Contacts of the helix formed by residues 68 - 78 (chain B) in PDB entry 4OA5
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 68 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65B THR* 3.0 27.3 + - - +
66B CYS 3.4 1.2 + - - -
67B VAL* 1.3 78.8 - - - +
69B PHE* 1.3 59.4 + - - +
70B SER 3.5 2.0 - - - -
71B ALA* 3.7 8.1 - - - +
72B ILE* 2.8 42.9 + - - +
97B ALA* 4.3 4.9 - - - -
101B ILE* 5.3 4.0 - - - -
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Residues in contact with PHE 69 (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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19B VAL* 5.0 0.9 - - + -
24B ALA* 3.3 36.3 - - + -
25B LEU* 5.0 0.2 - - - -
27B ALA* 4.6 6.5 - - - +
28B HIS* 3.6 26.0 - + + +
39B GLN* 3.6 16.4 - - + +
40B LEU* 3.2 34.1 - - + -
41B GLY 3.6 20.6 - - - -
42B THR* 4.1 17.0 - - + -
45B GLY* 4.9 0.4 - - - -
67B VAL 3.5 3.4 + - - +
68B GLY* 1.3 76.9 - - - +
70B SER* 1.3 68.1 + - - +
72B ILE* 3.3 2.8 + - - +
73B CYS* 3.0 48.0 + - - -
301B SAH 3.3 16.2 + - - +
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Residues in contact with SER 70 (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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40B LEU* 4.1 13.9 - - - -
48B LEU* 4.8 0.9 - - - -
62B GLU* 2.5 28.7 + - - -
65B THR 4.6 0.5 + - - -
69B PHE* 1.3 84.0 - - - +
71B ALA* 1.3 56.6 + - - +
73B CYS* 3.3 6.8 + - - +
74B MET* 3.0 34.9 + - - +
134B PHE* 4.0 13.5 - - - -
301B SAH 2.8 36.8 + - - -
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Residues in contact with ALA 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B GLU* 3.5 19.5 - - - +
65B THR* 5.1 0.2 - - + -
68B GLY* 3.3 14.7 + - - +
69B PHE 3.2 0.8 - - - -
70B SER* 1.3 80.9 + - - +
72B ILE* 1.3 56.3 + - - +
74B MET* 3.4 8.9 + - - -
75B ALA* 2.8 27.5 + - - +
84B ILE* 3.3 15.2 - - + +
86B THR* 4.4 6.1 - - + -
101B ILE* 5.6 0.4 - - + -
110B ILE* 3.8 27.4 - - + -
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Residues in contact with ILE 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B ALA* 4.0 18.2 - - + -
27B ALA* 3.8 26.2 - - + -
68B GLY 2.8 23.7 + - - +
69B PHE* 3.7 3.8 - - - +
71B ALA* 1.3 72.8 - - - +
73B CYS* 1.3 64.2 + - - +
75B ALA* 3.3 1.9 + - - +
76B HIS* 3.2 44.3 + - - +
100B ASN* 4.1 16.8 - - + +
101B ILE* 4.4 7.4 - - + +
104B CYS* 3.9 22.2 - - + -
106B LEU* 3.9 16.6 - - + +
110B ILE* 4.1 12.3 - - + -
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Residues in contact with CYS 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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19B VAL* 3.9 22.9 - - - -
24B ALA* 4.3 2.9 - - - -
45B GLY* 4.0 21.3 - - - +
48B LEU* 5.9 0.9 - - + -
49B GLN* 2.9 33.4 + - - +
69B PHE* 3.0 54.1 + - - -
70B SER* 3.6 9.0 - - - +
72B ILE* 1.3 77.7 - - - +
74B MET* 1.3 64.7 + - + +
75B ALA 3.4 0.2 + - - -
76B HIS* 3.4 7.9 + - - +
77B ALA 3.7 0.2 + - - -
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Residues in contact with MET 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B LEU* 3.8 27.6 - - + -
49B GLN* 4.8 2.0 - - - -
52B ILE* 3.5 29.9 - - + +
60B ILE* 4.1 24.7 - - + -
62B GLU* 3.3 34.1 - - + +
70B SER* 3.0 19.0 + - - +
71B ALA* 4.1 5.8 - - - -
73B CYS* 1.3 76.5 - - - +
75B ALA* 1.3 57.7 + - - +
77B ALA* 3.0 22.0 + - - +
78B LEU* 3.3 12.9 + - - +
84B ILE* 3.7 14.8 - - + -
132B MET* 4.1 12.3 - - - -
134B PHE* 4.0 11.0 - - + -
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Residues in contact with ALA 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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71B ALA 2.8 18.1 + - - +
72B ILE 3.3 4.7 + - - +
74B MET* 1.3 76.9 - - - +
76B HIS* 1.3 58.1 + - - +
78B LEU* 3.0 21.8 + - - +
84B ILE* 3.5 12.1 - - + +
106B LEU* 4.1 15.4 - - + +
109B LYS* 3.1 28.9 + - + -
110B ILE* 3.8 22.4 - - + -
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Residues in contact with HIS 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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19B VAL* 5.8 0.7 - - + -
21B THR* 3.8 32.1 + - + -
24B ALA* 5.1 0.9 - - + -
49B GLN* 3.9 11.4 - - - +
53B ARG* 4.0 3.1 + - - -
72B ILE* 3.2 31.9 + - + +
73B CYS* 3.7 11.0 - - - +
74B MET 3.3 0.2 - - - -
75B ALA* 1.3 75.1 - - - +
77B ALA* 1.3 59.0 + - - +
78B LEU 4.3 3.0 - - - +
104B CYS* 5.1 3.1 - - + -
106B LEU* 3.7 28.9 - - + +
109B LYS* 5.1 1.7 + - - +
305B IOD 3.8 13.6 - - + +
307B IOD 4.2 21.1 - - + +
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Residues in contact with ALA 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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49B GLN* 3.7 45.5 - - + +
52B ILE* 3.8 14.8 - - + +
53B ARG* 3.3 30.0 + - - +
73B CYS 3.7 1.2 + - - -
74B MET 3.0 11.3 + - - +
76B HIS* 1.3 77.7 - - - +
78B LEU* 1.3 64.5 + - - +
79B PRO* 3.8 2.4 - - - +
305B IOD 4.0 4.5 - - + -
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Residues in contact with LEU 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B ILE* 3.8 14.6 - - + -
57B ILE 3.4 22.9 - - - +
58B HIS 3.6 12.3 - - - +
60B ILE* 3.9 12.8 - - + -
74B MET 3.6 10.1 - - - +
75B ALA* 3.0 14.7 + - + +
76B HIS 4.3 3.1 - - - +
77B ALA* 1.3 80.4 - - - +
79B PRO* 1.3 72.9 - - + +
82B GLY* 3.9 2.9 - - - +
83B HIS* 3.6 22.7 - - - +
84B ILE* 3.6 34.1 - - + -
109B LYS* 2.8 21.4 + - - +
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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