - + -
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Residues in contact with ALA 78 (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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74A PRO 3.0 18.6 + - - +
75A GLY 3.8 2.0 - - - +
77A PHE* 1.3 83.4 - - + +
79A HIS* 1.3 62.7 + - - +
81A ARG* 3.5 17.8 + - - +
82A GLU* 3.1 22.0 + - - +
74B PRO* 3.5 41.2 - - + +
75B GLY* 3.8 1.3 - - - +
78B ALA* 4.0 4.7 - - + -
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Residues in contact with HIS 79 (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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75A GLY 3.1 17.6 + - - +
76A GLN* 3.9 3.1 - - - +
78A ALA* 1.3 73.8 - - - +
80A ALA* 1.3 66.9 + - - +
82A GLU* 3.0 7.1 + - - +
83A ILE* 3.0 45.3 + - + +
102A LEU 5.2 1.6 + - - -
106A GLY* 4.5 8.3 - - - -
109A ALA* 4.6 1.8 - - + -
115A SER* 3.4 42.3 + - - -
118A ALA* 4.3 5.6 - - + -
119A ILE* 5.5 1.4 - - - +
71B ALA* 3.7 37.7 - - + +
72B GLY* 3.7 12.1 + - - -
75B GLY* 4.3 3.7 - - - +
114B LEU* 3.6 20.9 - - + +
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Residues in contact with ALA 80 (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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20A ILE* 3.7 13.2 - - + -
50A LEU* 3.8 20.4 - - + -
76A GLN 2.9 18.8 + - - +
77A PHE* 3.5 4.9 - - - +
79A HIS* 1.3 76.1 - - - +
81A ARG* 1.3 57.8 + - - +
83A ILE* 3.4 1.7 + - - -
84A ALA* 2.9 33.1 + - - +
118A ALA* 3.9 7.5 - - + +
122A PHE* 3.6 26.8 - - + -
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Residues in contact with ARG 81 (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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20A ILE* 3.2 18.5 - - + +
77A PHE* 2.8 38.7 + - + +
78A ALA* 3.6 21.8 + - - +
79A HIS 3.2 0.2 - - - -
80A ALA* 1.3 78.1 - - - +
82A GLU* 1.3 61.7 + - - +
83A ILE 3.5 0.2 + - - -
84A ALA* 3.7 3.6 + - - +
85A PRO* 3.5 16.5 - - - +
377A GLU* 4.4 8.1 + - - -
378A GLU 5.6 1.0 + - - -
379A ALA* 3.9 25.5 - - + +
74B PRO* 5.0 7.1 - - - +
377B GLU* 5.5 6.1 + - - -
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Residues in contact with GLU 82 (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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78A ALA 3.1 12.2 + - - +
79A HIS* 3.0 12.6 + - - +
81A ARG* 1.3 79.2 - - - +
83A ILE* 1.3 59.1 + - + +
85A PRO* 3.6 10.0 - - - +
24B TYR* 5.0 4.0 + - - -
70B ARG 4.4 3.3 - - - +
71B ALA* 3.4 26.1 + - + +
72B GLY* 2.8 22.7 + - - -
73B GLY 4.6 0.3 + - - -
74B PRO* 3.2 32.9 - - + +
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Residues in contact with ILE 83 (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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79A HIS* 3.0 39.0 + - + +
80A ALA* 3.7 5.8 - - - +
82A GLU* 1.3 75.2 - - - +
84A ALA* 1.3 70.0 + - - +
85A PRO* 3.2 4.0 - - - -
86A ALA* 2.9 23.0 + - - +
102A LEU* 3.6 28.5 - - + +
105A ALA* 4.6 13.5 - - + -
119A ILE* 3.8 31.4 - - + +
122A PHE* 4.1 12.1 - - + -
71B ALA* 3.6 31.0 - - + -
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Residues in contact with ALA 84 (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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18A VAL* 4.4 10.4 - - + +
20A ILE* 5.2 4.9 - - + -
80A ALA 2.9 19.5 + - - +
81A ARG* 3.9 7.0 - - - +
83A ILE* 1.3 76.4 - - - +
85A PRO* 1.3 69.6 - - + +
87A LEU* 2.9 25.1 + - - +
88A ILE* 4.1 1.6 + - - +
122A PHE* 4.1 19.7 - - + -
381A VAL* 4.1 18.4 - - + +
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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