Contacts of the helix formed by residues 68 - 78 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65A THR* 3.0 26.3 + - - +
66A CYS 3.4 1.2 + - - -
67A VAL* 1.3 79.3 - - - +
69A PHE* 1.3 58.2 + - - +
70A SER 3.5 2.0 - - - -
71A ALA* 3.4 8.3 + - - +
72A ILE* 2.8 41.8 + - - +
97A ALA* 4.4 3.6 - - - -
101A ILE* 5.2 5.2 - - - -
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Residues in contact with PHE 69 (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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19A VAL* 5.1 0.7 - - + -
24A ALA* 3.3 35.9 - - + -
25A LEU 4.6 0.4 - - - -
27A ALA* 4.6 7.3 - - + +
28A HIS* 3.6 26.7 - + + +
39A GLN* 3.6 16.3 + - - +
40A LEU* 3.1 34.3 - - + -
41A GLY 3.6 21.3 - - - -
42A THR* 4.1 17.0 - - + -
45A GLY* 4.9 0.7 - - - -
67A VAL 3.5 2.6 - - - -
68A GLY* 1.3 77.3 - - - +
70A SER* 1.3 68.2 + - - +
72A ILE* 3.3 3.5 + - - +
73A CYS* 3.0 48.3 + - - -
301A SAH 3.4 16.4 + - - +
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Residues in contact with SER 70 (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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40A LEU* 4.1 12.3 - - - -
48A LEU* 4.7 1.1 - - - +
62A GLU* 2.5 28.2 + - - -
65A THR 4.7 0.9 + - - -
69A PHE* 1.3 83.1 - - - +
71A ALA* 1.3 57.0 + - - +
73A CYS* 3.3 6.9 + - - +
74A MET* 3.0 34.3 + - - +
134A PHE* 4.0 13.5 - - - -
301A SAH 2.8 36.9 + - - -
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Residues in contact with ALA 71 (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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62A GLU* 3.5 20.2 + - - +
65A THR* 5.1 0.2 - - + -
68A GLY* 3.4 15.1 + - - +
69A PHE 3.2 0.4 - - - -
70A SER* 1.3 78.6 + - - +
72A ILE* 1.3 58.7 + - - +
74A MET* 3.4 8.6 + - - -
75A ALA* 2.9 27.7 + - - +
84A ILE* 3.3 15.3 - - + +
86A THR* 4.4 5.6 - - + -
101A ILE* 5.6 0.7 - - + -
110A ILE* 3.8 27.4 - - + -
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Residues in contact with ILE 72 (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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24A ALA* 3.9 18.2 - - + -
27A ALA* 3.8 26.5 - - + -
68A GLY 2.8 23.2 + - - +
69A PHE* 3.7 3.8 - - - +
71A ALA* 1.3 76.6 - - - +
73A CYS* 1.3 63.2 + - - +
75A ALA* 3.3 1.7 + - - +
76A HIS* 3.2 44.8 + - + -
100A ASN* 4.1 16.8 - - + +
101A ILE* 4.4 7.4 - - + +
104A CYS* 3.8 21.8 - - + -
106A LEU* 3.9 16.1 - - + +
110A ILE* 4.1 12.8 - - + -
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Residues in contact with CYS 73 (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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19A VAL* 3.9 23.3 - - - -
24A ALA* 4.3 3.6 - - - -
45A GLY* 4.1 21.8 - - - +
48A LEU* 5.9 0.9 - - + -
49A GLN* 2.9 33.5 + - - +
69A PHE* 3.0 55.0 + - - -
70A SER* 3.6 8.5 - - - +
72A ILE* 1.3 77.5 - - - +
74A MET* 1.3 65.3 + - + +
75A ALA 3.4 0.2 + - - -
76A HIS* 3.4 7.5 + - - -
77A ALA 3.6 0.3 + - - -
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Residues in contact with MET 74 (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 LEU* 3.8 28.7 - - + -
49A GLN* 4.8 2.2 - - - -
52A ILE* 3.5 29.8 - - + +
60A ILE* 4.1 25.1 - - + -
62A GLU* 3.3 35.4 - - + +
70A SER* 3.0 20.3 + - - +
71A ALA* 4.0 5.4 - - - -
73A CYS* 1.3 75.9 - - - +
75A ALA* 1.3 58.4 + - - +
77A ALA* 2.9 21.3 + - - +
78A LEU* 3.3 12.7 + - - +
84A ILE* 3.7 14.6 - - + -
132A MET* 4.1 12.3 - - - -
134A PHE* 4.0 9.9 - - + -
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Residues in contact with ALA 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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71A ALA 2.9 17.9 + - - +
72A ILE 3.7 4.5 - - - +
73A CYS 3.3 0.4 - - - -
74A MET* 1.3 77.7 - - - +
76A HIS* 1.3 61.4 + - - +
78A LEU* 3.1 17.0 + - - +
84A ILE* 3.5 12.7 - - + +
106A LEU* 4.1 14.4 - - + -
109A LYS* 3.1 29.7 + - + -
110A ILE* 3.8 22.4 - - + -
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Residues in contact with HIS 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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19A VAL* 5.9 0.8 - - - +
21A THR* 3.8 32.0 + - + +
24A ALA* 5.2 0.6 - - + +
49A GLN* 3.9 11.4 + - - +
53A ARG* 3.9 7.1 + - - -
72A ILE* 3.2 31.6 + - + +
73A CYS* 3.7 10.6 - - - +
74A MET 3.3 0.2 - - - -
75A ALA* 1.3 76.8 - - - +
77A ALA* 1.3 59.8 + - - +
78A LEU 3.4 3.3 - - - +
104A CYS 5.1 1.8 + - - -
106A LEU* 3.8 25.3 - - + +
109A LYS* 5.1 1.5 + - - +
305A IOD 3.6 11.4 - - - +
306A IOD 4.2 23.1 - - + +
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Residues in contact with ALA 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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49A GLN* 3.7 45.1 - - + +
52A ILE* 3.8 14.4 - - + +
53A ARG* 3.2 30.4 + - - +
73A CYS 3.6 1.0 + - - -
74A MET 2.9 11.1 + - - +
76A HIS* 1.3 77.1 - - - +
78A LEU* 1.3 64.7 + - - +
79A PRO* 3.8 2.8 - - - +
305A IOD 3.9 6.3 - - + +
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Residues in contact with LEU 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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52A ILE* 3.8 13.7 - - + -
53A ARG* 5.3 2.4 + - - -
57A ILE 3.4 23.8 - - - +
58A HIS 3.6 13.2 - - - +
60A ILE* 3.9 13.0 - - + -
74A MET 3.3 10.3 + - - +
75A ALA* 3.1 14.5 + - + +
76A HIS 4.3 3.3 - - - +
77A ALA* 1.3 81.0 - - - +
79A PRO* 1.3 72.0 - - + +
82A GLY* 3.9 3.1 - - - -
83A HIS* 3.6 22.7 - - - +
84A ILE* 3.6 34.8 - - + -
109A LYS* 2.8 22.6 + - + +
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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